https://genomewiki.ucsc.edu/api.php?action=feedcontributions&user=Kuhn&feedformat=atomgenomewiki - User contributions [en]2024-03-29T09:53:11ZUser contributionsMediaWiki 1.38.4https://genomewiki.ucsc.edu/index.php?title=File:UcscLinks.xlsx&diff=25716File:UcscLinks.xlsx2020-10-21T00:44:06Z<p>Kuhn: Kuhn uploaded a new version of File:UcscLinks.xlsx</p>
<hr />
<div>changed mm10 links, too.</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Spreadsheet_links_to_Genome_Browser_views&diff=25061Spreadsheet links to Genome Browser views2018-10-25T22:32:02Z<p>Kuhn: updated links to new version of spreadsheet -- removed disambiguation page for rsIDs</p>
<hr />
<div>Many users of the Genome Browser gather data of their own in Excel spreadsheets and would like to create links to the Browser using data in the spreadsheet. For example, a clinical geneticist may have lists of regions or genes for a patient that are duplicated or deleted, as determined by comparative genomic hybridization (CGH). These regions can be the source information for a browser view allowing access to each region with a single click.<br />
<br />
<TABLE><TR><TD><br />
[[Image:ucscLinks.gif]]<br />
<br />
</TD><TD><br />
'''&nbsp;&nbsp;&nbsp;Click to download the spreadsheet:'''<BR><br />
&nbsp;&nbsp;&nbsp;[http://genomewiki.ucsc.edu/images/8/81/UcscLinks.xlsx ucscLinks.xlsx]<br />
<br />
</TD></TR></TABLE><br />
<br />
Careful use of Excel's "copy" and "move" functions will allow the links on this sheet to be used without modification.<br />
<br />
==Customizing the links==<br />
<br />
Postion-based link. The contents of the last cell in the image above are as follows:<br />
<br />
<PRE><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position="&E22&"&dgv=pack&knownGene=pack&omimGene2=pack","ucsc")<br />
</PRE><br />
<br />
Gene-name link. The URL for a link to a gene name is made in this way:<br />
<br />
<pre><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&singleSearch=knownCanonical&position="&E16&"&omimGene2=pack&decipher=pack&snp150=dense","ucsc")<br />
</pre><br />
<br />
Gene details link. A link to the UCSC Genes details page would look like this:<br />
<br />
<pre><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgGene?org=human&db=hg19&hgg_gene="&E16,"ucsc")<br />
</pre><br />
<br />
For example, you can create a link to hg38 for a region such as chr3:13000000-15000000, by modifying the following URL:<br />
<pre><br />
* http://genome.ucsc.edu/cgi-bin/hgTracks?db=[db]&position=[position]<br />
</pre><br />
to<br />
<pre><br />
* http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr3:13000000-15000000<br />
</pre><br />
<br />
The position-based link above shows how to create a link that turns on three specific tracks of interest. In this case, these tracks are explicitly turned on:<br />
<br />
Database of Genomic Variants (table: dgv)<br />
UCSC Genes (table: knownGene)<br />
OMIM Genes (table: omimGene2) <br />
<br />
Each track is set to "pack" in the link as follows, separated by ampersands (&):<br />
<br />
dgv=pack<br />
knownGene=pack<br />
omimGene2=pack<br />
<br />
A new track can be added using the tablename and a visibility of choice. e.g.:<br />
<br />
&snp150=dense<br />
<br />
Simply add to the end of the url any other desired <tablename>=visibility, appended to the url by an ampersand. Any track that has been open in on your Browser will remain in the view when the new browser window opens. Any track that is on by default must be turned off using:<br />
<br />
<tablename>=hide<br />
<br />
Or turn off all tracks except those you name using:<br />
<br />
hideTracks=1<br />
<br />
separated by ampersands.<br />
<br />
The simplest way to learn the name of the table underlying a track is to do a mouseover in a Genome Browser image and read the url at the bottom of the browser page. The table is shown in the url as<br />
<br />
g=tablename<br />
<br />
You can also see the tablename by clicking into an item in the track and then clicking "show table schema" on the next page.<br />
<br />
Visibility options include:<br />
<br />
hide<br />
dense<br />
squish<br />
pack<br />
full<br />
<br />
There is a short video describing various ways to discover the name of a table associated with a particular tracks: https://www.youtube.com/watch?v=RQZ4EeYS6Zk&list=UUQnUJepyNOw0p8s2otX4RYQ<br />
<br />
==Other documentation==<br />
<br />
Documentation for making links, including other parameters you can use, can be found on the Browser:<br />
<br />
https://genome.ucsc.edu/FAQ/FAQlink.html<br />
<br />
https://genome.ucsc.edu/goldenpath/help/customTrack.html#SHARE</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=File:UcscLinks.xlsx&diff=25060File:UcscLinks.xlsx2018-10-25T21:56:08Z<p>Kuhn: changed mm10 links, too.</p>
<hr />
<div>changed mm10 links, too.</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=File:UcscLinks.xls&diff=25059File:UcscLinks.xls2018-10-25T21:46:04Z<p>Kuhn: Kuhn uploaded a new version of File:UcscLinks.xls</p>
<hr />
<div>spreadsheet to create links that open Genome Browser views when a user types in a variety of entries, including genomic coordinates, gene names or chromosome bands.</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Spreadsheet_links_to_Genome_Browser_views&diff=24919Spreadsheet links to Genome Browser views2018-08-24T21:25:58Z<p>Kuhn: /* Other parameters */ added a link about making links</p>
<hr />
<div>Many users of the Genome Browser gather data of their own in Excel spreadsheets and would like to create links to the Browser using data in the spreadsheet. For example, a clinical geneticist may have lists of regions or genes for a patient that are duplicated or deleted, as determined by comparative genomic hybridization (CGH). These regions can be the source information for a browser view allowing access to each region with a single click.<br />
<br />
<TABLE><TR><TD><br />
[[Image:ucscLinks.gif]]<br />
<br />
</TD><TD><br />
'''Click to download the spreadsheet:'''<BR><br />
[http://genomewiki.ucsc.edu/images/0/01/UcscLinks.xls ucscLinks.xls]<br />
<br />
</TD></TR></TABLE><br />
<br />
Careful use of Excel's "copy" and "move" functions should allow the links on this sheet to be used without modification.<br />
<br />
==Customizing the links==<br />
<br />
Postion-based link. The contents of the last cell in the image above are as follows:<br />
<br />
<PRE><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position="&E22&"&dgv=pack&knownGene=pack&omimGene2=pack","ucsc")<br />
</PRE><br />
<br />
Gene-name link. The URL for a link to a gene name is made in this way:<br />
<br />
<pre><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&singleSearch=knownCanonical&position="&E16&"&omimGene2=pack&decipher=pack&snp150=dense","ucsc")<br />
</pre><br />
<br />
Gene details link. A link to the UCSC Genes details page would look like this:<br />
<br />
<pre><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgGene?org=human&db=hg19&hgg_gene="&E16,"ucsc")<br />
</pre><br />
<br />
For example, you can create a link to hg38 for a region such as chr3:13000000-15000000, by modifying the following URL:<br />
<pre><br />
* http://genome.ucsc.edu/cgi-bin/hgTracks?db=[db]&position=[position]<br />
</pre><br />
to<br />
<pre><br />
* http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr3:13000000-15000000<br />
</pre><br />
<br />
The position-based link above shows how to create a link that turns on three specific tracks of interest. In this case, these tracks are explicitly turned on:<br />
<br />
Database of Genomic Variants (table: dgv)<br />
UCSC Genes (table: knownGene)<br />
OMIM Genes (table: omimGene2) <br />
<br />
Each track is set to "pack" in the link as follows, separated by ampersands (&):<br />
<br />
dgv=pack<br />
knownGene=pack<br />
omimGene2=pack<br />
<br />
A new track can be added using the tablename and a visibility of choice. e.g.:<br />
<br />
&snp150=dense<br />
<br />
Simply add to the end of the url any other desired <tablename>=visibility, appended to the url by an ampersand. Any track that has been open in on your Browser will remain in the view when the new browser window opens. Any track that is on by default must be turned off using:<br />
<br />
<tablename>=hide<br />
<br />
Or turn off all tracks except those you name using:<br />
<br />
hideTracks=1<br />
<br />
separated by ampersands.<br />
<br />
The simplest way to learn the name of the table underlying a track is to do a mouseover in a Genome Browser image and read the url at the bottom of the browser page. The table is shown in the url as<br />
<br />
g=tablename<br />
<br />
You can also see the tablename by clicking into an item in the track and then clicking "show table schema" on the next page.<br />
<br />
Visibility options include:<br />
<br />
hide<br />
dense<br />
squish<br />
pack<br />
full<br />
<br />
There is a short video describing various ways to discover the name of a table associated with a particular tracks: https://www.youtube.com/watch?v=RQZ4EeYS6Zk&list=UUQnUJepyNOw0p8s2otX4RYQ<br />
<br />
==Other documentation==<br />
<br />
Documentation for making links, including other parameters you can use, can be found on the Browser:<br />
<br />
https://genome.ucsc.edu/FAQ/FAQlink.html<br />
<br />
https://genome.ucsc.edu/goldenpath/help/customTrack.html#SHARE</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Spreadsheet_links_to_Genome_Browser_views&diff=24749Spreadsheet links to Genome Browser views2018-04-17T20:01:18Z<p>Kuhn: </p>
<hr />
<div>Many users of the Genome Browser gather data of their own in Excel spreadsheets and would like to create links to the Browser using data in the spreadsheet. For example, a clinical geneticist may have lists of regions or genes for a patient that are duplicated or deleted, as determined by comparative genomic hybridization (CGH). These regions can be the source information for a browser view allowing access to each region with a single click.<br />
<br />
<TABLE><TR><TD><br />
[[Image:ucscLinks.gif]]<br />
<br />
</TD><TD><br />
'''Click to download the spreadsheet:'''<BR><br />
[http://genomewiki.ucsc.edu/images/0/01/UcscLinks.xls ucscLinks.xls]<br />
<br />
</TD></TR></TABLE><br />
<br />
Careful use of Excel's "copy" and "move" functions should allow the links on this sheet to be used without modification.<br />
<br />
==Customizing the links==<br />
<br />
Postion-based link. The contents of the last cell in the image above are as follows:<br />
<br />
<PRE><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position="&E22&"&dgv=pack&knownGene=pack&omimGene2=pack","ucsc")<br />
</PRE><br />
<br />
Gene-name link. The URL for a link to a gene name is made in this way:<br />
<br />
<pre><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&singleSearch=knownCanonical&position="&E16&"&omimGene2=pack&decipher=pack&snp150=dense","ucsc")<br />
</pre><br />
<br />
Gene details link. A link to the UCSC Genes details page would look like this:<br />
<br />
<pre><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgGene?org=human&db=hg19&hgg_gene="&E16,"ucsc")<br />
</pre><br />
<br />
For example, you can create a link to hg38 for a region such as chr3:13000000-15000000, by modifying the following URL:<br />
<pre><br />
* http://genome.ucsc.edu/cgi-bin/hgTracks?db=[db]&position=[position]<br />
</pre><br />
to<br />
<pre><br />
* http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr3:13000000-15000000<br />
</pre><br />
<br />
The position-based link above shows how to create a link that turns on three specific tracks of interest. In this case, these tracks are explicitly turned on:<br />
<br />
Database of Genomic Variants (table: dgv)<br />
UCSC Genes (table: knownGene)<br />
OMIM Genes (table: omimGene2) <br />
<br />
Each track is set to "pack" in the link as follows, separated by ampersands (&):<br />
<br />
dgv=pack<br />
knownGene=pack<br />
omimGene2=pack<br />
<br />
A new track can be added using the tablename and a visibility of choice. e.g.:<br />
<br />
&snp150=dense<br />
<br />
Simply add to the end of the url any other desired <tablename>=visibility, appended to the url by an ampersand. Any track that has been open in on your Browser will remain in the view when the new browser window opens. Any track that is on by default must be turned off using:<br />
<br />
<tablename>=hide<br />
<br />
Or turn off all tracks except those you name using:<br />
<br />
hideTracks=1<br />
<br />
separated by ampersands.<br />
<br />
The simplest way to learn the name of the table underlying a track is to do a mouseover in a Genome Browser image and read the url at the bottom of the browser page. The table is shown in the url as<br />
<br />
g=tablename<br />
<br />
You can also see the tablename by clicking into an item in the track and then clicking "show table schema" on the next page.<br />
<br />
Visibility options include:<br />
<br />
hide<br />
dense<br />
squish<br />
pack<br />
full<br />
<br />
There is a short video describing various ways to discover the name of a table associated with a particular tracks: https://www.youtube.com/watch?v=RQZ4EeYS6Zk&list=UUQnUJepyNOw0p8s2otX4RYQ<br />
<br />
==Other parameters==<br />
<br />
Other parameters you can use are documented on the Browser:<br />
<br />
https://genome.ucsc.edu/goldenpath/help/customTrack.html#SHARE</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=24593Other genome browsers2018-02-14T17:51:29Z<p>Kuhn: </p>
<hr />
<div>== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
* [http://genome-asia.ucsc.edu/ asianode] RIKEN. Yokahama, Japan.<br />
<br />
These mirrors are maintained by the Browser staff.<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome-mirror.cshl.edu/ Cold Spring Harbor Laboratory]. CSHL, NY<br />
<br />
* [http://genome-mirror.moma.ki.au.dk/ Aarhus University]. The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
== Other locations hosting UCSC Genome Browsers ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, including <I>Arabidopsis</I>, Trypanosome, herpes virus, phage lambda and others. University College, Cork, Ireland.<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.<br />
<br />
* [http://genomaize.org/cgi-bin/hgGateway Maize] at Florida State University.<br />
<br />
* [http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway Xenopus laevis] Frog at Medical Research Council, UK.<br />
<br />
* [http://old-gander.wustl.edu/gonramphubs/index.html various hubs] At WashU for: <I>Amazona vittata</I> (Puerto Rican Parrot), <I>Chlamydomonas reinhardtii</I> (single-celled alga), <I>Kryptolebias marmoratus</I>, <I>Sebastes rubrivinctus</I>, <I>Xenopus laevis</I> (frog commonly used used in research)<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway plants]. Oak, Rice, <I>Arabidopsis</I>, <i>Chlamydomonas</i>, <i>Volvox</i>, soybean, diatom, <i>Chromochlorus</i> algae, prune, some fungi, bacteria. At UCLA.<br />
<br />
* [http://em-x1.gurdon.cam.ac.uk/cgi-bin/hgGateway vertebrates]. Various new fish. At Cambridge University, UK.<br />
<br />
* [http://rohsdb.cmb.usc.edu/index.html DNA Shape] at University of Southern California. G-shape. Genome Browser Database for Shape Annotations. Many genomes. Some plants.<br />
* [http://genome.genetics.rutgers.edu/ Rutgers]. G-shape. Genome Browserfor several genomes. Some plants (incl. millet, switchgrass, soybean, rice), insects.<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly Assembly Hub] mechanism.<br />
<br />
If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=24592Other genome browsers2018-02-12T20:57:08Z<p>Kuhn: /* Locations using UCSC software on other organisms (or people) or additional content on our organisms, including assembly hubs */ Rutgers mirror</p>
<hr />
<div>== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
* [http://genome-asia.ucsc.edu/ asianode] RIKEN. Yokahama, Japan.<br />
<br />
These mirrors are maintained by the Browser staff.<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome-mirror.cshl.edu/ Cold Spring Harbor Laboratory]. CSHL, NY<br />
<br />
* [http://genome-mirror.moma.ki.au.dk/ Aarhus University]. The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms, including assembly hubs ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, including <I>Arabidopsis</I>, Trypanosome, herpes virus, phage lambda and others. University College, Cork, Ireland.<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.<br />
<br />
* [http://genomaize.org/cgi-bin/hgGateway Maize] at Florida State University.<br />
<br />
* [http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway Xenopus laevis] Frog at Medical Research Council, UK.<br />
<br />
* [http://old-gander.wustl.edu/gonramphubs/index.html various hubs] At WashU for: <I>Amazona vittata</I> (Puerto Rican Parrot), <I>Chlamydomonas reinhardtii</I> (single-celled alga), <I>Kryptolebias marmoratus</I>, <I>Sebastes rubrivinctus</I>, <I>Xenopus laevis</I> (frog commonly used used in research)<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway plants]. Oak, Rice, <I>Arabidopsis</I>, <i>Chlamydomonas</i>, <i>Volvox</i>, soybean, diatom, <i>Chromochlorus</i> algae, prune, some fungi, bacteria. At UCLA.<br />
<br />
* [http://em-x1.gurdon.cam.ac.uk/cgi-bin/hgGateway vertebrates]. Various new fish. At Cambridge University, UK.<br />
<br />
* [http://rohsdb.cmb.usc.edu/index.html DNA Shape] at University of Southern California. G-shape. Genome Browser Database for Shape Annotations. Many genomes. Some plants.<br />
* [http://genome.genetics.rutgers.edu/ Rutgers]. G-shape. Genome Browserfor several genomes. Some plants (incl. millet, switchgrass, soybean, rice), insects.<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly Assembly Hub] mechanism.<br />
<br />
If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=24531Other genome browsers2018-01-15T21:49:53Z<p>Kuhn: added details abt UCLA hub, dropped hub in China that does not work anymore.</p>
<hr />
<div>== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
* [http://genome-asia.ucsc.edu/ asianode] RIKEN. Yokahama, Japan.<br />
<br />
These mirrors are maintained by the Browser staff.<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome-mirror.cshl.edu/ Cold Spring Harbor Laboratory]. CSHL, NY<br />
<br />
* [http://genome-mirror.moma.ki.au.dk/ Aarhus University]. The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms, including assembly hubs ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, including <I>Arabidopsis</I>, Trypanosome, herpes virus, phage lambda and others. University College, Cork, Ireland.<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.<br />
<br />
* [http://genomaize.org/cgi-bin/hgGateway Maize] at Florida State University.<br />
<br />
* [http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway Xenopus laevis] Frog at Medical Research Council, UK.<br />
<br />
* [http://old-gander.wustl.edu/gonramphubs/index.html various hubs] At WashU for: <I>Amazona vittata</I> (Puerto Rican Parrot), <I>Chlamydomonas reinhardtii</I> (single-celled alga), <I>Kryptolebias marmoratus</I>, <I>Sebastes rubrivinctus</I>, <I>Xenopus laevis</I> (frog commonly used used in research)<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway plants]. Oak, Rice, <I>Arabidopsis</I>, <i>Chlamydomonas</i>, <i>Volvox</i>, soybean, diatom, <i>Chromochlorus</i> algae, prune, some fungi, bacteria. At UCLA.<br />
<br />
* [http://em-x1.gurdon.cam.ac.uk/cgi-bin/hgGateway vertebrates]. Various new fish. At Cambridge University, UK.<br />
<br />
* [http://rohsdb.cmb.usc.edu/index.html DNA Shape] at University of Southern California. G-shape. Genome Browser Database for Shape Annotations. Many genomes. Some plants.<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly Assembly Hub] mechanism.<br />
<br />
If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=24056Other genome browsers2017-05-11T00:43:58Z<p>Kuhn: /* Locations using UCSC software on other organisms (or people) or additional content on our organisms, including assembly hubs */</p>
<hr />
<div>== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
* [http://genome-asia.ucsc.edu/ asianode] RIKEN. Yokahama, Japan.<br />
<br />
These mirrors are maintained by the Browser staff.<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome-mirror.cshl.edu/ Cold Spring Harbor Laboratory]. CSHL, NY<br />
<br />
* [http://genome-mirror.moma.ki.au.dk/ Aarhus University]. The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms, including assembly hubs ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway?clade=plant&org=Glycine+max&db=0 soybean] and others at UCLA.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, including <I>Arabidopsis</I>, Trypanosome, herpes virus, phage lambda and others. University College, Cork, Ireland.<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.<br />
<br />
* [http://genomaize.org/cgi-bin/hgGateway Maize] at Florida State University.<br />
<br />
* [http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway Xenopus laevis] Frog at Medical Research Council, UK.<br />
<br />
* [http://old-gander.wustl.edu/gonramphubs/index.html various hubs] At WashU for: <I>Amazona vittata</I> (Puerto Rican Parrot), <I>Chlamydomonas reinhardtii</I> (single-celled alga), <I>Kryptolebias marmoratus</I>, <I>Sebastes rubrivinctus</I>, <I>Xenopus laevis</I> (frog commonly used used in research)<br />
<br />
* [http://structuralbiology.cau.edu.cn/cgi-bin/hgGateway plants]. Rice, <I>Arabidopsis</I>, cotton, maize. At China Agricultural University.<br />
<br />
* [http://em-x1.gurdon.cam.ac.uk/cgi-bin/hgGateway vertebrates]. Various new fish. At Cambridge University, UK.<br />
<br />
* [http://rohsdb.cmb.usc.edu/index.html DNA Shape] at University of Southern California. G-shape. Genome Browser Database for Shape Annotations. Many genomes. Some plants.<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly Assembly Hub] mechanism.<br />
<br />
If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=24055Other genome browsers2017-05-11T00:37:55Z<p>Kuhn: /* Locations using UCSC software on other organisms (or people) or additional content on our organisms, including assembly hubs */</p>
<hr />
<div>== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
* [http://genome-asia.ucsc.edu/ asianode] RIKEN. Yokahama, Japan.<br />
<br />
These mirrors are maintained by the Browser staff.<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome-mirror.cshl.edu/ Cold Spring Harbor Laboratory]. CSHL, NY<br />
<br />
* [http://genome-mirror.moma.ki.au.dk/ Aarhus University]. The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms, including assembly hubs ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway?clade=plant&org=Glycine+max&db=0 soybean] and others at UCLA.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, including <I>Arabidopsis</I>, Trypanosome, herpes virus, phage lambda and others. University College, Cork, Ireland.<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.<br />
<br />
* [http://genomaize.org/cgi-bin/hgGateway Maize] at Florida State University.<br />
<br />
* [http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway Xenopus laevis] Frog at Medical Research Council, UK.<br />
<br />
* [http://old-gander.wustl.edu/gonramphubs/index.html various hubs] At WashU for: <I>Amazona vittata</I> (Puerto Rican Parrot), <I>Chlamydomonas reinhardtii</I> (single-celled alga), <I>Kryptolebias marmoratus</I>, <I>Sebastes rubrivinctus</I>, <I>Xenopus laevis</I> (frog commonly used used in research)<br />
<br />
* [http://structuralbiology.cau.edu.cn/cgi-bin/hgGateway plants]. Rice, <I>Arabidopsis</I>, cotton, maize. At China Agricultural University.<br />
<br />
* [http://em-x1.gurdon.cam.ac.uk/cgi-bin/hgGateway vertebrates]. Various new fish. At Cambridge University, UK.<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly Assembly Hub] mechanism.<br />
<br />
If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=24054Other genome browsers2017-05-11T00:21:23Z<p>Kuhn: /* Locations using UCSC software on other organisms (or people) or additional content on our organisms, including assembly hubs */</p>
<hr />
<div>== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
* [http://genome-asia.ucsc.edu/ asianode] RIKEN. Yokahama, Japan.<br />
<br />
These mirrors are maintained by the Browser staff.<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome-mirror.cshl.edu/ Cold Spring Harbor Laboratory]. CSHL, NY<br />
<br />
* [http://genome-mirror.moma.ki.au.dk/ Aarhus University]. The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms, including assembly hubs ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway?clade=plant&org=Glycine+max&db=0 soybean] and others at UCLA.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, including <I>Arabidopsis</I>, Trypanosome, herpes virus, phage lambda and others. University College, Cork, Ireland.<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.<br />
<br />
* [http://genomaize.org/cgi-bin/hgGateway Maize] at Florida State University.<br />
<br />
* [http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway Xenopus laevis] Frog at Medical Research Council, UK.<br />
<br />
* [http://old-gander.wustl.edu/gonramphubs/index.html various hubs] At WashU for: <I>Amazona vittata</I> (Puerto Rican Parrot), <I>Chlamydomonas reinhardtii</I> (single-celled alga), <I>Kryptolebias marmoratus</I>, <I>Sebastes rubrivinctus</I>, <I>Xenopus laevis</I> (frog commonly used used in research)<br />
<br />
* [http://structuralbiology.cau.edu.cn/cgi-bin/hgGateway plants]. Rice, <I>Arabidopsis</I>, cotton, maize. At China Agricultural University.<br />
<br />
* [http://em-x1.gurdon.cam.ac.uk/cgi-bin/hgGateway vertebrates]. Various vertebrates, including several fish. At Cambridge University, UK.<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly Assembly Hub] mechanism.<br />
<br />
If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Spreadsheet_links_to_Genome_Browser_views&diff=23917Spreadsheet links to Genome Browser views2017-03-29T20:55:09Z<p>Kuhn: </p>
<hr />
<div>Many users of the Genome Browser gather data of their own in Excel spreadsheets and would like to create links to the Browser using data in the spreadsheet. For example, a clinical geneticist may have lists of regions or genes for a patient that are duplicated or deleted, as determined by comparative genomic hybridization (CGH). These regions can be the source information for a browser view allowing access to each region with a single click.<br />
<br />
<TABLE><TR><TD><br />
[[Image:ucscLinks.gif]]<br />
<br />
</TD><TD><br />
'''Click to download the spreadsheet:'''<BR><br />
[http://genomewiki.ucsc.edu/images/0/01/UcscLinks.xls ucscLinks.xls]<br />
<br />
</TD></TR></TABLE><br />
<br />
Careful use of Excel's "copy" and "move" functions should allow the links on this sheet to be used without modification.<br />
<br />
==Customizing the links==<br />
<br />
Postion-based link. The contents of the last cell in the image above are as follows:<br />
<br />
<PRE><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position="&E22&"&dgv=pack&knownGene=pack&omimGene2=pack","ucsc")<br />
</PRE><br />
<br />
Gene-name link. The URL for a link to a gene name is made in this way:<br />
<br />
<pre><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&singleSearch=knownCanonical&position="&E16&"&omimGene2=pack&decipher=pack&snp141=dense","ucsc")<br />
</pre><br />
<br />
Gene details link. A link to the UCSC Genes details page would look like this:<br />
<br />
<pre><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgGene?org=human&db=hg19&hgg_gene="&E16,"ucsc")<br />
</pre><br />
<br />
Add tracks of choice. The position-based link above shows how to create a link that turns on three specific tracks of interest. In this case, these tracks are explicitly turned on:<br />
<br />
Database of Genomic Variants (table: dgv)<br />
UCSC Genes (table: knownGene)<br />
OMIM Genes (table: omimGene2) <br />
<br />
Each track is set to "pack" in the link as follows:<br />
<br />
dgv=pack<br />
knownGene=pack<br />
omimGene2=pack<br />
<br />
Any track that has been open in on your Browser will remain in the view when the new browser window opens. Any track that is on by default must be turned off using:<br />
<br />
<tablename>=hide<br />
<br />
A new track can be added using the tablename and a visibility of choice. e.g.:<br />
<br />
&snp141=dense<br />
<br />
Simply add to the end of the url any other desired <tablename>=visibility, appended to the url by an ampersand (&). The simplest way to learn the name of the table underlying a track is to do a mouseover in a Genome Browser image and read the url at the bottom of the browser page. The table is shown in the url as<br />
<br />
g=tablename<br />
<br />
You can also see the tablename by clicking into an item in the track and then clicking "show table schema" on the next page.<br />
<br />
Visibility options include:<br />
<br />
hide<br />
dense<br />
squish<br />
pack<br />
full<br />
<br />
==Other parameters==<br />
<br />
Other parameters you can use are documented on the Browser:<br />
<br />
https://genome.ucsc.edu/goldenpath/help/customTrack.html#SHARE</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Spreadsheet_links_to_Genome_Browser_views&diff=23916Spreadsheet links to Genome Browser views2017-03-29T20:53:39Z<p>Kuhn: </p>
<hr />
<div>Many users of the Genome Browser gather data of their own in Excel spreadsheets and would like to create links to the Browser using data in the spreadsheet. For example, a clinical geneticist may have lists of regions or genes for a patient that are duplicated or deleted, as determined by comparative genomic hybridization (CGH). These regions can be the source information for a browser view allowing access to each region with a single click.<br />
<br />
<TABLE><TR><TD><br />
[[Image:ucscLinks.gif]]<br />
<br />
</TD><TD><br />
'''Click to download the spreadsheet:'''<BR><br />
[http://genomewiki.ucsc.edu/images/0/01/UcscLinks.xls ucscLinks.xls]<br />
<br />
</TD></TR></TABLE><br />
<br />
Careful use of Excel's "copy" and "move" functions should allow the links on this sheet to be used without modification.<br />
<br />
==Customizing the links==<br />
<br />
Postion-based link. The contents of the last cell in the image above are as follows:<br />
<br />
<PRE><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position="&E22&"&dgv=pack&knownGene=pack&omimGene2=pack","ucsc")<br />
</PRE><br />
<br />
Gene-name link. The URL for a link to a gene name is made in this way:<br />
<br />
<pre><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&singleSearch=knownCanonical&position="&E16&"&omimGene2=pack&decipher=pack&snp141=dense","ucsc")<br />
</pre><br />
<br />
Gene details link. A link to the UCSC Genes details page would look like this:<br />
<br />
<pre><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgGene?org=human&db=hg19&hgg_gene="&E16,"ucsc")<br />
</pre><br />
<br />
Add tracks of choice. The position-based link above shows how to create a link that turns on three specific tracks of interest. In this case, these tracks are explicitly turned on:<br />
<br />
Database of Genomic Variants (table: dgv)<br />
UCSC Genes (table: knownGene)<br />
OMIM Genes (table: omimGene2) <br />
<br />
Each track is set to "pack" in the link as follows:<br />
<br />
dgv=pack<br />
knownGene=pack<br />
omimGene2=pack<br />
<br />
Any track that has been open in on your Browser will remain in the view when the new browser window opens. Any track that is on by default must be turned off using:<br />
<br />
<tablename>=hide<br />
<br />
A new track can be added using the tablename and a visibility of choice. e.g.:<br />
<br />
&snp141=dense<br />
<br />
Simply add to the end of the url any other desired <tablename>=visibility, appended to the url by an ampersand (&). The simplest way to learn the name of the table underlying a track is to do a mouseover in a Genome Browser image and read the url at the bottom of the browser page. The table is shown in the url as<br />
<br />
g=tablename<br />
<br />
You can also see the tablename by clicking into an item in the track and then clicking "show table schema" on the next page.<br />
<br />
Visibility options include:<br />
<br />
hide<br />
dense<br />
squish<br />
pack<br />
full<br />
<br />
Other parameters you can use are documented on the Browser:<br />
<br />
https://genome.ucsc.edu/goldenpath/help/customTrack.html#SHARE</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=23629Other genome browsers2016-11-10T20:07:00Z<p>Kuhn: /* Locations using UCSC software on other organisms (or people) or additional content on our organisms, including assembly hubs */</p>
<hr />
<div>== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
* [http://genome-asia.ucsc.edu/ asianode] RIKEN. Yokahama, Japan.<br />
<br />
These mirrors are maintained by the Browser staff.<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome-mirror.cshl.edu/ Cold Spring Harbor Laboratory]. CSHL, NY<br />
<br />
* [http://genome-mirror.moma.ki.au.dk/ Aarhus University]. The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms, including assembly hubs ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway?clade=plant&org=Glycine+max&db=0 soybean] and others at UCLA.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, including <I>Arabidopsis</I>, Trypanosome, herpes virus, phage lambda and others. University College, Cork, Ireland.<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.<br />
<br />
* [http://genomaize.org/cgi-bin/hgGateway Maize] at Florida State University.<br />
<br />
* [http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway Xenopus laevis] Frog at Medical Research Council, UK.<br />
<br />
* [http://old-gander.wustl.edu/gonramphubs/index.html various hubs] At WashU for: <I>Amazona vittata</I> (Puerto Rican Parrot), <I>Chlamydomonas reinhardtii</I> (single-celled alga), <I>Kryptolebias marmoratus</I>, <I>Sebastes rubrivinctus</I>, <I>Xenopus laevis</I> (frog commonly used used in research)<br />
<br />
* [http://structuralbiology.cau.edu.cn/cgi-bin/hgGateway plants]. Rice, <I>Arabidopsis</I>, cotton, maize. At China Agricultural University.<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly Assembly Hub] mechanism.<br />
<br />
If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=23628Other genome browsers2016-11-10T20:03:36Z<p>Kuhn: /* UCSC Genome mirror sites */ australia mirror retired</p>
<hr />
<div>== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
* [http://genome-asia.ucsc.edu/ asianode] RIKEN. Yokahama, Japan.<br />
<br />
These mirrors are maintained by the Browser staff.<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome-mirror.cshl.edu/ Cold Spring Harbor Laboratory]. CSHL, NY<br />
<br />
* [http://genome-mirror.moma.ki.au.dk/ Aarhus University]. The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms, including assembly hubs ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway?clade=plant&org=Glycine+max&db=0 soybean] and others at UCLA.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, including <I>Arabidopsis</I>, Trypanosome, herpes virus, phage lambda and others. University College, Cork, Ireland.<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.<br />
<br />
* [http://genomaize.org/cgi-bin/hgGateway Maize] at Florida State University.<br />
<br />
* [http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway Xenopus laevis] Frog at Medical Research Council, UK.<br />
<br />
* [http://old-gander.wustl.edu/gonramphubs/index.html various hubs] At WashU for: <I>Amazona vittata</I> (Puerto Rican Parrot), <I>Chlamydomonas reinhardtii</I> (single-celled alga), <I>Kryptolebias marmoratus</I>, <I>Sebastes rubrivinctus</I>, <I>Xenopus laevis</I> (frog commonly used used in research)<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly Assembly Hub] mechanism.<br />
<br />
If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=23520Other genome browsers2016-10-04T18:32:06Z<p>Kuhn: /* Locations using UCSC software on other organisms (or people) or additional content on our organisms */</p>
<hr />
<div>== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
* [http://genome-asia.ucsc.edu/ asianode] RIKEN. Yokahama, Japan.<br />
<br />
These mirrors are maintained by the Browser staff.<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome-mirror.cshl.edu/ Cold Spring Harbor Laboratory]. CSHL, NY<br />
<br />
* [http://genome-mirror.moma.ki.au.dk/ Aarhus University]. The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
* [https://ucsc.genome.edu.au/ Genomics Virtual Lab]. QFAB mirror in Australia.<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms, including assembly hubs ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway?clade=plant&org=Glycine+max&db=0 soybean] and others at UCLA.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, including <I>Arabidopsis</I>, Trypanosome, herpes virus, phage lambda and others. University College, Cork, Ireland.<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.<br />
<br />
* [http://genomaize.org/cgi-bin/hgGateway Maize] at Florida State University.<br />
<br />
* [http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway Xenopus laevis] Frog at Medical Research Council, UK.<br />
<br />
* [http://old-gander.wustl.edu/gonramphubs/index.html various hubs] At WashU for: <I>Amazona vittata</I> (Puerto Rican Parrot), <I>Chlamydomonas reinhardtii</I> (single-celled alga), <I>Kryptolebias marmoratus</I>, <I>Sebastes rubrivinctus</I>, <I>Xenopus laevis</I> (frog commonly used used in research)<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly Assembly Hub] mechanism.<br />
<br />
If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=23519Other genome browsers2016-10-04T18:26:48Z<p>Kuhn: /* Official UCSC Genome mirror site */</p>
<hr />
<div>== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
* [http://genome-asia.ucsc.edu/ asianode] RIKEN. Yokahama, Japan.<br />
<br />
These mirrors are maintained by the Browser staff.<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome-mirror.cshl.edu/ Cold Spring Harbor Laboratory]. CSHL, NY<br />
<br />
* [http://genome-mirror.moma.ki.au.dk/ Aarhus University]. The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
* [https://ucsc.genome.edu.au/ Genomics Virtual Lab]. QFAB mirror in Australia.<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway?clade=plant&org=Glycine+max&db=0 soybean] and others at UCLA.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, including <I>Arabidopsis</I>, Trypanosome, herpes virus, phage lambda and others. University College, Cork, Ireland.<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.<br />
<br />
* [http://genomaize.org/cgi-bin/hgGateway Maize] at Florida State University.<br />
<br />
* [http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway Xenopus laevis] Frog at Medical Research Council, UK.<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly Assembly Hub] mechanism.<br />
<br />
If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Presentations&diff=23397Presentations2016-08-26T17:33:38Z<p>Kuhn: /* 2011 */ added poster. Genomic Disorders meeting, Hinxton, 2011.</p>
<hr />
<div>An archive of presentations by staff and researchers of the UCSC Genome Browser group and the Center for Biomolecular Science and Engineering (CBSE). Please keep the list in order by date, newest ones at the top.<br />
<!-- presentation present --><br />
<br />
==2016==<br />
* 20 Aug 2016, Max Haeussler, Evaluation of scoring algorithms for Crispor and the UCSC Genome Browser, CSHL Crispr Meeting 2016, Poster [[File:CrisporCshl2016.pdf | PDF]]<br />
* 12 July 2016, Kate Rosenbloom, GTEx in the UCSC Genome Browser: July 2016 Update (presentation to the GTEx Steering Committee, Stanford) [[Media:GtexAtUcscTalkJuly2016.pptx | PPTX]]<br />
* 11 July 2016, Christopher Lee poster presented at the 2016 GTEx Community Meeting at Stanford [[:File:GTEX_2016_Poster.pdf | PDF]]<br />
* 09 June 2016, Hiram Clawson presentation to Bejerano Lab, Stanford, assembly nomenclature, assembly hubs, lastz/chain/net procedures [[:File:BejeranoLab_2016-06-09.pptx | PPTX]]<br />
* 24 May 2016, Chris Eisenhart phone conference presentation, explaining the new data transfer to the CIRM CRP and CIP labs [https://docs.google.com/presentation/d/16tsxBkYvrTVLlyYrTKIcTJnkKYTWIO0mUbViU0d7tlQ/edit?usp=sharing google doc]<br />
* 10 May 2016, Galt Barber, Multi-Region (Exon Mostly) at Biology of Genomes [[Media:Multi-region-BoG2016.pdf | PDF]]<br />
* 29 April 2016, Chris Eisenhart presentation at the 2nd Annual CIRM retreat, CDW, Stem cell hub, current lab status [https://docs.google.com/presentation/d/1xmxfROdgSkqlxXhQwBiQ2cPnfV1N8BPp6ChkXFG-IJk/edit?usp=sharing google doc]<br />
* 29 April 2016, Clay Fischer poster presented at the 2nd Annual CIRM retreat [[:File:CIRMposter2016.pdf | PDF]]<br />
* 04 April 2016, Robert Kuhn. poster presented at International Congress of Human Genetics (ICHG) in Kyoto. Reformatted from Luvina's ACMG poster. Thanks, Luvina [[:File:PosterIchg2016.pdf | PDF]]<br />
* 11 March 2016, Luvina Guruvado presented poster about about accessing variation data in the GBiB and Data Integrator at the American College of Medical Genetics (ACMG) annual meeting in Tampa [[:File:ACMGposter2016.pdf | PDF]]<br />
* 17 February 2016, Kate Rosenbloom, GTEx in the UCSC Genome Browser (presentation at Genecats) [[Media:GTExAtUcscFeb2016.pptx | PPTX]] [[Media:GTExAtUcscFeb2016.pdf | PDF]]<br />
* 12 January 2016 Hiram Clawson, BME230 browser introduction, assembly hub demonstration, table browser intersection [[:File:BME230_Winter_2016.ppt|PPT]]<br />
<br />
==2015==<br />
* 4 December 2015, Kate Rosenbloom, GTEx in the UCSC Genome Browser (presentation at the December 2015 GTEx Steering Committee meeting) [[Media:GTExAtUcsc_Dec2015.pptx | PPTX]] [[Media:GTExAtUcsc_Dec2015.pdf | PDF]]<br />
* 28-30 September 2015, Kate Rosenbloom, Visualizing proteomics data in genomic context using the UCSC Genome Browser (poster presented by collaborator Eric Deutsch (PeptideAtlas Project, Institute for Systems Biology) at the HUPO2015 (Human Proteomics Organization) Congress in Vancouver) [[Media:UCSC_Proteomics_HUPO2015_Poster.pptx | PPTX]] <br />
* 29 June - 1 July 2015, Pauline Fujita, [https://www.encodeproject.org/tutorials/encode-users-meeting-2015/ ENCODE Users Meeting] Visualizing ENCODE Data in the UCSC Genome Browser. [[Media:ENCODEusersMtg.ppt | PPTX]]<br />
* 23 June 2015, Kate Rosenbloom, GTEx Data in the UCSC Genome Browser (poster presented at the June 2015 GTEx Community Meeting in Chicago) [[Media:GTEX2015Poster.pptx | PPTX]] [[Media:GTEX2015Poster.pdf | PDF]]<br />
* 22-24 June 2015, Matthew Speir, Use The UCSC Genome Browser To Visualize And Analyze Your Genomic Data (poster presented at [https://bioeng-symposium-2015.soe.ucsc.edu/ UC-wide Bioengineering Symposium 2015] at UCSC) [[BioengSymp2015Poster | wiki]] [[Media:bioengSymp2015Poster.pptx | PPTX]] [[Media:bioengSymp2015Poster.pdf | PDF]]<br />
* 9 May 2015, Angie Hinrichs, The Data Integrator: a new way to combine datasources underlying the UCSC Genome Browser (poster presented at [http://meetings.cshl.edu/meetings/2015/genome15.shtml Biology of Genomes 2015] at CSHL) [[BoG2015DataIntegratorPoster | wiki]] [[Media:BoG2015DataIntegrator.pptx | PPTX]] [[Media:BoG2015DataIntegrator.pdf | PDF]]<br />
* 11 March 2015, Angie Hinrichs, Annotation Integrator [[Media:HgAi_genecats_15_03_11.pdf|PDF]] [[Media:HgAi_genecats_15_03_11.pptx|PPTX]]<br />
* 5 March 2015, Brian Raney, Genome 10K, Poster on assembly hubs and GBiB. [[:File:G10K2015.pdf|PDF]]<br />
* 26 Feb 2015, Robert Kuhn, ACMG meeting, Salt Lake. UCSC Genome Browser and Variant Annotation Integrator [[Media:acmg2015poster.pdf|PDF]]<br />
<br />
==2014==<br />
* 13 October 2014, Brian Raney, The American Society of Human Genetics, Poster on assembly hubs and GBiB. [[:File:Ashg2014.pdf|PDF]]<br />
* 20 September 2014, Galt Barber, Genome Informatics 2014 Poster on hubs, security, and GBiB. [[:File:GenomeInformatics2014Poster.pdf|PDF]]<br />
* 19 Sept 2014 Jim Kent, Ebola Scramble [[Media:ebolaUcsfSept192014.pptx|PPTX]]<br />
* 22 Aug 2014 Jim Kent, hg38, mapping sponge, and ENCODE [[Media:spongeAwg.pptx|PPTX]]<br />
* 19 May 2014, Karen Miga, GRCh38 Centromere Reference Models [[:File:KarenMigaCentromere.pdf|PDF]]<br />
* 11 February 2014, Hiram Clawson, BME230 browser introduction, assembly hub demonstration, table browser intersection [[:File:BME230_Winter_2014.ppt|PPT]]<br />
<br />
==2013==<br />
* 19 June 2013, Tracy Ballinger, Track Hubs and Assembly Hubs presentation for Epigenome Roadmap working group meeting. [[:File:TrackHub_presentation.ppt|PPT]] [[:File:TrackHub_presentation.pdf|PDF]]<br />
* 10 May 2013, Brooke Rhead, New variation resources at the UCSC Genome Browser. Poster presented at [http://meetings.cshl.edu/meetings/2013/genome13.shtml Biology of Genomes 2013] at CSHL. [[BoG2013VariationPoster | wiki]], [[Media:BoG2013variation.pptx | PPTX]], [[Media:BoG2013variation.pdf | PDF]].<br />
* 08 May 2013, Hiram Clawson, Assembly Hubs poster presentation at [http://meetings.cshl.edu/meetings/2013/genome13.shtml Biology of Genomes 2013] at CSHL. [[Assembly_Hubs | wiki]], [[Media:AssemblyHubs_BoG_2013.pdf | PDF]], [[Media:AssemblyHubs_BoG_2013.pptx| PPTX]]<br />
* 20 Mar 2013, Brian Raney, UCSC Genes Genecats talk [[:File:ucscGenes.ppt|PPT]] [[:File:ucscGenes.pdf|PDF]]<br />
<br />
==2012==<br />
* 06 Sep 2012, Brian Raney, Remote Data Track Storage for Viewing on the UCSC Genome Browser [[GI2012TrackHubsPoster|wiki]], <br />
* 09 May 2012, Angie Hinrichs, Using the UCSC Genome Browser to evaluate putative genetic variants [[BoG2012VariationPoster|wiki]], [[:File:Hinrichs_BoG2012_GBVariants.pptx|PPTX]], [[:File:Hinrichs_BoG2012_GBVariants.pdf|PDF]]<br />
* 11 April 2012, Ted Pak, JavaScript/Ruby version of the UCSC Yeast Genome Browser [[:File:UCSC_talk.graffle.pdf|PDF]] <br />
* 21 March 2012, Larry Meyer, Genome Browser API. (Genecats) [[:File:hgApi.ppt|PPT]] <br />
* 15 February 2012, Greg Roe & Venkat Malladi, Selenium Testing [[:File:SeleniumTesting.pptx|PPTX]]<br />
* 26 January 2012, Hiram Clawson, BME230 browser introduction, table browser intersection [[:File:BME230_Winter_2012.ppt|PPT]]<br />
* 18 January 2012, Jim Kent, Software Engineering and Testing. (Genecats) [[:File:SoftwareEngTesting.pptx|PPTX]]<br />
* 11 January 2012, Brooke Rhead, The QA Release Process: what gets pushed and when. (Genecats) [[:File:QaReleaseProcess.pptx|PPTX]] or [[:File:QaReleaseProcess.pdf|PDF]]<br />
<br />
==2011==<br />
* 18-19 October 2011, [http://www-conf.slac.stanford.edu/xldb2011/Program.asp XLDB presentations] including from UCSC, the 5th lightning talk on the 18th of October. Note additional interesting genomics presentations, for example the NCBI sequence read archive architecture on the morning of the 19th.<br />
* 09 September 2011, Angie Hinrichs, Visually integrating genomic data in the UCSC Genome Browser. Poster presented at [http://hgvmeeting.org/hgv2011/ HGV2011]. [[Media:HGV2011_GenomeBrowser.pptx|.pptx]] [[Media:HGV2011_GenomeBrowser.pdf|PDF]]<br />
* 24 August 2011, Sol Katzman, Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hotspots [[File:Sol_GCBias_GeneCats_2011-08-24.pdf]]<br />
* 27 July 2011, Larry Meyer, Browser Performance and Architecture<br />
* May 2011, Ann Zweig, UCSC Genome Browser Track Data Hubs. Poster given at Biology of Genomes conference at CSHL. [[File:BoG2011.pdf]]<br />
* May 2011, Gabor Marth, Toward a unified view of human genetic variation. Talk given at Biology of Genomes conference at CSHL. [[Image:Marth-1000G-CSHL2011.pptx]]<br />
* 27 April 2011, Jim Kent, Accelerating Biomedical Research for 10 Years and Counting. [[Image:AcceleratingBiomedicine2011.pptx]]<br />
* 06 April 2011, Angie Hinrichs, Recent work on human variation tracks. [[Media:VariationGenecats20110406.pptx|.pptx]] [[Media:VariationGenecats20110406.pdf|PDF]] (PDF has squashed animations)<br />
* 24 March 2011, Robert Kuhn. poster presented at Genomic Disorders meeting, Hinxton. [[Image:genomicDisorders2011.pdf]]<br />
* 09 March 2011, Josh Stuart, Ph.D., Integrated Pathway Modeling. [[Image:jstuart.pptx]]<br />
* 03 March 2011, Andreas Sundquist, Ph.D., DNAnexus -- Data Management for the First 1,000,000 Human Genomes. [[Image:DNAnexus.pptx]]<br />
* 02 March 2011, MDB and CV in the shadow of the shadow of greatness. [[Image:mdbAndCvPresentation.pdf]] or [[Image:mdbAndCvPresentation.ppt]] Brian Raney and Tim Dreszer.<br />
* 02 February 2011, Benedict Paten, JobTree. [[Image:JobtreeSlides.pdf]]<br />
* 06 January 2011, BME 230 class, Hiram Clawson, introduction to the UCSC genome browser and programming with the kent source tree. [[Image:BME230_Winter_2011.ppt]]<br />
<br />
==2010==<br />
* 10 November 2010, Xin Zhou, Human Epigenomics Browser [[Image:2010-11-10_-_Genecats.pdf]]<br />
* 4 Novermber 2010, Kate Rosenbloom, Genome-wide ENCODE Data at UCSC (poster for ASHG2010) [[Media:ENCODE_ASHG2010.ppt]] <br />
* 29 September 2010, Andy Pohl, Investigation of the Nucleosome Linker [[Image:2010-09-29_-_Genecats.pdf]]<br />
* 25 August 2010, Ann Zweig, Redmine Task-Tracking Tool [[Image:Genecats08252010.ppt]] [[Image:Genecats082510.mp3]]<br />
* 18 August 2010, Kate Rosenbloom, Genome-wide ENCODE Data at UCSC (poster for CSB2010) [[Media:ENCODE_CSB2010.ppt]] <br />
* 18 August 2010, Melissa Cline, Genome-wide Mouse ENCODE Data at UCSC (presented at CSB2010) [[Image:Cline.MouseEncode.CSB2010.ppt]] <br />
* 11 August, 2010, Mary Goldman, Working with git [[Media:Genecats_08_11_10.mp3]]<br />
* 23 June, 2010, Ed Green, Detecting positive selection in humans using the Neandertal genome [[Media:Genecats062310.mp3]]<br />
* 17 June, 2010, Kate Rosenbloom, ENCODE Data at UCSC (presented at CSHL Integrated Analysis of Genome-Scale Data short course) [[Media:Rosenbloom.ENCODE_CSHL_Jun2010.ppt]]<br />
* 16 June, 2010, Larry Meyer, Bringing Web 2.0 to the UCSC Genome Browser [[Image:Genecats061610.pdf]] audio: [[Image:Genecats061610.mp3]]<br />
* 15 June, 2010, Steve Benz, Thesis Advancement [[Image:Sbenz_thesis_advancement.pdf]] audio: [[Image:BenzAdvancement061510.mp3]]<br />
* 09 June, 2010, Ann Zweig & Galt Barber, git Source Code Management [[Image:gitSourceCodeMgmt.pdf]] partial audio: [[Media:Genecats060910.mp3]]<br />
* 05 May 2010, Hiram Clawson, [[Unix environment]]<br />
* 21 April 2010, Mitchell Skinner, JBrowse - An AJAX Genome Browser [[Image:UCSC-4-21-10.pdf]]<br />
* 10 February 2010, Jorge Garcia, The Genome Browser - Under The Hood [[Image:Browsermap.pdf]] and 2013 review [[Image:Dependency-Review-20130826.pdf]] and 2016 review [[Image:Browsermap2016.pdf]]<br />
* 03 February 2010, Melissa Cline, Coordinated Alternative Splicing [[Image:CoordinatedSplicing.ppt]]<br />
* 05,07 January 2010 BME 230 class, Hiram Clawson, introduction to the UCSC genome browser and programming with the kent source tree. [[Image:BME230_Winter_2010.ppt]] Browser [[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=BME230%20Winter%202010 Session]] for example intersection.<br />
<br />
==2009==<br />
* 14 October Genecats meeting, [[Image:MonsatoIntroduction_Oct2009.pdf|Monsanto Introduction]] Brad Fabbri<br />
* 14 October Genecats meeting, Hiram Clawson - building the kent source tree and a UCSC genome browser assembly, [[Image:Genecats_2009_10_14.pptx|pptx power point]] or older style [[Image:Genecats_2009_10_14.ppt|ppt power point]]<br />
* 24 August Genecats meeting, Larry and Tim present 3 new hgTracks features coming down the shute: [[Media:Image20ui.pdf|image20ui.pdf]].<br />
* 29 July Genecats meeting, Mark's presentation on SVS/subversion proposal to replace CVS [[Image:svnForGb.pdf|svnForGb.pdf]].<br />
* 08 April Genecats meeting, Fan Hsu: "Some thoughts from Fan" [[Image:SomeThoughtsFromFan0408B.pdf|SomeThoughtsFromFan0408B.pdf]].<br />
* 08 January 2009 BME 230 class, Hiram Clawson, introduction to the UCSC genome browser and programming with the kent source tree. [[Image:BME230_Winter_2009.ppt]] Browser [[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=BME230%20Winter%202009 Session]] for example intersection.<br />
<br />
==2008==<br />
* 18 December 2008 [[Image:FrankJacobs181208.ppt]] - Frank Jacobs, Developmental Neurobiology, Rudolf Magnus Institute of Neuroscience, University of Utrecht, The Netherlands, "Pitx3 outSMRTs Nurr1 in dopamine neuron terminal differentiation"<br />
<br />
* Genecats - 17 December 2008 - [[Media:Matrix.ppt|Composite sketch]]: Nifty tricks for composite tracks (multi-view, dimensions, sorting, drag and drop, etc.). Tim Dreszer.<br />
<br />
* 11 December 2008, Paul Flicek, EBI, presenting 1,000 genomes project status [[Image:Flicek_11_DEC_2008.pdf]]<br />
<br />
* Genecats - 10 December 2008 - Ed Green from Max Planck Institute for Evolutionary Anthropology discusses the [[http://www.cell.com/retrieve/pii/S0092867408007733| Neandertal mtDNA]] project<br />
<br />
* Genecats - 15 October 2008 - [[Image:Metcalf.Richardson.2008-10-15.pdf]] Jake Metcalf, Sarah Richardson discussion of ethics controversy concerning Bruce T. Lahn of U. Chicago publications.<br />
<br />
* Sep. 2008 - Angie's "UCSC Genome Browser Tool Suite" poster presented at Genomics of Common Disease [[Media:UCSC_Genome_Browser_GCD_2008.ppt|PPT]] [[Media:UCSC_Genome_Browser_GCD_2008.pdf|PDF]]<br />
<br />
* 27 August 2008 - Jim Kent at the Computational Systems Bioinformatics Conference, Stanford CA, [[Image:Kent_decodingEncode.ppt]] a wide-ranging discussion of Encode research, using the Gene Sorter, using the Table browser, source code design issues<br />
<br />
* Genecats - 06 August 2008 - [[Image:ISMB2008_genecats_summary.ppt]] summary of ISMB 2008, Toronto, Hiram Clawson<br />
<br />
* Genecats - July 30, 2008 - [[Media:UBCSslides.ppt|Biased Clustered Subsitutions in the Human Genome: Sex, Gambling and Non-Darwinian Evolution]]. Tim Dreszer's presentation of his master's thesis work.<br />
<br />
* ISMB Toronto - July 2008 - Intelligent Systems for Molecular Biology [[Image:ISMB2008_UCSC.ppt]] presentation by Hiram Clawson. A brief tutorial on browser usage with special emphasis on how to perform intersections with the table browser. Task demonstrated: finding highly conserved non-coding regions of the genome.<br />
<br />
* Genecats - 05 July 2008 - Jim Kent describing the all.joiner file used by the UCSC genome browser to specify database table relationships - the database "schema" behind the browser [[Image:Kent_allJoiner.ppt]]<br />
<br />
* Genecats - 16 April 2008 - Rachel Harte trip report from Mouse Genome Annotation Summit Meeting and RefSeq/CCDS visit, NIH, Bethesda MD 12-14 March 2008 [[Image:MouseAnnotAndCCDSVisitReport041608.ppt]]<br />
<br />
* Genecats - 06 April 2008 - Jim Kent reviewing the Parasol super computer job management system [[Image:Kent_parasolArchitecture.ppt]]<br />
<br />
* Bejerano Lab (Stanford) - March 31, 2008 - [[Image:Bejerano Lab 2008 03 31.ppt]] Angie's crash course on using the kent/src tools and libraries. Did a brief live demo (TB intersection -> custom track) first. Group was already very familiar with browser and had their own mirror.<br />
<br />
* BME 230 Winter 2008, 10 January 2008, Robert Baertsch [[Image:Baertsch-code-talk.ppt]] genome browser introduction and kent src code preview<br />
<br />
==2007==<br />
* Genecats - 16 April 2008 - [[Image:ISMB2007TripReportGenecats.ppt]] Rachel Harte summary from ISMB 2007 meeting in Vienna, Austria<br />
* Jim's talk - 12 September 2007 - [[Image:geneSorter.ppt]] "Inside the Gene Sorter - A moderately complex CGI application" talk by Jim Kent<br />
<br />
==2006==<br />
<br />
* Genecats - September 12, 2006 - [[Image:Automation 2006 09 12 v2.ppt]] Overview of the automation scripts that are now in kent/src/hg/utils/automation/ (Angie).<br />
<br />
==2005==<br />
<br />
* Chicken Genome Meeting - May, 2005 - [[Image:Browsers CSHL Chicken 2005 05.ppt]] An intro to the Genome Browser and Table Browser (Angie).<br />
<br />
==2003==<br />
<br />
* CSHL June 2003 "Evolution and the Santa Cruz Genome Browser" [[Image:CSHL_2003_Jim_Kent.ppt]] presentation by Jim Kent. Recent new functions in the genome browser, using the chain and net process to highlight evolutionary processes, a new rat genome assembly with 3-way human-mouse-rat multiple alignment.<br />
<br />
==2002==<br />
<br />
* Charles Sugnet's talk January 2002 - "Adding tracks to the Human Genome Browser" [[Image:howToAddTrack_Sugnet.pdf|howToAddTrack_Sugnet.pdf]] and examples used in the talk - [[Image:sampTracksChr22.tab]]<br />
<br />
* Genecats October 2002 - "Software Sermon" [[Image:SoftwareSermon2002_Jim_Kent.ppt]] - software development philosophy and guidelines, Jim Kent.<br />
<br />
==2000==<br />
<br />
* October 2000 - "Details of the Genome Browser" [[Image:CompBioOct2000_Jim_Kent.ppt]] - Description of the genome browser software architecture, the early days. Jim Kent<br />
<br />
<br />
[[Category:Browser Development]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=File:GenomicDisorders2011.pdf&diff=23396File:GenomicDisorders2011.pdf2016-08-26T17:32:31Z<p>Kuhn: Genomic Disorders meeting, Hinxton. organized by DECIPHER.</p>
<hr />
<div>Genomic Disorders meeting, Hinxton. organized by DECIPHER.</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Presentations&diff=23395Presentations2016-08-26T17:22:11Z<p>Kuhn: /* 2016 */ added ICGH 2016 poster</p>
<hr />
<div>An archive of presentations by staff and researchers of the UCSC Genome Browser group and the Center for Biomolecular Science and Engineering (CBSE). Please keep the list in order by date, newest ones at the top.<br />
<!-- presentation present --><br />
<br />
==2016==<br />
* 20 Aug 2016, Max Haeussler, Evaluation of scoring algorithms for Crispor and the UCSC Genome Browser, CSHL Crispr Meeting 2016, Poster [[File:CrisporCshl2016.pdf | PDF]]<br />
* 12 July 2016, Kate Rosenbloom, GTEx in the UCSC Genome Browser: July 2016 Update (presentation to the GTEx Steering Committee, Stanford) [[Media:GtexAtUcscTalkJuly2016.pptx | PPTX]]<br />
* 11 July 2016, Christopher Lee poster presented at the 2016 GTEx Community Meeting at Stanford [[:File:GTEX_2016_Poster.pdf | PDF]]<br />
* 09 June 2016, Hiram Clawson presentation to Bejerano Lab, Stanford, assembly nomenclature, assembly hubs, lastz/chain/net procedures [[:File:BejeranoLab_2016-06-09.pptx | PPTX]]<br />
* 24 May 2016, Chris Eisenhart phone conference presentation, explaining the new data transfer to the CIRM CRP and CIP labs [https://docs.google.com/presentation/d/16tsxBkYvrTVLlyYrTKIcTJnkKYTWIO0mUbViU0d7tlQ/edit?usp=sharing google doc]<br />
* 10 May 2016, Galt Barber, Multi-Region (Exon Mostly) at Biology of Genomes [[Media:Multi-region-BoG2016.pdf | PDF]]<br />
* 29 April 2016, Chris Eisenhart presentation at the 2nd Annual CIRM retreat, CDW, Stem cell hub, current lab status [https://docs.google.com/presentation/d/1xmxfROdgSkqlxXhQwBiQ2cPnfV1N8BPp6ChkXFG-IJk/edit?usp=sharing google doc]<br />
* 29 April 2016, Clay Fischer poster presented at the 2nd Annual CIRM retreat [[:File:CIRMposter2016.pdf | PDF]]<br />
* 04 April 2016, Robert Kuhn. poster presented at International Congress of Human Genetics (ICHG) in Kyoto. Reformatted from Luvina's ACMG poster. Thanks, Luvina [[:File:PosterIchg2016.pdf | PDF]]<br />
* 11 March 2016, Luvina Guruvado presented poster about about accessing variation data in the GBiB and Data Integrator at the American College of Medical Genetics (ACMG) annual meeting in Tampa [[:File:ACMGposter2016.pdf | PDF]]<br />
* 17 February 2016, Kate Rosenbloom, GTEx in the UCSC Genome Browser (presentation at Genecats) [[Media:GTExAtUcscFeb2016.pptx | PPTX]] [[Media:GTExAtUcscFeb2016.pdf | PDF]]<br />
* 12 January 2016 Hiram Clawson, BME230 browser introduction, assembly hub demonstration, table browser intersection [[:File:BME230_Winter_2016.ppt|PPT]]<br />
<br />
==2015==<br />
* 4 December 2015, Kate Rosenbloom, GTEx in the UCSC Genome Browser (presentation at the December 2015 GTEx Steering Committee meeting) [[Media:GTExAtUcsc_Dec2015.pptx | PPTX]] [[Media:GTExAtUcsc_Dec2015.pdf | PDF]]<br />
* 28-30 September 2015, Kate Rosenbloom, Visualizing proteomics data in genomic context using the UCSC Genome Browser (poster presented by collaborator Eric Deutsch (PeptideAtlas Project, Institute for Systems Biology) at the HUPO2015 (Human Proteomics Organization) Congress in Vancouver) [[Media:UCSC_Proteomics_HUPO2015_Poster.pptx | PPTX]] <br />
* 29 June - 1 July 2015, Pauline Fujita, [https://www.encodeproject.org/tutorials/encode-users-meeting-2015/ ENCODE Users Meeting] Visualizing ENCODE Data in the UCSC Genome Browser. [[Media:ENCODEusersMtg.ppt | PPTX]]<br />
* 23 June 2015, Kate Rosenbloom, GTEx Data in the UCSC Genome Browser (poster presented at the June 2015 GTEx Community Meeting in Chicago) [[Media:GTEX2015Poster.pptx | PPTX]] [[Media:GTEX2015Poster.pdf | PDF]]<br />
* 22-24 June 2015, Matthew Speir, Use The UCSC Genome Browser To Visualize And Analyze Your Genomic Data (poster presented at [https://bioeng-symposium-2015.soe.ucsc.edu/ UC-wide Bioengineering Symposium 2015] at UCSC) [[BioengSymp2015Poster | wiki]] [[Media:bioengSymp2015Poster.pptx | PPTX]] [[Media:bioengSymp2015Poster.pdf | PDF]]<br />
* 9 May 2015, Angie Hinrichs, The Data Integrator: a new way to combine datasources underlying the UCSC Genome Browser (poster presented at [http://meetings.cshl.edu/meetings/2015/genome15.shtml Biology of Genomes 2015] at CSHL) [[BoG2015DataIntegratorPoster | wiki]] [[Media:BoG2015DataIntegrator.pptx | PPTX]] [[Media:BoG2015DataIntegrator.pdf | PDF]]<br />
* 11 March 2015, Angie Hinrichs, Annotation Integrator [[Media:HgAi_genecats_15_03_11.pdf|PDF]] [[Media:HgAi_genecats_15_03_11.pptx|PPTX]]<br />
* 5 March 2015, Brian Raney, Genome 10K, Poster on assembly hubs and GBiB. [[:File:G10K2015.pdf|PDF]]<br />
* 26 Feb 2015, Robert Kuhn, ACMG meeting, Salt Lake. UCSC Genome Browser and Variant Annotation Integrator [[Media:acmg2015poster.pdf|PDF]]<br />
<br />
==2014==<br />
* 13 October 2014, Brian Raney, The American Society of Human Genetics, Poster on assembly hubs and GBiB. [[:File:Ashg2014.pdf|PDF]]<br />
* 20 September 2014, Galt Barber, Genome Informatics 2014 Poster on hubs, security, and GBiB. [[:File:GenomeInformatics2014Poster.pdf|PDF]]<br />
* 19 Sept 2014 Jim Kent, Ebola Scramble [[Media:ebolaUcsfSept192014.pptx|PPTX]]<br />
* 22 Aug 2014 Jim Kent, hg38, mapping sponge, and ENCODE [[Media:spongeAwg.pptx|PPTX]]<br />
* 19 May 2014, Karen Miga, GRCh38 Centromere Reference Models [[:File:KarenMigaCentromere.pdf|PDF]]<br />
* 11 February 2014, Hiram Clawson, BME230 browser introduction, assembly hub demonstration, table browser intersection [[:File:BME230_Winter_2014.ppt|PPT]]<br />
<br />
==2013==<br />
* 19 June 2013, Tracy Ballinger, Track Hubs and Assembly Hubs presentation for Epigenome Roadmap working group meeting. [[:File:TrackHub_presentation.ppt|PPT]] [[:File:TrackHub_presentation.pdf|PDF]]<br />
* 10 May 2013, Brooke Rhead, New variation resources at the UCSC Genome Browser. Poster presented at [http://meetings.cshl.edu/meetings/2013/genome13.shtml Biology of Genomes 2013] at CSHL. [[BoG2013VariationPoster | wiki]], [[Media:BoG2013variation.pptx | PPTX]], [[Media:BoG2013variation.pdf | PDF]].<br />
* 08 May 2013, Hiram Clawson, Assembly Hubs poster presentation at [http://meetings.cshl.edu/meetings/2013/genome13.shtml Biology of Genomes 2013] at CSHL. [[Assembly_Hubs | wiki]], [[Media:AssemblyHubs_BoG_2013.pdf | PDF]], [[Media:AssemblyHubs_BoG_2013.pptx| PPTX]]<br />
* 20 Mar 2013, Brian Raney, UCSC Genes Genecats talk [[:File:ucscGenes.ppt|PPT]] [[:File:ucscGenes.pdf|PDF]]<br />
<br />
==2012==<br />
* 06 Sep 2012, Brian Raney, Remote Data Track Storage for Viewing on the UCSC Genome Browser [[GI2012TrackHubsPoster|wiki]], <br />
* 09 May 2012, Angie Hinrichs, Using the UCSC Genome Browser to evaluate putative genetic variants [[BoG2012VariationPoster|wiki]], [[:File:Hinrichs_BoG2012_GBVariants.pptx|PPTX]], [[:File:Hinrichs_BoG2012_GBVariants.pdf|PDF]]<br />
* 11 April 2012, Ted Pak, JavaScript/Ruby version of the UCSC Yeast Genome Browser [[:File:UCSC_talk.graffle.pdf|PDF]] <br />
* 21 March 2012, Larry Meyer, Genome Browser API. (Genecats) [[:File:hgApi.ppt|PPT]] <br />
* 15 February 2012, Greg Roe & Venkat Malladi, Selenium Testing [[:File:SeleniumTesting.pptx|PPTX]]<br />
* 26 January 2012, Hiram Clawson, BME230 browser introduction, table browser intersection [[:File:BME230_Winter_2012.ppt|PPT]]<br />
* 18 January 2012, Jim Kent, Software Engineering and Testing. (Genecats) [[:File:SoftwareEngTesting.pptx|PPTX]]<br />
* 11 January 2012, Brooke Rhead, The QA Release Process: what gets pushed and when. (Genecats) [[:File:QaReleaseProcess.pptx|PPTX]] or [[:File:QaReleaseProcess.pdf|PDF]]<br />
<br />
==2011==<br />
* 18-19 October 2011, [http://www-conf.slac.stanford.edu/xldb2011/Program.asp XLDB presentations] including from UCSC, the 5th lightning talk on the 18th of October. Note additional interesting genomics presentations, for example the NCBI sequence read archive architecture on the morning of the 19th.<br />
* 09 September 2011, Angie Hinrichs, Visually integrating genomic data in the UCSC Genome Browser. Poster presented at [http://hgvmeeting.org/hgv2011/ HGV2011]. [[Media:HGV2011_GenomeBrowser.pptx|.pptx]] [[Media:HGV2011_GenomeBrowser.pdf|PDF]]<br />
* 24 August 2011, Sol Katzman, Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hotspots [[File:Sol_GCBias_GeneCats_2011-08-24.pdf]]<br />
* 27 July 2011, Larry Meyer, Browser Performance and Architecture<br />
* May 2011, Ann Zweig, UCSC Genome Browser Track Data Hubs. Poster given at Biology of Genomes conference at CSHL. [[File:BoG2011.pdf]]<br />
* May 2011, Gabor Marth, Toward a unified view of human genetic variation. Talk given at Biology of Genomes conference at CSHL. [[Image:Marth-1000G-CSHL2011.pptx]]<br />
* 27 April 2011, Jim Kent, Accelerating Biomedical Research for 10 Years and Counting. [[Image:AcceleratingBiomedicine2011.pptx]]<br />
* 06 April 2011, Angie Hinrichs, Recent work on human variation tracks. [[Media:VariationGenecats20110406.pptx|.pptx]] [[Media:VariationGenecats20110406.pdf|PDF]] (PDF has squashed animations)<br />
* 09 March 2011, Josh Stuart, Ph.D., Integrated Pathway Modeling. [[Image:jstuart.pptx]]<br />
* 03 March 2011, Andreas Sundquist, Ph.D., DNAnexus -- Data Management for the First 1,000,000 Human Genomes. [[Image:DNAnexus.pptx]]<br />
* 02 March 2011, MDB and CV in the shadow of the shadow of greatness. [[Image:mdbAndCvPresentation.pdf]] or [[Image:mdbAndCvPresentation.ppt]] Brian Raney and Tim Dreszer.<br />
* 02 February 2011, Benedict Paten, JobTree. [[Image:JobtreeSlides.pdf]]<br />
* 06 January 2011, BME 230 class, Hiram Clawson, introduction to the UCSC genome browser and programming with the kent source tree. [[Image:BME230_Winter_2011.ppt]]<br />
<br />
==2010==<br />
* 10 November 2010, Xin Zhou, Human Epigenomics Browser [[Image:2010-11-10_-_Genecats.pdf]]<br />
* 4 Novermber 2010, Kate Rosenbloom, Genome-wide ENCODE Data at UCSC (poster for ASHG2010) [[Media:ENCODE_ASHG2010.ppt]] <br />
* 29 September 2010, Andy Pohl, Investigation of the Nucleosome Linker [[Image:2010-09-29_-_Genecats.pdf]]<br />
* 25 August 2010, Ann Zweig, Redmine Task-Tracking Tool [[Image:Genecats08252010.ppt]] [[Image:Genecats082510.mp3]]<br />
* 18 August 2010, Kate Rosenbloom, Genome-wide ENCODE Data at UCSC (poster for CSB2010) [[Media:ENCODE_CSB2010.ppt]] <br />
* 18 August 2010, Melissa Cline, Genome-wide Mouse ENCODE Data at UCSC (presented at CSB2010) [[Image:Cline.MouseEncode.CSB2010.ppt]] <br />
* 11 August, 2010, Mary Goldman, Working with git [[Media:Genecats_08_11_10.mp3]]<br />
* 23 June, 2010, Ed Green, Detecting positive selection in humans using the Neandertal genome [[Media:Genecats062310.mp3]]<br />
* 17 June, 2010, Kate Rosenbloom, ENCODE Data at UCSC (presented at CSHL Integrated Analysis of Genome-Scale Data short course) [[Media:Rosenbloom.ENCODE_CSHL_Jun2010.ppt]]<br />
* 16 June, 2010, Larry Meyer, Bringing Web 2.0 to the UCSC Genome Browser [[Image:Genecats061610.pdf]] audio: [[Image:Genecats061610.mp3]]<br />
* 15 June, 2010, Steve Benz, Thesis Advancement [[Image:Sbenz_thesis_advancement.pdf]] audio: [[Image:BenzAdvancement061510.mp3]]<br />
* 09 June, 2010, Ann Zweig & Galt Barber, git Source Code Management [[Image:gitSourceCodeMgmt.pdf]] partial audio: [[Media:Genecats060910.mp3]]<br />
* 05 May 2010, Hiram Clawson, [[Unix environment]]<br />
* 21 April 2010, Mitchell Skinner, JBrowse - An AJAX Genome Browser [[Image:UCSC-4-21-10.pdf]]<br />
* 10 February 2010, Jorge Garcia, The Genome Browser - Under The Hood [[Image:Browsermap.pdf]] and 2013 review [[Image:Dependency-Review-20130826.pdf]] and 2016 review [[Image:Browsermap2016.pdf]]<br />
* 03 February 2010, Melissa Cline, Coordinated Alternative Splicing [[Image:CoordinatedSplicing.ppt]]<br />
* 05,07 January 2010 BME 230 class, Hiram Clawson, introduction to the UCSC genome browser and programming with the kent source tree. [[Image:BME230_Winter_2010.ppt]] Browser [[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=BME230%20Winter%202010 Session]] for example intersection.<br />
<br />
==2009==<br />
* 14 October Genecats meeting, [[Image:MonsatoIntroduction_Oct2009.pdf|Monsanto Introduction]] Brad Fabbri<br />
* 14 October Genecats meeting, Hiram Clawson - building the kent source tree and a UCSC genome browser assembly, [[Image:Genecats_2009_10_14.pptx|pptx power point]] or older style [[Image:Genecats_2009_10_14.ppt|ppt power point]]<br />
* 24 August Genecats meeting, Larry and Tim present 3 new hgTracks features coming down the shute: [[Media:Image20ui.pdf|image20ui.pdf]].<br />
* 29 July Genecats meeting, Mark's presentation on SVS/subversion proposal to replace CVS [[Image:svnForGb.pdf|svnForGb.pdf]].<br />
* 08 April Genecats meeting, Fan Hsu: "Some thoughts from Fan" [[Image:SomeThoughtsFromFan0408B.pdf|SomeThoughtsFromFan0408B.pdf]].<br />
* 08 January 2009 BME 230 class, Hiram Clawson, introduction to the UCSC genome browser and programming with the kent source tree. [[Image:BME230_Winter_2009.ppt]] Browser [[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=BME230%20Winter%202009 Session]] for example intersection.<br />
<br />
==2008==<br />
* 18 December 2008 [[Image:FrankJacobs181208.ppt]] - Frank Jacobs, Developmental Neurobiology, Rudolf Magnus Institute of Neuroscience, University of Utrecht, The Netherlands, "Pitx3 outSMRTs Nurr1 in dopamine neuron terminal differentiation"<br />
<br />
* Genecats - 17 December 2008 - [[Media:Matrix.ppt|Composite sketch]]: Nifty tricks for composite tracks (multi-view, dimensions, sorting, drag and drop, etc.). Tim Dreszer.<br />
<br />
* 11 December 2008, Paul Flicek, EBI, presenting 1,000 genomes project status [[Image:Flicek_11_DEC_2008.pdf]]<br />
<br />
* Genecats - 10 December 2008 - Ed Green from Max Planck Institute for Evolutionary Anthropology discusses the [[http://www.cell.com/retrieve/pii/S0092867408007733| Neandertal mtDNA]] project<br />
<br />
* Genecats - 15 October 2008 - [[Image:Metcalf.Richardson.2008-10-15.pdf]] Jake Metcalf, Sarah Richardson discussion of ethics controversy concerning Bruce T. Lahn of U. Chicago publications.<br />
<br />
* Sep. 2008 - Angie's "UCSC Genome Browser Tool Suite" poster presented at Genomics of Common Disease [[Media:UCSC_Genome_Browser_GCD_2008.ppt|PPT]] [[Media:UCSC_Genome_Browser_GCD_2008.pdf|PDF]]<br />
<br />
* 27 August 2008 - Jim Kent at the Computational Systems Bioinformatics Conference, Stanford CA, [[Image:Kent_decodingEncode.ppt]] a wide-ranging discussion of Encode research, using the Gene Sorter, using the Table browser, source code design issues<br />
<br />
* Genecats - 06 August 2008 - [[Image:ISMB2008_genecats_summary.ppt]] summary of ISMB 2008, Toronto, Hiram Clawson<br />
<br />
* Genecats - July 30, 2008 - [[Media:UBCSslides.ppt|Biased Clustered Subsitutions in the Human Genome: Sex, Gambling and Non-Darwinian Evolution]]. Tim Dreszer's presentation of his master's thesis work.<br />
<br />
* ISMB Toronto - July 2008 - Intelligent Systems for Molecular Biology [[Image:ISMB2008_UCSC.ppt]] presentation by Hiram Clawson. A brief tutorial on browser usage with special emphasis on how to perform intersections with the table browser. Task demonstrated: finding highly conserved non-coding regions of the genome.<br />
<br />
* Genecats - 05 July 2008 - Jim Kent describing the all.joiner file used by the UCSC genome browser to specify database table relationships - the database "schema" behind the browser [[Image:Kent_allJoiner.ppt]]<br />
<br />
* Genecats - 16 April 2008 - Rachel Harte trip report from Mouse Genome Annotation Summit Meeting and RefSeq/CCDS visit, NIH, Bethesda MD 12-14 March 2008 [[Image:MouseAnnotAndCCDSVisitReport041608.ppt]]<br />
<br />
* Genecats - 06 April 2008 - Jim Kent reviewing the Parasol super computer job management system [[Image:Kent_parasolArchitecture.ppt]]<br />
<br />
* Bejerano Lab (Stanford) - March 31, 2008 - [[Image:Bejerano Lab 2008 03 31.ppt]] Angie's crash course on using the kent/src tools and libraries. Did a brief live demo (TB intersection -> custom track) first. Group was already very familiar with browser and had their own mirror.<br />
<br />
* BME 230 Winter 2008, 10 January 2008, Robert Baertsch [[Image:Baertsch-code-talk.ppt]] genome browser introduction and kent src code preview<br />
<br />
==2007==<br />
* Genecats - 16 April 2008 - [[Image:ISMB2007TripReportGenecats.ppt]] Rachel Harte summary from ISMB 2007 meeting in Vienna, Austria<br />
* Jim's talk - 12 September 2007 - [[Image:geneSorter.ppt]] "Inside the Gene Sorter - A moderately complex CGI application" talk by Jim Kent<br />
<br />
==2006==<br />
<br />
* Genecats - September 12, 2006 - [[Image:Automation 2006 09 12 v2.ppt]] Overview of the automation scripts that are now in kent/src/hg/utils/automation/ (Angie).<br />
<br />
==2005==<br />
<br />
* Chicken Genome Meeting - May, 2005 - [[Image:Browsers CSHL Chicken 2005 05.ppt]] An intro to the Genome Browser and Table Browser (Angie).<br />
<br />
==2003==<br />
<br />
* CSHL June 2003 "Evolution and the Santa Cruz Genome Browser" [[Image:CSHL_2003_Jim_Kent.ppt]] presentation by Jim Kent. Recent new functions in the genome browser, using the chain and net process to highlight evolutionary processes, a new rat genome assembly with 3-way human-mouse-rat multiple alignment.<br />
<br />
==2002==<br />
<br />
* Charles Sugnet's talk January 2002 - "Adding tracks to the Human Genome Browser" [[Image:howToAddTrack_Sugnet.pdf|howToAddTrack_Sugnet.pdf]] and examples used in the talk - [[Image:sampTracksChr22.tab]]<br />
<br />
* Genecats October 2002 - "Software Sermon" [[Image:SoftwareSermon2002_Jim_Kent.ppt]] - software development philosophy and guidelines, Jim Kent.<br />
<br />
==2000==<br />
<br />
* October 2000 - "Details of the Genome Browser" [[Image:CompBioOct2000_Jim_Kent.ppt]] - Description of the genome browser software architecture, the early days. Jim Kent<br />
<br />
<br />
[[Category:Browser Development]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=File:PosterIchg2016.pdf&diff=23394File:PosterIchg2016.pdf2016-08-26T17:09:41Z<p>Kuhn: Poster, reformatted from Luvina's ACMG. Used at ICHG Kyoto, 2016</p>
<hr />
<div>Poster, reformatted from Luvina's ACMG. Used at ICHG Kyoto, 2016</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Tuning-primer.sh&diff=23110Tuning-primer.sh2016-03-10T15:50:38Z<p>Kuhn: grammar nit - removing errant apostrophe</p>
<hr />
<div>This is a shell script I found on the net. It uses MySQL internals to make recommendations about tuning your MySQL installation by adjusting /etc/my.cnf - the mysql startup file.<br />
<br />
Run it at your own risk as root. It worked for me but otherwise comes with no guarantees except the usual one - if it breaks anything of yours, you still own all the pieces.<br />
<br />
(Note: The script has been extended. Download from mysqltuner.com, link is on the right-hand side. --[[User:Max|Max]] 18:03, 25 February 2010 (UTC))<br />
<br />
<code><br />
#!/usr/bin/env bash<br />
<br />
#########################################################################<br />
# #<br />
# MySQL performance tuning primer script #<br />
# Writen by: Matthew Montgomery <mmontgom@rackspace.com> #<br />
# Inspired by: MySQLARd (http://gert.sos.be/demo/mysqlar/) #<br />
# Version 1.2-r6 #<br />
# Licenced under GPLv2 #<br />
# #<br />
#########################################################################<br />
#########################################################################<br />
# #<br />
# Set this socket variable if you have multiple instances running or if # <br />
# we are unable to find your socket otherwise #<br />
# #<br />
#########################################################################<br />
<br />
socket=<br />
<br />
function cecho ()<br />
<br />
## -- Function to easliy print colored text -- ##<br />
<br />
# Color-echo.<br />
# Argument $1 = message<br />
# Argument $2 = color<br />
{<br />
export black='\E[0m\c'<br />
export boldblack='\E[1;0m\c'<br />
export red='\E[31m\c'<br />
export boldred='\E[1;31m\c'<br />
export green='\E[32m\c'<br />
export boldgreen='\E[1;32m\c'<br />
export yellow='\E[33m\c'<br />
export boldyellow='\E[1;33m\c'<br />
export blue='\E[34m\c'<br />
export boldblue='\E[1;34m\c'<br />
export magenta='\E[35m\c'<br />
export boldmagenta='\E[1;35m\c'<br />
export cyan='\E[36m\c'<br />
export boldcyan='\E[1;36m\c'<br />
export white='\E[37m\c'<br />
export boldwhite='\E[1;37m\c'<br />
<br />
local default_msg="No message passed."<br />
# Doesn't really need to be a local variable.<br />
<br />
message=${1:-$default_msg} # Defaults to default message.<br />
color=${2:-$black} # Defaults to black, if not specified.<br />
<br />
echo -e "$color"<br />
echo -e "$message"<br />
tput sgr0 # Reset to normal.<br />
echo -e "$black"<br />
return<br />
} <br />
<br />
function print_banner () {<br />
<br />
## -- Banner -- ##<br />
<br />
cecho "\t\c " $black<br />
cecho "-- MYSQL PERFORMANCE TUNING PRIMER --" $boldblue<br />
cecho "\t - By: Matthew Montgomery -" $black<br />
<br />
}<br />
<br />
## -- Find the location of the mysql.sock file -- ##<br />
<br />
function check_for_socket () {<br />
if [ -z "$socket" ] ; then<br />
if [ -S /var/lib/mysql/mysql.sock ] ; then<br />
socket=/var/lib/mysql/mysql.sock<br />
elif [ -S /tmp/mysql.sock ] ; then<br />
socket=/tmp/mysql.sock<br />
else<br />
ps_socket=`netstat -ln | egrep "mysql(d)?\.sock" | awk '{ print $9 }'`<br />
if [ "$ps_socket" ] ; then<br />
socket=$ps_socket<br />
fi<br />
fi<br />
fi<br />
if [ -S "$socket" ] ; then<br />
echo UP > /dev/null<br />
else<br />
cecho "No valid socket file "$socket" found!" $boldred<br />
cecho "mysqld is not running or it is installed in a custom location" $red<br />
cecho "Please set the $socket variable at the top of this script."<br />
exit 1<br />
fi<br />
}<br />
<br />
<br />
function check_for_plesk_passwords () {<br />
<br />
## -- Check for the existance of plesk and login using its credentials -- ##<br />
<br />
if [ -f /etc/psa/.psa.shadow ] ; then<br />
mysql="mysql -S $socket -u admin -p`cat /etc/psa/.psa.shadow`"<br />
mysqladmin="mysqladmin -S $socket -u admin -p`cat /etc/psa/.psa.shadow`"<br />
else<br />
mysql="mysql -S $socket"<br />
mysqladmin="mysqladmin -S $socket"<br />
fi<br />
}<br />
<br />
function check_mysql_login () {<br />
<br />
## -- Test for running mysql -- ##<br />
<br />
is_up=`$mysqladmin ping 2>&1`<br />
if [ "$is_up" = "mysqld is alive" ] ; then<br />
echo UP > /dev/null<br />
elif [ "$is_up" != "mysqld is alive" ] ; then<br />
cecho "\n\c"<br />
cecho "- INITIAL LOGIN ATTEMPT FAILED -\n" $boldred<br />
if [ -z $prompted ] ; then<br />
find_webmin_passwords<br />
else<br />
return 1<br />
fi<br />
<br />
else <br />
cecho "Unknow exit status" $red<br />
exit -1<br />
fi<br />
}<br />
<br />
function final_login_attempt () {<br />
is_up=`$mysqladmin ping 2>&1`<br />
if [ "$is_up" = "mysqld is alive" ] ; then<br />
echo UP > /dev/null<br />
elif [ "$is_up" != "mysqld is alive" ] ; then<br />
cecho "- FINAL LOGIN ATTEMPT FAILED -\n" $boldred<br />
exit 1<br />
fi<br />
}<br />
<br />
function second_login_failed () {<br />
<br />
## -- create a ~/.my.cnf and exit when all else fails -- ##<br />
<br />
cecho "- RETRY LOGIN ATTEMPT FAILED -\n" $boldred<br />
cecho "Could not auto detect login info!\n"<br />
read -p "Do you have your login handy ? [y/N] : "<br />
case $REPLY in <br />
yes | y | Y | YES)<br />
answer1='yes'<br />
read -p "User: " user<br />
read -rsp "Password: " pass<br />
export mysql="$mysql -u$user -p$pass"<br />
export mysqladmin="$mysqladmin -u$user -p$pass"<br />
;;<br />
*)<br />
cecho "\nPlease create a valid login to MySQL"<br />
cecho "Or, set correct values for 'user=' and 'password=' in ~/.my.cnf"<br />
;;<br />
esac<br />
cecho "\n\c"<br />
read -p "Would you like me to create a ~/.my.cnf file for you? [y/N] : "<br />
case $REPLY in<br />
yes | y | Y | YES)<br />
answer2='yes'<br />
if [ ! -f ~/.my.cnf ] ; then<br />
umask 077<br />
echo -e "[client]\nuser=$user\npassword=$pass" > ~/.my.cnf<br />
if [ "$answer1" != 'yes' ] ; then<br />
exit 1<br />
else<br />
final_login_attempt<br />
return 0<br />
fi<br />
else<br />
cecho "\n~/.my.cnf already exists!\n" $boldred<br />
read -p "Replace ? [y/N] : "<br />
if [ "$REPLY" = 'y' ] || [ "$REPLY = 'Y' " ] ; then <br />
echo -e "[client]\nuser=$user\npassword=$pass" > ~/.my.cnf<br />
if [ "$answer1" != 'yes' ] ; then<br />
exit 1<br />
else<br />
final_login_attempt<br />
return 0<br />
fi<br />
else<br />
cecho "Please set the 'user=' and 'password=' values in ~/.my.cnf"<br />
exit 1<br />
fi<br />
fi<br />
;;<br />
*)<br />
if [ "$answer1" != 'yes' ] ; then<br />
exit 1<br />
else<br />
final_login_attempt<br />
return 0<br />
fi<br />
;;<br />
esac<br />
}<br />
<br />
function find_webmin_passwords () {<br />
<br />
## -- populate the .my.cnf file using values harvested from Webmin -- ##<br />
<br />
cecho "Testing Stored for passwords:\c"<br />
if [ -f /etc/webmin/mysql/config ] ; then<br />
user=`grep ^login= /etc/webmin/mysql/config | cut -d "=" -f 2`<br />
pass=`grep ^pass= /etc/webmin/mysql/config | cut -d "=" -f 2`<br />
if [ $user ] && [ $pass ] && [ ! -f ~/.my.cnf ] ; then<br />
cecho "Setting login info as User: $user Password: $pass"<br />
touch ~/.my.cnf<br />
chmod 600 ~/.my.cnf<br />
echo -e "[client]\nuser=$user\npassword=$pass" > ~/.my.cnf <br />
cecho "Retrying login"<br />
is_up=`$mysqladmin ping 2>&1`<br />
if [ "$is_up" = "mysqld is alive" ] ; then<br />
echo UP > /dev/null<br />
else<br />
second_login_failed<br />
fi<br />
echo<br />
else<br />
second_login_failed<br />
echo<br />
fi<br />
else<br />
cecho " None Found\n" $boldred<br />
second_login_failed<br />
fi<br />
}<br />
<br />
#########################################################################<br />
# #<br />
# Function to pull MySQL status variable #<br />
# #<br />
# Call using : #<br />
# mysql_status \'Mysql_status_variable\' bash_dest_variable #<br />
# #<br />
#########################################################################<br />
<br />
function mysql_status () {<br />
local status=`$mysql -Bse "show /*!50000 global */ status like $1" | <br />
awk '{ print $2 }'`<br />
export "$2"=$status<br />
}<br />
<br />
#########################################################################<br />
# #<br />
# Function to pull MySQL server runtime variable #<br />
# #<br />
# Call using : #<br />
# mysql_variable \'Mysql_server_variable\' bash_dest_variable #<br />
# - OR - #<br />
# mysql_variableTSV \'Mysql_server_variable\' bash_dest_variable #<br />
# #<br />
#########################################################################<br />
<br />
function mysql_variable () {<br />
local variable=`$mysql -e "show /*!500000 global */ variables like $1" | <br />
grep -v Variable_name | awk '{ print $2 }'`<br />
export "$2"=$variable<br />
}<br />
function mysql_variableTSV () {<br />
local variable=`$mysql -e "show variables like $1" | <br />
grep -v Variable_name | awk -F \t '{ print $2 }'`<br />
export "$2"=$variable<br />
}<br />
<br />
function divide () {<br />
<br />
# -- Divide two intigers -- #<br />
<br />
usage="$0 dividend divisor '$variable' scale"<br />
if [ $1 -ge 1 ] ; then<br />
dividend=$1<br />
else<br />
cecho "Invalid Dividend" $red<br />
echo $usage<br />
exit 1<br />
fi<br />
if [ $2 -ge 1 ] ; then<br />
divisor=$2<br />
else<br />
cecho "Invalid Divisor" $red<br />
echo $usage<br />
exit 1<br />
fi<br />
if [ ! -n $3 ] ; then<br />
cecho "Invalid variable name" $red<br />
echo $usage<br />
exit 1<br />
fi<br />
if [ -z $4 ] ; then<br />
scale=2<br />
elif [ $4 -ge 0 ] ; then<br />
scale=$4<br />
else<br />
cecho "Invalid scale" $red<br />
echo $usage<br />
exit 1<br />
fi<br />
export $3=$(echo "scale=$scale; $dividend / $divisor" | bc -l)<br />
}<br />
<br />
function human_readable () {<br />
<br />
#########################################################################<br />
# #<br />
# Convert a value in to human readable size and populate a variable #<br />
# with the result. #<br />
# #<br />
# Call using: #<br />
# human_readable $value 'variable name' #<br />
# #<br />
#########################################################################<br />
<br />
## value=$1<br />
## variable=$2<br />
scale=$3<br />
<br />
if [ $1 -gt 1048576 ] ; then<br />
if [ -z $3 ] ; then <br />
scale=0<br />
fi<br />
divide $1 1048576 "$2" $scale<br />
unit="M"<br />
elif [ $1 -gt 1024 ] ; then<br />
if [ -z $3 ] ; then<br />
scale=2<br />
fi<br />
divide $1 1024 "$2" $scale<br />
unit="K"<br />
else<br />
export "$2"=$1<br />
unit="bytes"<br />
fi<br />
# let "$2"=$HR<br />
}<br />
<br />
function human_readable_time () {<br />
<br />
########################################################################<br />
# #<br />
# Function to produce human readable time #<br />
# #<br />
########################################################################<br />
<br />
usage="$0 seconds 'variable'"<br />
if [ -z $1 ] || [ -z $2 ] ; then<br />
cecho $usage $red<br />
exit 1<br />
fi<br />
days=$(echo "scale=0 ; $1 / 86400" | bc -l)<br />
remainder=$(echo "scale=0 ; $1 % 86400" | bc -l)<br />
hours=$(echo "scale=0 ; $remainder / 3600" | bc -l)<br />
remainder=$(echo "scale=0 ; $remainder % 3600" | bc -l)<br />
minutes=$(echo "scale=0 ; $remainder / 60" | bc -l)<br />
seconds=$(echo "scale=0 ; $remainder % 60" | bc -l)<br />
export $2="$days days $hours hrs $minutes min $seconds sec"<br />
}<br />
<br />
function check_mysql_version () {<br />
<br />
## -- Print Version Info -- ##<br />
<br />
mysql_variable \'version\' mysql_version<br />
mysql_variable \'version_compile_machine\' mysql_version_compile_machine<br />
<br />
cecho "MySQL Version $mysql_version $mysql_version_compile_machine"<br />
}<br />
<br />
function post_uptime_warning () {<br />
<br />
#########################################################################<br />
# #<br />
# Present a reminder that mysql must run for a couple of days to #<br />
# build up good numbers in server status variables before these tuning #<br />
# suggestions should be used. #<br />
# #<br />
#########################################################################<br />
<br />
mysql_status \'Uptime\' uptime<br />
mysql_status \'Threads_connected\' threads<br />
let queries_per_sec=$questions/$uptime<br />
human_readable_time $uptime uptimeHR<br />
<br />
cecho "Uptime = $uptimeHR"<br />
cecho "Avg. qps = $queries_per_sec"<br />
cecho "Total Questions = $questions"<br />
cecho "Threads Connected = $threads"<br />
echo<br />
<br />
if [ $uptime -gt 172800 ] ; then<br />
cecho "Server has been running for over 48hrs."<br />
cecho "It should be safe to follow these recommendations"<br />
else<br />
cecho "Warning: \c" $boldred<br />
cecho "Server has not been running for at least 48hrs." $boldred<br />
cecho "It may not be safe to use these recommendations" $boldred<br />
<br />
fi<br />
echo ""<br />
cecho "To find out more information on how each of these" $red<br />
cecho "runtime variables effects performance visit:" $red<br />
if [ $major_version == '3.23' ] || [ $major_version == '4.0' ] || [ $major_version == '4.1' ]; then<br />
cecho "http://dev.mysql.com/doc/refman/4.1/en/server-system-variables.html" $boldblue<br />
elif [ $major_version == '5.0' ] || [ $major_version == '5.1' ] ; then<br />
cecho "http://dev.mysql.com/doc/refman/$major_version/en/server-system-variables.html" $boldblue<br />
else<br />
echo "UNSUPPORTED MYSQL VERSION"<br />
exit 1<br />
fi<br />
}<br />
<br />
function check_slow_queries () {<br />
<br />
## -- Slow Queries -- ## <br />
<br />
cecho "SLOW QUERIES" $boldblue<br />
<br />
mysql_status \'Slow_queries\' slow_queries<br />
mysql_variable \'long_query_time\' long_query_time<br />
mysql_variable \'log%queries\' log_slow_queries<br />
prefered_query_time=5<br />
if [ -e /etc/my.cnf ] ; then<br />
if [ -z $log_slow_queries ] ; then<br />
log_slow_queries=`grep log-slow-queries /etc/my.cnf`<br />
fi<br />
fi<br />
cecho "Current long_query_time = $long_query_time sec."<br />
cecho "You have \c"<br />
cecho "$slow_queries \c" $boldred <br />
cecho "out of \c"<br />
cecho "$questions \c" $boldred<br />
cecho "that take longer than $long_query_time sec. to complete"<br />
<br />
if [ "$log_slow_queries" = 'ON' ] ; then<br />
cecho "The slow query log is enabled."<br />
elif [ "$log_slow_queries" = 'OFF' ] ; then<br />
cecho "The slow query log is \c"<br />
cecho "NOT \c" $boldred<br />
cecho "enabled."<br />
elif [ -z $log_slow_queries ] ; then<br />
cecho "The slow query log is \c"<br />
cecho "NOT \c" $boldred<br />
cecho "enabled."<br />
else<br />
cecho "Error: $log_slow_queries" $boldred<br />
fi<br />
<br />
if [ $long_query_time -gt $prefered_query_time ] ; then<br />
cecho "Your long_query_time may be too high, I typically set this under $prefered_query_time sec." $red<br />
else<br />
cecho "Your long_query_time seems to be fine" $green<br />
fi <br />
}<br />
<br />
function check_used_connections () {<br />
<br />
## -- Used Connections -- ##<br />
<br />
mysql_variable \'max_connections\' max_connections<br />
mysql_status \'Max_used_connections\' max_used_connections<br />
mysql_status \'Threads_connected\' threads_connected<br />
<br />
let connections_ratio=$max_used_connections*100/$max_connections<br />
<br />
cecho "MAX CONNECTIONS" $boldblue<br />
cecho "Current max_connections = $max_connections"<br />
cecho "Current threads_connected = $threads_connected"<br />
cecho "Historic max_used_connections = $max_used_connections"<br />
cecho "The number of used connections is \c"<br />
if [ $connections_ratio -ge 85 ] ; then<br />
txt_color=$red<br />
else <br />
txt_color=$green<br />
fi<br />
# cecho "$max_used_connections \c" $txt_color<br />
# cecho "which is \c"<br />
cecho "$connections_ratio% \c" $txt_color<br />
cecho "of the configured maximum."<br />
unset txt_color<br />
<br />
if [ $connections_ratio -ge 85 ] ; then<br />
cecho "You should raise max_connections" $red<br />
else <br />
cecho "Your max_connections variable seems to be fine." $green<br />
fi<br />
}<br />
<br />
function check_threads() {<br />
<br />
## -- Worker Threads -- ##<br />
<br />
cecho "WORKER THREADS" $boldblue<br />
<br />
mysql_status \'Threads_created\' threads_created1<br />
sleep 1<br />
mysql_status \'Threads_created\' threads_created2<br />
<br />
mysql_status \'Threads_cached\' threads_cached<br />
mysql_status \'Uptime\' uptime<br />
mysql_variable \'thread_cache_size\' thread_cache_size<br />
<br />
let historic_threads_per_sec=$threads_created1/$uptime<br />
let current_threads_per_sec=$threads_created2-$threads_created1;<br />
<br />
cecho "Current thread_cache_size = $thread_cache_size"<br />
cecho "Current threads_cached = $threads_cached"<br />
cecho "Current threads_per_sec = $current_threads_per_sec"<br />
cecho "Historic threads_per_sec = $historic_threads_per_sec"<br />
<br />
if [ $historic_threads_per_sec -ge 2 ] && [ $threads_cached -le 1 ] ; then<br />
cecho "Threads created per/sec are overrunning threads cached" $red<br />
cecho "You should raise thread_cache_size" $red<br />
elif [ $current_threads_per_sec -ge 2 ] ; then<br />
cecho "Threads created per/sec are overrunning threads cached" $red<br />
cecho "You should raise thread_cache_size" $red<br />
else<br />
cecho "Your thread_cache_size is fine" $green<br />
fi<br />
}<br />
<br />
function check_key_buffer_size () {<br />
<br />
## -- Key buffer Size -- ##<br />
<br />
cecho "KEY BUFFER" $boldblue<br />
<br />
mysql_status \'Key_read_requests\' key_read_requests<br />
mysql_status \'Key_reads\' key_reads<br />
mysql_status \'Key_blocks_used\' key_blocks_used<br />
mysql_status \'Key_blocks_unused\' key_blocks_unused<br />
mysql_variable \'key_buffer_size\' key_buffer_size<br />
mysql_variable \'datadir\' datadir<br />
<br />
<br />
myisam_indexes=`$mysql -Bse "/*!50000 SELECT SUM(INDEX_LENGTH) from information_schema.TABLES where ENGINE='MyISAM' <br />
*/"`<br />
OS=$(uname)<br />
<br />
if [ "$OS" == 'Darwin' ] || [ "$OS" == 'FreeBSD' ] || [ "$OS" == 'OpenBSD' ] ; then<br />
duflags=''<br />
else<br />
duflags='-b'<br />
fi<br />
if [ -z "$myisam_indexes" ] ; then<br />
myisam_indexes=`find $datadir -name '*.MYI' -exec du $duflags '{}' \; | awk '{ s += $1 } END { <br />
printf("%i\n", s )}'`<br />
fi<br />
<br />
if [ $key_reads -eq 0 ] ; then<br />
cecho "No key reads?!" $boldred<br />
cecho "Seriously look into using some indexes" $red<br />
key_cache_miss_rate=0<br />
key_buffer_ratio=0<br />
key_buffer_ratioRND=0<br />
else<br />
let key_cache_miss_rate=$key_read_requests/$key_reads<br />
if [ ! -z $key_blocks_unused ] ; then<br />
let key_blocks_total=$key_blocks_used+$key_blocks_unused<br />
divide $key_blocks_used $key_blocks_total key_buffer_fill 2<br />
key_buffer_ratio=$(echo "$key_buffer_fill * 100" | bc -l)<br />
key_buffer_ratioRND=$(echo "scale=0; $key_buffer_ratio / 1" | bc -l)<br />
else<br />
key_buffer_ratio='Unknown'<br />
key_buffer_ratioRND=75<br />
fi<br />
fi<br />
<br />
human_readable $myisam_indexes myisam_indexes_HR 0<br />
cecho "Current MyISAM index space = $myisam_indexes_HR $unit" <br />
<br />
human_readable $key_buffer_size key_buffer_size_HR 0<br />
cecho "Current key_buffer_size = $key_buffer_size_HR $unit"<br />
cecho "Key cache miss rate is 1 / $key_cache_miss_rate"<br />
cecho "Key buffer fill ratio = $key_buffer_ratio %" <br />
<br />
if [ $key_cache_miss_rate -le 100 ] && [ $key_cache_miss_rate -gt 0 ] && [ $key_buffer_ratioRND -ge 80 ]; then<br />
cecho "You could increase key_buffer_size" $boldred<br />
cecho "It is safe to raise this up to 1/4 of total system memory;"<br />
cecho "assuming this is a dedicated database server."<br />
elif [ $key_buffer_ratioRND -ge 80 ] && [ $key_buffer_size -le $myisam_indexes ] ; then<br />
cecho "You could increase key_buffer_size" $boldred<br />
cecho "It is safe to raise this up to 1/4 of total system memory;"<br />
cecho "assuming this is a dedicated database server."<br />
elif [ $key_cache_miss_rate -ge 10000 ] || [ $key_buffer_ratioRND -le 50 ] ; then<br />
cecho "Your key_buffer_size seems to be too high." $red <br />
cecho "Perhaps you can use these resources elsewhere" $red<br />
else<br />
cecho "Your key_buffer_size seems to be fine" $green<br />
fi<br />
}<br />
<br />
function check_query_cache () {<br />
<br />
## -- Query Cache -- ##<br />
<br />
cecho "QUERY CACHE" $boldblue<br />
<br />
mysql_variable \'version\' mysql_version<br />
mysql_variable \'query_cache_size\' query_cache_size<br />
mysql_status \'Qcache_free_memory\' qcache_free_memory<br />
mysql_status \'Qcache_lowmem_prunes\' qcache_lowmem_prunes<br />
<br />
if [ -z $query_cache_size ] ; then<br />
cecho "You are using MySQL $mysql_version, no query cache is supported. \nI recommend an upgrade to MySQL <br />
4.0 or better" $red<br />
elif [ $query_cache_size -eq 0 ] ; then<br />
cecho "Query cache is supported but not enabled" $red<br />
cecho "Perhaps you should set the query_cache_size" $red<br />
else<br />
let qcache_used_memory=$query_cache_size-$qcache_free_memory<br />
qcache_fill_ratio=$(echo "scale=2; $qcache_used_memory * 100 / $query_cache_size" | bc -l)<br />
qcache_fill_ratio_HR=$(echo "scale=0; $qcache_fill_ratio / 1" | bc -l)<br />
cecho "Query cache is enabled" $green<br />
human_readable $query_cache_size query_cache_size_HR<br />
cecho "Current query_cache_size = $query_cache_size_HR $unit"<br />
human_readable $qcache_used_memory qcache_used_memory_HR<br />
cecho "Current query_cache_used = $qcache_used_memory_HR $unit"<br />
cecho "Current Query cache fill ratio = $qcache_fill_ratio %"<br />
if [ $qcache_fill_ratio_HR -le 25 ] ; then<br />
cecho "Your query_cache_size seems to be too high." $red<br />
cecho "Perhaps you can use these resources elsewhere" $red<br />
fi<br />
if [ $qcache_lowmem_prunes -ge 50 ] && [ $qcache_fill_ratio_HR -ge 80 ]; then<br />
cecho "However, \c"<br />
cecho "$qcache_lowmem_prunes \c" $boldred<br />
cecho "queries have been removed from the query cache due to lack of memory"<br />
cecho "Perhaps you should raise query_cache_size" $boldred<br />
fi<br />
fi<br />
<br />
}<br />
<br />
function check_sort_operations () {<br />
<br />
## -- Sort Operations -- ##<br />
<br />
cecho "SORT OPERATIONS" $boldblue<br />
<br />
mysql_status \'Sort_merge_passes\' sort_merge_passes<br />
mysql_status \'Sort_scan\' sort_scan<br />
mysql_status \'Sort_range\' sort_range<br />
mysql_variable \'sort_buffer%\' sort_buffer_size <br />
mysql_variable \'read_rnd_buffer_size\' read_rnd_buffer_size <br />
<br />
let total_sorts=$sort_scan+$sort_range<br />
if [ -z $read_rnd_buffer_size ] ; then<br />
mysql_variable \'record_buffer\' read_rnd_buffer_size<br />
fi<br />
<br />
## Correct rounding error in mysqld where 512K != 524288 ##<br />
let sort_buffer_size=$sort_buffer_size+8<br />
let read_rnd_buffer_size=$read_rnd_buffer_size+8<br />
<br />
human_readable $sort_buffer_size sort_buffer_size_HR<br />
cecho "Current sort_buffer_size = $sort_buffer_size_HR $unit"<br />
<br />
human_readable $read_rnd_buffer_size read_rnd_buffer_size_HR<br />
cecho "Current record/read_rnd_buffer_size = $read_rnd_buffer_size_HR $unit"<br />
<br />
if [ $total_sorts -eq 0 ] ; then <br />
cecho "No sort operations have been performed"<br />
passes_per_sort=0<br />
fi<br />
if [ $sort_merge_passes -ne 0 ] ; then<br />
let passes_per_sort=$sort_merge_passes/$total_sorts<br />
else<br />
passes_per_sort=0<br />
fi<br />
<br />
if [ $passes_per_sort -ge 2 ] ; then<br />
cecho "On average \c"<br />
cecho "$passes_per_sort \c" $boldred<br />
cecho "sort merge passes are made per sort operation"<br />
cecho "You should raise your sort_buffer_size"<br />
cecho "You should also raise your \c"<br />
if [ $major_version == '3.23' ] ; then <br />
cecho "record_rnd_buffer_size"<br />
else<br />
cecho "read_rnd_buffer_size"<br />
fi<br />
else<br />
cecho "Sort buffer seems to be fine" $green<br />
fi<br />
}<br />
<br />
function check_join_operations () {<br />
<br />
## -- Joins -- ##<br />
<br />
cecho "JOINS" $boldblue<br />
<br />
mysql_status \'Select_full_join\' select_full_join<br />
mysql_status \'Select_range_check\' select_range_check<br />
mysql_variable \'join_buffer%\' join_buffer_size<br />
<br />
human_readable $join_buffer_size join_buffer_size_HR<br />
<br />
cecho "Current join_buffer_size = $join_buffer_size_HR $unit"<br />
cecho "You have had $select_full_join queries where a join could not use an index properly"<br />
<br />
if [ $select_range_check -eq 0 ] && [ $select_full_join -eq 0 ] ; then<br />
cecho "Your joins seem to be using indexes properly" $green<br />
fi<br />
if [ $select_full_join -gt 0 ] ; then<br />
print_error='true'<br />
fi<br />
if [ $select_range_check -gt 0 ] ; then<br />
cecho "You have had $select_range_check joins without keys that check for key usage after each row" $red<br />
print_error='true'<br />
fi<br />
## Debuging ##<br />
# print_error='true'<br />
if [ $print_error ] ; then <br />
if [ $major_version == '3.23' ] || [ $major_version == '4.0' ] ; then<br />
cecho "You should enable \"log-long-format\" "<br />
elif [ $major_version == '4.1' ] || [ $major_version == '5.0' ] || [ $major_version == '5.1' ] ; then<br />
cecho "You should enable \"log-queries-not-using-indexes\""<br />
fi<br />
cecho "Then look for non indexed joins in the slow query log."<br />
cecho "If you are unable to optimize your queries you may want to increase your"<br />
cecho "join_buffer_size to accommodate larger joins in one pass."<br />
fi<br />
<br />
# XXX Add test for join_buffer_size <br />
}<br />
<br />
check_tmp_tables () {<br />
<br />
## -- Temp Tables -- ##<br />
<br />
cecho "TEMP TABLES" $boldblue<br />
<br />
mysql_status \'Created_tmp_tables\' created_tmp_tables <br />
mysql_status \'Created_tmp_disk_tables\' created_tmp_disk_tables<br />
mysql_variable \'tmp_table_size\' tmp_table_size<br />
<br />
human_readable $tmp_table_size tmp_table_size_HR <br />
<br />
if [ $created_tmp_tables -eq 0 ] ; then<br />
tmp_disk_tables=0<br />
else<br />
let tmp_disk_tables=created_tmp_disk_tables*100/created_tmp_tables<br />
fi<br />
cecho "Current tmp_table_size = $tmp_table_size_HR $unit"<br />
cecho "$tmp_disk_tables% of tmp tables created were disk based"<br />
if [ $tmp_disk_tables -ge 25 ] ; then<br />
cecho "Perhaps you should increase your tmp_table_size" $red<br />
else<br />
cecho "Created disk tmp tables ratio seems fine" $green<br />
fi<br />
}<br />
<br />
function check_table_cache () {<br />
<br />
## -- Table Cache -- ##<br />
<br />
cecho "TABLE CACHE" $boldblue<br />
<br />
mysql_variable \'datadir\' datadir<br />
mysql_variable \'table_cache\' table_cache<br />
<br />
## /* MySQL +5.1 version of table_cache */ ## <br />
mysql_variable \'table_open_cache\' table_open_cache<br />
mysql_variable \'table_definition_cache\' table_definition_cache<br />
<br />
mysql_status \'Open_tables\' open_tables<br />
mysql_status \'Opened_tables\' opened_tables<br />
mysql_status \'Open_table_definitions\' open_table_definitions<br />
<br />
# socket_owner=`find $socket -printf '%u\n'`<br />
socket_owner=`ls -l $socket | awk '{ print $3 }'`<br />
script_runner=`whoami`<br />
<br />
table_count=`$mysql -Bse "/*!50000 SELECT COUNT(*) FROM INFORMATION_SCHEMA.TABLES WHERE TABLE_TYPE='BASE TABLE' <br />
*/"`<br />
<br />
if [ -z $table_count ] ; then<br />
if [ "$script_runner" != "$socket_owner" ] && [ "$script_runner" != "root" ] ; then<br />
cecho "You are not '$socket_owner' or 'root'" $red<br />
cecho "I am unable to determine the table_count!" $red<br />
else<br />
table_count=`find $datadir 2>&1 | grep -c .frm$`<br />
fi<br />
fi<br />
if [ $table_open_cache ] ; then<br />
table_cache=$table_open_cache<br />
fi<br />
<br />
if [ $opened_tables -ne 0 ] && [ $table_cache -ne 0 ] ; then <br />
let table_cache_hit_rate=$open_tables*100/$opened_tables<br />
let table_cache_fill=$open_tables*100/$table_cache<br />
elif [ $opened_tables -eq 0 ] && [ $table_cache -ne 0 ] ; then<br />
table_cache_hit_rate=100<br />
let table_cache_fill=$open_tables*100/$table_cache<br />
else<br />
cecho "ERROR no table_cache ?!" $boldred<br />
exit 1<br />
fi<br />
if [ $table_cache ] && [ ! $table_open_cache ] ; then<br />
cecho "Current table_cache value = $table_cache tables"<br />
fi<br />
if [ $table_open_cache ] ; then<br />
cecho "Current table_open_cache = $table_open_cache tables"<br />
cecho "Current table_definition_cache = $table_definition_cache tables"<br />
fi<br />
if [ $table_count ] ; then<br />
cecho "You have a total of $table_count tables"<br />
fi<br />
<br />
if [ $table_cache_fill -lt 95 ] ; then<br />
cecho "You have \c"<br />
cecho "$open_tables \c" $green<br />
cecho "open tables." <br />
cecho "The table_cache value seems to be fine" $green<br />
elif [ $table_cache_hit_rate -le 85 -o $table_cache_fill -ge 95 ]; then<br />
cecho "You have \c"<br />
cecho "$open_tables \c" $boldred<br />
cecho "open tables."<br />
cecho "Current table_cache hit rate is \c" <br />
cecho "$table_cache_hit_rate%\c" $boldred<br />
cecho ", while \c"<br />
cecho "$table_cache_fill% \c" $boldred<br />
cecho "of your table cache is in use"<br />
cecho "You should probably increase your table_cache" $red<br />
else<br />
cecho "Current table_cache hit rate is \c"<br />
cecho "$table_cache_hit_rate%\c" $green<br />
cecho ", while \c"<br />
cecho "$table_cache_fill% \c" $green<br />
cecho "of your table cache is in use"<br />
cecho "The table cache value seems to be fine" $green<br />
fi<br />
if [ $table_definition_cache ] && [ $table_definition_cache -le $table_count ] && [ $table_count -ge 100 ] ; then<br />
cecho "You should probably increase your table_definition_cache value." $red<br />
fi<br />
}<br />
<br />
function check_table_locking () {<br />
<br />
## -- Table Locking -- ##<br />
<br />
cecho "TABLE LOCKING" $boldblue<br />
<br />
mysql_status \'Table_locks_waited\' table_locks_waited<br />
mysql_status \'Table_locks_immediate\' table_locks_immediate<br />
mysql_variable \'concurrent_insert\' concurrent_insert<br />
mysql_variable \'low_priority_updates\' low_priority_updates<br />
if [ "$concurrent_insert" = 'ON' ]; then<br />
let concurrent_insert=1<br />
elif [ "$concurrent_insert" = 'OFF' ]; then<br />
let concurrent_insert=0<br />
fi<br />
<br />
cecho "Current Lock Wait ratio = \c"<br />
if [ $table_locks_waited -gt 0 ]; then<br />
let immediate_locks_miss_rate=$table_locks_immediate/$table_locks_waited<br />
cecho "1 : $immediate_locks_miss_rate" $red <br />
else<br />
let immediate_locks_miss_rate=99999 # perfect<br />
cecho "0 : $questions" $green<br />
fi<br />
if [ $immediate_locks_miss_rate -lt 5000 ] ; then<br />
cecho "You may benefit from selective use of InnoDB."<br />
if [ "$low_priority_updates" == 'OFF' ] ; then<br />
cecho "If you have long running SELECT's against MyISAM tables \c"<br />
cecho "and perform frequent updates consider setting 'low_priority_updates=1'"<br />
fi<br />
if [ $concurrent_insert -le 1 ] && [ $major_version == '5.0' ] ; then<br />
cecho "If you have a high concurrentcy of inserts on Dynamic row-lenght tables \c"<br />
cecho "consider setting 'concurrent_insert=2'."<br />
elif [ $concurrent_insert -le 1 ] && [ $major_version == '5.1' ] ; then<br />
cecho "If you have a high concurrentcy of inserts on Dynamic row-lenght tables \c"<br />
cecho "consider setting 'concurrent_insert=2'."<br />
fi<br />
else<br />
cecho "Your table locking seems to be fine" $green<br />
fi<br />
}<br />
<br />
function check_table_scans () {<br />
<br />
## -- Table Scans -- ##<br />
<br />
cecho "TABLE SCANS" $boldblue<br />
<br />
mysql_status \'Com_select\' com_select<br />
mysql_status \'Handler_read_rnd_next\' read_rnd_next<br />
mysql_variable \'read_buffer_size\' read_buffer_size<br />
<br />
if [ -z $read_buffer_size ] ; then<br />
mysql_variable \'record_buffer\' read_buffer_size<br />
fi<br />
<br />
human_readable $read_buffer_size read_buffer_size_HR<br />
cecho "Current read_buffer_size = $read_buffer_size_HR $unit"<br />
<br />
if [ $com_select -gt 0 ] ; then<br />
let full_table_scans=$read_rnd_next/$com_select <br />
cecho "Current table scan ratio = $full_table_scans : 1"<br />
if [ $full_table_scans -ge 4000 ] && [ $read_buffer_size -le 2097152 ] ; then<br />
cecho "You have a high ratio of sequential access requests to SELECTs" $red<br />
cecho "You may benefit from raising \c" $red<br />
if [ $major_version == '3.23' ] ; then <br />
cecho "record_buffer \c" $red<br />
else<br />
cecho "read_buffer_size \c" $red<br />
fi<br />
cecho "and/or improving your use of indexes." $red<br />
elif [ $read_buffer_size -gt 2097152 ] ; then <br />
cecho "read_buffer_size is over 2 MB \c" $red <br />
cecho "there is probably no need for such a large read_buffer" $red<br />
<br />
else<br />
cecho "read_buffer_size seems to be fine" $green<br />
fi<br />
else<br />
cecho "read_buffer_size seems to be fine" $green<br />
fi<br />
}<br />
<br />
<br />
function check_innodb_status () {<br />
<br />
## -- InnoDB -- ##<br />
<br />
mysql_variable \'have_innodb\' have_innodb<br />
<br />
if [ "$have_innodb" = "YES" ] ; then<br />
mysql_variable \'innodb_buffer_pool_size\' innodb_buffer_pool_size<br />
echo<br />
cecho "INNODB STATUS" $boldblue<br />
innodb_indexes=`$mysql -Bse "/*!50000 SELECT SUM(INDEX_LENGTH) from information_schema.TABLES where <br />
ENGINE='InnoDB' */"`<br />
<br />
if [ ! -z "$innodb_indexes" ] ; then<br />
human_readable $innodb_indexes innodb_indexes_HR 0<br />
cecho "Current InnoDB index space = $innodb_indexes_HR $unit"<br />
else<br />
cecho "Cannot find InnoDB index space prior to 5.0.x" $red<br />
fi<br />
<br />
human_readable $innodb_buffer_pool_size innodb_buffer_pool_sizeHR<br />
cecho "Current innodb_buffer_pool_size = $innodb_buffer_pool_sizeHR $unit"<br />
cecho "Depending on how much space your innodb indexes take up it may be safe" <br />
cecho "to increase this value to up to 1 / 3 of total system memory"<br />
echo<br />
$mysql -s -e "SHOW /*!50000 ENGINE */INNODB STATUS\G"<br />
else<br />
cecho "No InnoDB Support Enabled!" $boldred<br />
fi<br />
}<br />
<br />
function total_memory_used () {<br />
<br />
## -- Total Memory Usage -- ##<br />
cecho "MEMORY USAGE" $boldblue<br />
<br />
mysql_variable \'read_buffer_size\' read_buffer_size<br />
mysql_variable \'sort_buffer_size\' sort_buffer_size<br />
mysql_variable \'thread_stack\' thread_stack<br />
mysql_variable \'max_connections\' max_connections<br />
mysql_status \'Max_used_connections\' max_used_connections<br />
<br />
let per_thread_buffers=($read_buffer_size+$sort_buffer_size+$thread_stack)*$max_used_connections<br />
let per_thread_max_buffers=($read_buffer_size+$sort_buffer_size+$thread_stack)*$max_connections<br />
<br />
mysql_variable \'innodb_buffer_pool_size\' innodb_buffer_pool_size<br />
if [ -z $innodb_buffer_pool_size ] ; then<br />
innodb_buffer_pool_size=0<br />
fi<br />
<br />
mysql_variable \'innodb_additional_mem_pool_size\' innodb_additional_mem_pool_size<br />
if [ -z $innodb_additional_mem_pool_size ] ; then<br />
innodb_additional_mem_pool_size=0<br />
fi<br />
<br />
mysql_variable \'innodb_log_buffer_size\' innodb_log_buffer_size<br />
if [ -z $innodb_log_buffer_size ] ; then<br />
innodb_log_buffer_size=0<br />
fi<br />
<br />
mysql_variable \'key_buffer_size\' key_buffer_size<br />
<br />
mysql_variable \'query_cache_size\' query_cache_size<br />
if [ -z $query_cache_size ] ; then<br />
query_cache_size=0<br />
fi<br />
<br />
<br />
let <br />
global_buffers=$innodb_buffer_pool_size+$innodb_additional_mem_pool_size+$innodb_log_buffer_size+$key_buffer_size+$query_cache_size<br />
<br />
let total_memory=$global_buffers+$per_thread_buffers<br />
let max_memory=$global_buffers+$per_thread_max_buffers<br />
human_readable $total_memory total_memoryHR 0<br />
cecho "Max Memory Ever Allocated : $total_memoryHR $unit" $boldred<br />
human_readable $max_memory max_memoryHR 0<br />
cecho "Configured Max Memory Limit : $max_memoryHR $unit" $boldred<br />
<br />
total_system_memory=`free -b | grep -v buffers | awk '{ s += $2 } END { printf("%ld\n", s ) }'`<br />
human_readable $total_system_memory total_system_memoryHR 0<br />
cecho "Total System Memory : $total_system_memoryHR $unit" $boldred<br />
}<br />
<br />
function snarky () {<br />
<br />
## -- Be Snarky -- ##<br />
<br />
fortune=`which fortune 2>/dev/null` <br />
if [ -z $fortune ] ; then<br />
echo "What the hell sort of straight-lace bastard doesn't have fortune installed?"<br />
else<br />
$fortune<br />
fi<br />
}<br />
<br />
## Required Functions ## <br />
<br />
function login_validation () {<br />
check_for_socket # determine the socket location -- 1st login<br />
check_for_plesk_passwords # determine the login method -- 2nd login<br />
check_mysql_login # determine if mysql is accepting login -- 3rd login<br />
export major_version=`$mysql -Bse 'select substring_index(version(), ".", +2)'`<br />
export OS=`uname`<br />
mysql_status \'Questions\' questions<br />
}<br />
<br />
## Optional Components Groups ##<br />
<br />
function banner_info () {<br />
print_banner ; echo<br />
check_mysql_version ; echo<br />
post_uptime_warning ; echo<br />
}<br />
<br />
function misc () {<br />
check_slow_queries ; echo<br />
check_used_connections ; echo<br />
check_threads ; echo<br />
}<br />
<br />
function memory () {<br />
total_memory_used ; echo<br />
check_key_buffer_size ; echo<br />
check_query_cache ; echo<br />
check_sort_operations ; echo<br />
check_join_operations ; echo<br />
}<br />
<br />
function file () {<br />
check_table_cache ; echo<br />
check_tmp_tables ; echo<br />
check_table_scans ; echo<br />
check_table_locking ; echo<br />
}<br />
<br />
function all () {<br />
banner_info<br />
misc<br />
memory<br />
file<br />
# snarky<br />
}<br />
<br />
function prompt () {<br />
prompted='true'<br />
read -p "Username [anonymous] : " user<br />
read -rsp "Password [<none>] : " pass<br />
cecho "\n\c"<br />
read -p "Socket [ /var/lib/mysql/mysql.sock ] : " socket<br />
if [ -z $socket ] ; then<br />
export socket='/var/lib/mysql/mysql.sock'<br />
fi<br />
if [ -n $pass ] ; then<br />
pass_flag='-p'<br />
fi<br />
mysql="mysql -S $socket -u$user $pass_flag$pass"<br />
mysqladmin="mysqladmin -S $socket -u$user $pass_flag$pass"<br />
echo $mysql<br />
check_for_socket<br />
check_mysql_login<br />
if [ $? = 1 ] ; then<br />
exit 1<br />
fi<br />
read -p "Mode to test (see usage:) [all] : " pmode<br />
case $pmode in<br />
banner )<br />
banner_info <br />
;;<br />
misc )<br />
misc<br />
;;<br />
memory )<br />
memory<br />
;; <br />
file )<br />
file<br />
;;<br />
innodb )<br />
innodb<br />
;;<br />
all | *)<br />
all<br />
;;<br />
esac <br />
}<br />
<br />
if [ -z $1 ] ; then<br />
login_validation<br />
mode='ALL'<br />
elif [ "$1" != "prompt" ] || [ "$1" != "PROMPT" ] ; then<br />
login_validation<br />
mode=$1<br />
elif [ "$1" = "prompt" ] || [ "$1" = "PROMPT" ] ; then<br />
mode=$1<br />
fi<br />
<br />
case $mode in <br />
ALL | all )<br />
cecho "\n\c"<br />
all<br />
;;<br />
mem | memory | MEM | MEMORY )<br />
cecho "\n\c"<br />
memory<br />
;;<br />
file | FILE | disk | DISK )<br />
cecho "\n\c"<br />
file<br />
;;<br />
banner | BANNER | header | HEADER | head)<br />
banner_info<br />
;;<br />
misc | MISC | miscelaneous )<br />
cecho "\n\c"<br />
misc<br />
;;<br />
innodb | INNODB )<br />
banner_info<br />
check_innodb_status ; echo<br />
;;<br />
prompt | PROMPT )<br />
prompt<br />
;;<br />
*)<br />
cecho "usage: $0 [ all | banner | file | innodb | memory | misc | promp ]" $boldred<br />
exit 1<br />
;;<br />
esac<br />
<br />
<br />
<br />
</code><br />
<br />
<br />
[[Category:User Developed Scripts]]<br />
[[Category:Mirror Site FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Learn_about_the_Browser&diff=23034Learn about the Browser2016-01-10T23:29:08Z<p>Kuhn: /* Use the browser website */</p>
<hr />
<div>This page links to various pages that will help you to learn more about the UCSC Genome Browser. It is sorted by increasing technical complexity: the first steps require only a webbrowser, the last ones administrator access to a Linux webserver.<br />
<br />
== Use the browser website ==<br />
* Bob Kuhn is giving workshops throughout the year at several US conferences, in Europe, Australia and Asia<br />
** Read about how to [http://genome.ucsc.edu/training/ | host]<br />
* Video tutorials and slides by [http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml Openhelix]<br />
* An introduction on [http://www.nature.com/scitable/ebooks/guide-to-the-ucsc-genome-browser-16569863/contents Nature Education]<br />
* Basic materials written by the gurus: The [http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html User's guide] and the [http://genome.ucsc.edu/FAQ/ FAQs]. <br />
* View a [[Genome_Browser_Session_Gallery|gallery]] of browser sessions that highlight interesting data sets.<br />
* Type in (manually) a couple of [http://genome.ucsc.edu/FAQ/FAQcustom custom tracks] in [http://genome.ucsc.edu/FAQ/FAQformat.html different formats] (just try bed for a start, you mostly won't need the others)<br />
** Try typing "chr1 1 1000 Hello_World!" as a custom track<br />
** If you need to graph data, there are [[Selecting_a_graphing_track_data_format|different graphing formats]]<br />
* Subscribe to the [http://www.soe.ucsc.edu/mailman/listinfo/genome mailing list] or [http://genome.ucsc.edu/contacts.html search through it]. Most everyday questions have already been asked by someone else so searching gives you an answer usually faster than asking on the mailing list.<br />
<br />
== Download the data of the genome browser (sequences and annotations) ==<br />
* Be aware that internal coordinates (not those shown on the website) are [[Coordinate_Transforms|0-based]]!<br />
* Unlike Gbrowse and Ensembl, UCSC is storing the data partially in SQL (coordiantes, outline of x-y-plots) and partially in flat text files (sequences, alignments, details of x-y-plots)<br />
* Table Browser: The easiest way to access data (you don't have to care whether data is stored in MySQL or in textfiles):<br />
** [http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Table Browser], [[Image:ISMB2008_UCSC.ppt|Example session]]<br />
* SQL-stored data ([http://genome.ucsc.edu/FAQ/FAQdownloads FAQ]):<br />
** [http://genome.ucsc.edu/FAQ/FAQdownloads#download29 Public mysql access]<br />
** [[Image:Kent_allJoiner.ppt|The all.joiner file]], describes relations between all database tables<br />
** For all genes-related tables, there is a [http://genome-test.cse.ucsc.edu/images/knownGeneSchema.gif graphical map] (sub-optimal layout :-)<br />
* Flat-file data: Download from the [http://genome.ucsc.edu/FAQ/FAQdownloads#download1 ftp server] (stored in /gbdb on browser servers)<br />
** [http://genome.ucsc.edu/FAQ/FAQformat.html Text file formats]<br />
<br />
== Install a copy of the browser on your own machine (Unix or Mac) ==<br />
* Create a mirror of the UCSC site:<br />
** [http://genome.ucsc.edu/admin/mirror.html Official FAQ: mirror a complete browser], the main reference for browser installation<br />
** [[Browser_Installation|Inofficial FAQ: Browser Installation]], on the wiki, a lot more info<br />
** [[Minimal Browser Installation|Mirror only selected genomes]]<br />
** Adapt your cgi-bin/[[Hg.conf]] file for your mirror<br />
** Be prepared that you'll need to create at least and also download parts of the hg18. At least mouse genomes still depend on it.<br />
** Make sure that you keep your own tracks separate, read this before loading any local data: [[Local_tracks_at_mirror_sites|Local TrackDB table]]<br />
** [[Browser_Mirrors|Updating the data automatically from UCSC]]<br />
** [[Using_custom_track_database|Pro and cons of storing custom tracks in MySQL or as flat files]]<br />
** [[Cookie_Session|How are cookies handled by the browser?]]<br />
** [[Category:Mirror_Site_FAQ|All other documents in this category]]<br />
** The [http://genome-test.cse.ucsc.edu/eng/ old documentation website with developer documentation]<br />
**[[Running your own gfServer]] (=BLAT server), needed in cases where you don't want or cannot use the UCSC BLAT servers.<br />
<br />
== Compile the UCSC source tree and analyze genomes yourself ==<br />
* The '''source tree''' (aka Kent source) is the collection of all tools used at the UCSC browser group<br />
* You could also call this an '''API''', as you can use these tools from your own programs<br />
* General introduction to the [[the source tree]] <br />
* What is documented to be available in the [[Kent source utilities]] <br />
** ... and what is [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/sources really available] in the source tree?<br />
* Some important tools are already compiled (even for windows!) [http://hgdownload.cse.ucsc.edu/admin/exe/ from here]<br />
* [http://genome.ucsc.edu/admin/jk-install.html Compile all tools (includes the browser webserver)] yourself<br />
** The best starting point is the main zipfile: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip<br />
** You need to set some [[Build_Environment_Variables|environment variables]] before you start the compilation<br />
** Walkthroughs for...<br />
*** [http://bergmanlab.smith.man.ac.uk/?p=32 MacOS X users]<br />
*** [[Source tree compilation on Debian/Ubuntu|Debian and Ubuntu]]<br />
*** [[CentOS Notes]]<br />
*** Windows: see [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2008-November/001059.html] but your mileage may vary to get everything to compile.<br />
<br />
** The most common problem on the mailing list are harmless warnings that trigger errors. "cc1: warnings being treated as errors". To ignore them, which is usually safe, [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2006-November/000251.html remove the -Wall option from the makefile]<br />
** See also the textfile README.building.source [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.building.source README.building.source]<br />
** [http://genome.ucsc.edu/contacts.html Search through the archives] or the [[:Category:Technical FAQ| Technical-FAQ-Category of the wiki]] when you have problems<br />
** Send an email to the mailing list if you cannot find the answer yourself<br />
** Some more sophisticated genome pipelines<br />
*** Create your own [[Whole_genome_alignment_howto|whole-genome alignment]]<br />
*** Create your own [[LiftOver_Howto|liftOver file]]<br />
<br />
== Modify your own copy of the browser ==<br />
* You load track data into your mirror <br />
** with the hgLoadxxx utils (e.g. hgLoadBed)<br />
** and show meta data (name, type, possible controls, etc) on the browser by editing a textfile called trackDb.ra<br />
* TrackDB documentation:<br />
** [http://www.soe.ucsc.edu/~sugnet/doc/trackHowto/browserTalk.pdf Charles Sugnet's presentation about TrackDB] <br />
** [[How_to_add_a_track_to_a_mirror]]<br />
** [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.trackDb The structure of the trackDB]<br />
** [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/trackDb/ Full TrackDB-Documentation: shows all possible trackDB statements]<br />
*** Examples: [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/trackDb/human/hg19/trackDb.ra UCSC trackDb for hg19]<br />
*** Examples for the composite statements in trackDb, from the [Encode trackDb http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra]<br />
* When you run into problems, search through the [http://genome.ucsc.edu/mirror.html mailing list] when you have problems and read the documentation in the directory [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/ kent/src/product]<br />
** [http://genome-test.cse.ucsc.edu/~hiram/rgbItemExamples.html|RGB color codes]<br />
** [http://genome-test.cse.ucsc.edu/admin/ a similar place with hgSearchSpec docs and statistics (the system to search for ids)] can be found completely off-track<br />
* Create a browser for a [[Building a new genome database|completely new genome]]<br />
** Slides of a class on [https://banana-slug.soe.ucsc.edu/_media/lecture_notes:genomebrowsersetup.pdf Creating a browser for new bacterial genome] <br />
* The most difficult part: [[Writing_a_new_track_type|Adding a completely new track type and visualisation code to the browser]]<br />
<br />
== Making Of: How the UCSC genome annotations are created ==<br />
* How the UCSC folks created their tracks:<br />
** The [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/doc/ UCSC's makeDb-files] are a log of all commands that are necessary to re-create all annotations for a particular genome. <br />
** Some explanations how to read the makeDb files: [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/doc/bashVsCsh.txt bashVsCsh] <br />
** The [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/trackDb/ trackDb-files] are the "track database" of the browser. They include all instructions on how annotations are displayed (e.g. the type of display, colors, settings, options, filenames, etc.)<br />
** [[Implementation_Notes|Notes on the history of the internal tools: Autosql. Blastz. Chains and nets]]<br />
* Whole-genome multiple alignments ([[Chains_Nets]])<br />
** [[Mm9_multiple_alignment]]<br />
** Whole-genome alignment pipeline: [[Chains_Nets|Angies mental model]] and [[Whole genome alignment howto|Max's howto]]<br />
* [http://genome.ucsc.edu/FAQ/FAQlicense#license4 How to create a browser for a new genome from scratch]<br />
* [http://users.soe.ucsc.edu/~markd/genbank-update/ Genbank Updates]<br />
* Cross-links to other databases<br />
** Outlinks for genes are copied from uniProt. The whole uniProt update process is rather complicated, see [[UCSC_Genes_Staging_Process]]<br />
<br />
== Developing with the UCSC API ==<br />
* [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-March/001677.html Debug the cgi-scripts with GDB]<br />
* Understand the [http://biostar.stackexchange.com/questions/3669/is-there-such-a-thing-as-a-ucsc-api/3723#3723 binning scheme]<br />
<br />
== Statistics, overviews ==<br />
*[[Gene_Set_Summary_Statistics]]<br />
* [http://genome-test.cse.ucsc.edu/~hiram/WEBStats/ Web hit statistics of the UCSC browser] <br />
<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Custom_track&diff=22906Custom track2015-10-03T21:22:03Z<p>Kuhn: redirecting to custom track category</p>
<hr />
<div>#REDIRECT [[Category:Custom_tracks]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Custom_track&diff=22905Custom track2015-10-03T21:19:34Z<p>Kuhn: removing redirect. New tracks in a browser installation are not custom tracks.</p>
<hr />
<div></div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Spreadsheet_links_to_Genome_Browser_views&diff=22903Spreadsheet links to Genome Browser views2015-10-02T22:01:07Z<p>Kuhn: added link to parameter documentation on Genome Browser</p>
<hr />
<div>Many users of the Genome Browser gather data of their own in Excel spreadsheets and would like to create links to the Browser using data in the spreadsheet. For example, a clinical geneticist may have lists of regions or genes for a patient that are duplicated or deleted, as determined by comparative genomic hybridization (CGH). These regions can be the source information for a browser view allowing access to each region with a single click.<br />
<br />
<TABLE><TR><TD><br />
[[Image:ucscLinks.gif]]<br />
<br />
</TD><TD><br />
'''Click to download the spreadsheet:'''<BR><br />
[http://genomewiki.ucsc.edu/images/0/01/UcscLinks.xls ucscLinks.xls]<br />
<br />
</TD></TR></TABLE><br />
<br />
Careful use of Excel's "copy" and "move" functions should allow the links on this sheet to be used without modification.<br />
<br />
==Customizing the links==<br />
<br />
Postion-based link. The contents of the last cell in the image above are as follows:<br />
<br />
<PRE><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position="&E22&"&dgv=pack&knownGene=pack&omimGene2=pack","ucsc")<br />
</PRE><br />
<br />
Gene-name link. The URL for a link to a gene name is made in this way:<br />
<br />
<pre><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&singleSearch=knownCanonical&position="&E16&"&omimGene2=pack&decipher=pack&snp141=dense","ucsc")<br />
</pre><br />
<br />
Gene details link. A link to the UCSC Genes details page would look like this:<br />
<br />
<pre><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgGene?org=human&db=hg19&hgg_gene="&E16,"ucsc")<br />
</pre><br />
<br />
Add tracks of choice. The position-based link above shows how to create a link that turns on three specific tracks of interest. In this case, these tracks are explicitly turned on:<br />
<br />
Database of Genomic Variants (table: dgv)<br />
UCSC Genes (table: knownGene)<br />
OMIM Genes (table: omimGene2) <br />
<br />
Each track is set to "pack" in the link as follows:<br />
<br />
dgv=pack<br />
knownGene=pack<br />
omimGene2=pack<br />
<br />
Any track that has been open in on your Browser will remain in the view when the new browser window opens. Any track that is on by default must be turned off using:<br />
<br />
<tablename>=hide<br />
<br />
A new track can be added using the tablename and a visibility of choice. e.g.:<br />
<br />
&snp141=dense<br />
<br />
Simply add to the end of the url any other desired <tablename>=visibility, appended to the url by an ampersand (&). The simplest way to learn the name of the table underlying a track is to do a mouseover in a Genome Browser image and read the url at the bottom of the browser page. The table is shown in the url as<br />
<br />
g=tablename<br />
<br />
You can also see the tablename by clicking into an item in the track and then clicking "show table schema" on the next page.<br />
<br />
Visibility options include:<br />
<br />
hide<br />
dense<br />
squish<br />
pack<br />
full<br />
<br />
Other parameters you can use are documented on the Browser:<br />
<br />
http://hgwdev-max.soe.ucsc.edu/goldenPath/help/customTrackText.html#optParams</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=File:UcscLinks.xls&diff=22603File:UcscLinks.xls2015-05-01T19:48:20Z<p>Kuhn: uploaded a new version of &quot;File:UcscLinks.xls&quot;: new version with mm10 replacing hg18.</p>
<hr />
<div>spreadsheet to create links that open Genome Browser views when a user types in a variety of entries, including genomic coordinates, gene names or chromosome bands.</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Presentations&diff=22602Presentations2015-05-01T18:49:22Z<p>Kuhn: added ACMG poster</p>
<hr />
<div>An archive of presentations by staff and researchers of the UCSC Genome Browser group and the Center for Biomolecular Science and Engineering (CBSE). Please keep the list in order by date, newest ones at the top.<br />
<!-- presentation present --><br />
<br />
==2015==<br />
<br />
* 9 May 2015, Angie Hinrichs, The Data Integrator: a new way to combine datasources underlying the UCSC Genome Browser (poster presented at [http://meetings.cshl.edu/meetings/2015/genome15.shtml Biology of Genomes 2015] at CSHL) [[BoG2015DataIntegratorPoster | wiki]] [[Media:BoG2015DataIntegrator.pptx | PPTX]] [[Media:BoG2015DataIntegrator.pdf | PDF]]<br />
* 11 March 2015, Angie Hinrichs, Annotation Integrator [[Media:HgAi_genecats_15_03_11.pdf|PDF]] [[Media:HgAi_genecats_15_03_11.pptx|PPTX]]<br />
* 26 Feb 2015, Robert Kuhn, ACMG meeting, Salt Lake. UCSC Genome Browser and Variant Annotation Integrator [[Media:acmg2015poster.pdf|PDF]] <br />
<br />
==2014==<br />
* 20 September 2014, Galt Barber, Genome Informatics 2014 Poster on hubs, security, and GBiB. [[:File:GenomeInformatics2014Poster.pdf|PDF]]<br />
* 19 Sept 2014 Jim Kent, Ebola Scramble [[Media:ebolaUcsfSept192014.pptx|PPTX]]<br />
* 22 Aug 2014 Jim Kent, hg38, mapping sponge, and ENCODE [[Media:spongeAwg.pptx|PPTX]]<br />
* 19 May 2014, Karen Miga, GRCh38 Centromere Reference Models [[:File:KarenMigaCentromere.pdf|PDF]]<br />
* 11 February 2014, Hiram Clawson, BME230 browser introduction, assembly hub demonstration, table browser intersection [[:File:BME230_Winter_2014.ppt|PPT]]<br />
<br />
==2013==<br />
* 19 June 2013, Tracy Ballinger, Track Hubs and Assembly Hubs presentation for Epigenome Roadmap working group meeting. [[:File:TrackHub_presentation.ppt|PPT]] [[:File:TrackHub_presentation.pdf|PDF]]<br />
* 10 May 2013, Brooke Rhead, New variation resources at the UCSC Genome Browser. Poster presented at [http://meetings.cshl.edu/meetings/2013/genome13.shtml Biology of Genomes 2013] at CSHL. [[BoG2013VariationPoster | wiki]], [[Media:BoG2013variation.pptx | PPTX]], [[Media:BoG2013variation.pdf | PDF]].<br />
* 08 May 2013, Hiram Clawson, Assembly Hubs poster presentation at [http://meetings.cshl.edu/meetings/2013/genome13.shtml Biology of Genomes 2013] at CSHL. [[Assembly_Hubs | wiki]], [[Media:AssemblyHubs_BoG_2013.pdf | PDF]], [[Media:AssemblyHubs_BoG_2013.pptx| PPTX]]<br />
* 20 Mar 2013, Brian Raney, UCSC Genes Genecats talk [[:File:ucscGenes.ppt|PPT]] [[:File:ucscGenes.pdf|PDF]]<br />
<br />
==2012==<br />
* 06 Sep 2012, Brian Raney, Remote Data Track Storage for Viewing on the UCSC Genome Browser [[GI2012TrackHubsPoster|wiki]], <br />
* 09 May 2012, Angie Hinrichs, Using the UCSC Genome Browser to evaluate putative genetic variants [[BoG2012VariationPoster|wiki]], [[:File:Hinrichs_BoG2012_GBVariants.pptx|PPTX]], [[:File:Hinrichs_BoG2012_GBVariants.pdf|PDF]]<br />
* 11 April 2012, Ted Pak, JavaScript/Ruby version of the UCSC Yeast Genome Browser [[:File:UCSC_talk.graffle.pdf|PDF]] <br />
* 21 March 2012, Larry Meyer, Genome Browser API. (Genecats) [[:File:hgApi.ppt|PPT]] <br />
* 15 February 2012, Greg Roe & Venkat Malladi, Selenium Testing [[:File:SeleniumTesting.pptx|PPTX]]<br />
* 26 January 2012, Hiram Clawson, BME230 browser introduction, table browser intersection [[:File:BME230_Winter_2012.ppt|PPT]]<br />
* 18 January 2012, Jim Kent, Software Engineering and Testing. (Genecats) [[:File:SoftwareEngTesting.pptx|PPTX]]<br />
* 11 January 2012, Brooke Rhead, The QA Release Process: what gets pushed and when. (Genecats) [[:File:QaReleaseProcess.pptx|PPTX]] or [[:File:QaReleaseProcess.pdf|PDF]]<br />
<br />
==2011==<br />
* 18-19 October 2011, [http://www-conf.slac.stanford.edu/xldb2011/Program.asp XLDB presentations] including from UCSC, the 5th lightning talk on the 18th of October. Note additional interesting genomics presentations, for example the NCBI sequence read archive architecture on the morning of the 19th.<br />
* 09 September 2011, Angie Hinrichs, Visually integrating genomic data in the UCSC Genome Browser. Poster presented at [http://hgvmeeting.org/hgv2011/ HGV2011]. [[Media:HGV2011_GenomeBrowser.pptx|.pptx]] [[Media:HGV2011_GenomeBrowser.pdf|PDF]]<br />
* 24 August 2011, Sol Katzman, Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hotspots [[File:Sol_GCBias_GeneCats_2011-08-24.pdf]]<br />
* 27 July 2011, Larry Meyer, Browser Performance and Architecture<br />
* May 2011, Ann Zweig, UCSC Genome Browser Track Data Hubs. Poster given at Biology of Genomes conference at CSHL. [[File:BoG2011.pdf]]<br />
* May 2011, Gabor Marth, Toward a unified view of human genetic variation. Talk given at Biology of Genomes conference at CSHL. [[Image:Marth-1000G-CSHL2011.pptx]]<br />
* 27 April 2011, Jim Kent, Accelerating Biomedical Research for 10 Years and Counting. [[Image:AcceleratingBiomedicine2011.pptx]]<br />
* 06 April 2011, Angie Hinrichs, Recent work on human variation tracks. [[Media:VariationGenecats20110406.pptx|.pptx]] [[Media:VariationGenecats20110406.pdf|PDF]] (PDF has squashed animations)<br />
* 09 March 2011, Josh Stuart, Ph.D., Integrated Pathway Modeling. [[Image:jstuart.pptx]]<br />
* 03 March 2011, Andreas Sundquist, Ph.D., DNAnexus -- Data Management for the First 1,000,000 Human Genomes. [[Image:DNAnexus.pptx]]<br />
* 02 March 2011, MDB and CV in the shadow of the shadow of greatness. [[Image:mdbAndCvPresentation.pdf]] or [[Image:mdbAndCvPresentation.ppt]] Brian Raney and Tim Dreszer.<br />
* 02 February 2011, Benedict Paten, JobTree. [[Image:JobtreeSlides.pdf]]<br />
* 06 January 2011, BME 230 class, Hiram Clawson, introduction to the UCSC genome browser and programming with the kent source tree. [[Image:BME230_Winter_2011.ppt]]<br />
<br />
==2010==<br />
* 10 November 2010, Xin Zhou, Human Epigenomics Browser [[Image:2010-11-10_-_Genecats.pdf]]<br />
* 4 Novermber 2010, Kate Rosenbloom, Genome-wide ENCODE Data at UCSC (poster for ASHG2010) [[Media:ENCODE_ASHG2010.ppt]] <br />
* 29 September 2010, Andy Pohl, Investigation of the Nucleosome Linker [[Image:2010-09-29_-_Genecats.pdf]]<br />
* 25 August 2010, Ann Zweig, Redmine Task-Tracking Tool [[Image:Genecats08252010.ppt]] [[Image:Genecats082510.mp3]]<br />
* 18 August 2010, Kate Rosenbloom, Genome-wide ENCODE Data at UCSC (poster for CSB2010) [[Media:ENCODE_CSB2010.ppt]] <br />
* 18 August 2010, Melissa Cline, Genome-wide Mouse ENCODE Data at UCSC (presented at CSB2010) [[Image:Cline.MouseEncode.CSB2010.ppt]] <br />
* 11 August, 2010, Mary Goldman, Working with git [[Media:Genecats_08_11_10.mp3]]<br />
* 23 June, 2010, Ed Green, Detecting positive selection in humans using the Neandertal genome [[Media:Genecats062310.mp3]]<br />
* 17 June, 2010, Kate Rosenbloom, ENCODE Data at UCSC (presented at CSHL Integrated Analysis of Genome-Scale Data short course) [[Media:Rosenbloom.ENCODE_CSHL_Jun2010.ppt]]<br />
* 16 June, 2010, Larry Meyer, Bringing Web 2.0 to the UCSC Genome Browser [[Image:Genecats061610.pdf]] audio: [[Image:Genecats061610.mp3]]<br />
* 15 June, 2010, Steve Benz, Thesis Advancement [[Image:Sbenz_thesis_advancement.pdf]] audio: [[Image:BenzAdvancement061510.mp3]]<br />
* 09 June, 2010, Ann Zweig & Galt Barber, git Source Code Management [[Image:gitSourceCodeMgmt.pdf]] partial audio: [[Media:Genecats060910.mp3]]<br />
* 05 May 2010, Hiram Clawson, [[Unix environment]]<br />
* 21 April 2010, Mitchell Skinner, JBrowse - An AJAX Genome Browser [[Image:UCSC-4-21-10.pdf]]<br />
* 10 February 2010, Jorge Garcia, The Genome Browser - Under The Hood [[Image:Browsermap.pdf]] and 2013 review [[Image:Dependency-Review-20130826.pdf]]<br />
* 03 February 2010, Melissa Cline, Coordinated Alternative Splicing [[Image:CoordinatedSplicing.ppt]]<br />
* 05,07 January 2010 BME 230 class, Hiram Clawson, introduction to the UCSC genome browser and programming with the kent source tree. [[Image:BME230_Winter_2010.ppt]] Browser [[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=BME230%20Winter%202010 Session]] for example intersection.<br />
<br />
==2009==<br />
* 14 October Genecats meeting, [[Image:MonsatoIntroduction_Oct2009.pdf|Monsanto Introduction]] Brad Fabbri<br />
* 14 October Genecats meeting, Hiram Clawson - building the kent source tree and a UCSC genome browser assembly, [[Image:Genecats_2009_10_14.pptx|pptx power point]] or older style [[Image:Genecats_2009_10_14.ppt|ppt power point]]<br />
* 24 August Genecats meeting, Larry and Tim present 3 new hgTracks features coming down the shute: [[Media:Image20ui.pdf|image20ui.pdf]].<br />
* 29 July Genecats meeting, Mark's presentation on SVS/subversion proposal to replace CVS [[Image:svnForGb.pdf|svnForGb.pdf]].<br />
* 08 April Genecats meeting, Fan Hsu: "Some thoughts from Fan" [[Image:SomeThoughtsFromFan0408B.pdf|SomeThoughtsFromFan0408B.pdf]].<br />
* 08 January 2009 BME 230 class, Hiram Clawson, introduction to the UCSC genome browser and programming with the kent source tree. [[Image:BME230_Winter_2009.ppt]] Browser [[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=BME230%20Winter%202009 Session]] for example intersection.<br />
<br />
==2008==<br />
* 18 December 2008 [[Image:FrankJacobs181208.ppt]] - Frank Jacobs, Developmental Neurobiology, Rudolf Magnus Institute of Neuroscience, University of Utrecht, The Netherlands, "Pitx3 outSMRTs Nurr1 in dopamine neuron terminal differentiation"<br />
<br />
* Genecats - 17 December 2008 - [[Media:Matrix.ppt|Composite sketch]]: Nifty tricks for composite tracks (multi-view, dimensions, sorting, drag and drop, etc.). Tim Dreszer.<br />
<br />
* 11 December 2008, Paul Flicek, EBI, presenting 1,000 genomes project status [[Image:Flicek_11_DEC_2008.pdf]]<br />
<br />
* Genecats - 10 December 2008 - Ed Green from Max Planck Institute for Evolutionary Anthropology discusses the [[http://www.cell.com/retrieve/pii/S0092867408007733| Neandertal mtDNA]] project<br />
<br />
* Genecats - 15 October 2008 - [[Image:Metcalf.Richardson.2008-10-15.pdf]] Jake Metcalf, Sarah Richardson discussion of ethics controversy concerning Bruce T. Lahn of U. Chicago publications.<br />
<br />
* Sep. 2008 - Angie's "UCSC Genome Browser Tool Suite" poster presented at Genomics of Common Disease [[Media:UCSC_Genome_Browser_GCD_2008.ppt|PPT]] [[Media:UCSC_Genome_Browser_GCD_2008.pdf|PDF]]<br />
<br />
* 27 August 2008 - Jim Kent at the Computational Systems Bioinformatics Conference, Stanford CA, [[Image:Kent_decodingEncode.ppt]] a wide-ranging discussion of Encode research, using the Gene Sorter, using the Table browser, source code design issues<br />
<br />
* Genecats - 06 August 2008 - [[Image:ISMB2008_genecats_summary.ppt]] summary of ISMB 2008, Toronto, Hiram Clawson<br />
<br />
* Genecats - July 30, 2008 - [[Media:UBCSslides.ppt|Biased Clustered Subsitutions in the Human Genome: Sex, Gambling and Non-Darwinian Evolution]]. Tim Dreszer's presentation of his master's thesis work.<br />
<br />
* ISMB Toronto - July 2008 - Intelligent Systems for Molecular Biology [[Image:ISMB2008_UCSC.ppt]] presentation by Hiram Clawson. A brief tutorial on browser usage with special emphasis on how to perform intersections with the table browser. Task demonstrated: finding highly conserved non-coding regions of the genome.<br />
<br />
* Genecats - 05 July 2008 - Jim Kent describing the all.joiner file used by the UCSC genome browser to specify database table relationships - the database "schema" behind the browser [[Image:Kent_allJoiner.ppt]]<br />
<br />
* Genecats - 16 April 2008 - Rachel Harte trip report from Mouse Genome Annotation Summit Meeting and RefSeq/CCDS visit, NIH, Bethesda MD 12-14 March 2008 [[Image:MouseAnnotAndCCDSVisitReport041608.ppt]]<br />
<br />
* Genecats - 06 April 2008 - Jim Kent reviewing the Parasol super computer job management system [[Image:Kent_parasolArchitecture.ppt]]<br />
<br />
* Bejerano Lab (Stanford) - March 31, 2008 - [[Image:Bejerano Lab 2008 03 31.ppt]] Angie's crash course on using the kent/src tools and libraries. Did a brief live demo (TB intersection -> custom track) first. Group was already very familiar with browser and had their own mirror.<br />
<br />
* BME 230 Winter 2008, 10 January 2008, Robert Baertsch [[Image:Baertsch-code-talk.ppt]] genome browser introduction and kent src code preview<br />
<br />
==2007==<br />
* Genecats - 16 April 2008 - [[Image:ISMB2007TripReportGenecats.ppt]] Rachel Harte summary from ISMB 2007 meeting in Vienna, Austria<br />
* Jim's talk - 12 September 2007 - [[Image:geneSorter.ppt]] "Inside the Gene Sorter - A moderately complex CGI application" talk by Jim Kent<br />
<br />
==2006==<br />
<br />
* Genecats - September 12, 2006 - [[Image:Automation 2006 09 12 v2.ppt]] Overview of the automation scripts that are now in kent/src/hg/utils/automation/ (Angie).<br />
<br />
==2005==<br />
<br />
* Chicken Genome Meeting - May, 2005 - [[Image:Browsers CSHL Chicken 2005 05.ppt]] An intro to the Genome Browser and Table Browser (Angie).<br />
<br />
==2003==<br />
<br />
* CSHL June 2003 "Evolution and the Santa Cruz Genome Browser" [[Image:CSHL_2003_Jim_Kent.ppt]] presentation by Jim Kent. Recent new functions in the genome browser, using the chain and net process to highlight evolutionary processes, a new rat genome assembly with 3-way human-mouse-rat multiple alignment.<br />
<br />
==2002==<br />
<br />
* Charles Sugnet's talk January 2002 - "Adding tracks to the Human Genome Browser" [[Image:howToAddTrack_Sugnet.pdf|howToAddTrack_Sugnet.pdf]] and examples used in the talk - [[Image:sampTracksChr22.tab]]<br />
<br />
* Genecats October 2002 - "Software Sermon" [[Image:SoftwareSermon2002_Jim_Kent.ppt]] - software development philosophy and guidelines, Jim Kent.<br />
<br />
==2000==<br />
<br />
* October 2000 - "Details of the Genome Browser" [[Image:CompBioOct2000_Jim_Kent.ppt]] - Description of the genome browser software architecture, the early days. Jim Kent<br />
<br />
<br />
[[Category:Browser Development]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=File:Acmg2015poster.pdf&diff=22601File:Acmg2015poster.pdf2015-05-01T18:47:26Z<p>Kuhn: Annual meeting American Society for Medical Genetics, Salt Lake City.</p>
<hr />
<div>Annual meeting American Society for Medical Genetics, Salt Lake City.</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=22474Other genome browsers2015-03-06T19:04:09Z<p>Kuhn: /* Locations using UCSC software on other organisms (or people) or additional content on our organisms */ adding X. leavis mirror in UK</p>
<hr />
<div><br />
== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
<br />
This mirror is maintained by the Browser staff.<br />
<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome.hmgc.mcw.edu/ Medical College of Wisconsin]. Milwaukee, WI<br />
<br />
* [http://genome-mirror.cshl.edu/ Cold Spring Harbor Laboratory]. CSHL, NY<br />
<br />
* [http://moma.ki.au.dk/genome-mirror/ Aarhus University]. The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
* [https://ucsc.genome.edu.au/ Genomics Virtual Lab]. QFAB mirror in Australia.<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway?clade=plant&org=Glycine+max&db=0 soybean] and others at UCLA.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, including <I>Arabidopsis</I>, Trypanosome, herpes virus, phage lambda and others. University College, Cork, Ireland.<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.<br />
<br />
* [http://genomaize.org/cgi-bin/hgGateway Maize] at Florida State University.<br />
<br />
* [http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway Xenopus laevis] Frog at Medical Research Council, UK.<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly Assembly Hub] mechanism.<br />
<br />
If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=22456Other genome browsers2015-02-24T16:24:49Z<p>Kuhn: /* Locations using UCSC software on other organisms (or people) or additional content on our organisms */ added maize browser at Florida State</p>
<hr />
<div><br />
== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
<br />
This mirror is maintained by the Browser staff.<br />
<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome.hmgc.mcw.edu/ Medical College of Wisconsin]. Milwaukee, WI<br />
<br />
* [http://genome-mirror.bscb.cornell.edu/ Cornell University]. Ithaca, NY<br />
<br />
* [http://moma.ki.au.dk/genome-mirror/ Aarhus University]. The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
* [https://ucsc.genome.edu.au/ Genomics Virtual Lab]. QFAB mirror in Australia.<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway?clade=plant&org=Glycine+max&db=0 soybean] and others at UCLA.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, including <I>Arabidopsis</I>, Trypanosome, herpes virus, phage lambda and others. University College, Cork, Ireland.<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.<br />
<br />
* [http://genomaize.org/cgi-bin/hgGateway Maize] at Florida State University.<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly Assembly Hub] mechanism.<br />
<br />
If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=22364Other genome browsers2015-01-29T16:40:16Z<p>Kuhn: /* Locations using UCSC software on other organisms (or people) or additional content on our organisms */ listed some novel orgs hosted at the Irish site.</p>
<hr />
<div><br />
== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
<br />
This mirror is maintained by the Browser staff.<br />
<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome.hmgc.mcw.edu/ Medical College of Wisconsin]. Milwaukee, WI<br />
<br />
* [http://genome-mirror.bscb.cornell.edu/ Cornell University]. Ithaca, NY<br />
<br />
* [http://moma.ki.au.dk/genome-mirror/ Aarhus University]. The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
* [https://ucsc.genome.edu.au/ Genomics Virtual Lab]. QFAB mirror in Australia.<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway?clade=plant&org=Glycine+max&db=0 soybean] and others at UCLA.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, including <I>Arabidopsis</I>, Trypanosome, herpes virus, phage lambda and others. University College, Cork, Ireland.<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly Assembly Hub] mechanism.<br />
<br />
If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Spreadsheet_links_to_Genome_Browser_views&diff=22318Spreadsheet links to Genome Browser views2014-12-11T20:51:54Z<p>Kuhn: /* Customizing the links */</p>
<hr />
<div>Many users of the Genome Browser gather data of their own in Excel spreadsheets and would like to create links to the Browser using data in the spreadsheet. For example, a clinical geneticist may have lists of regions or genes for a patient that are duplicated or deleted, as determined by comparative genomic hybridization (CGH). These regions can be the source information for a browser view allowing access to each region with a single click.<br />
<br />
<TABLE><TR><TD><br />
[[Image:ucscLinks.gif]]<br />
<br />
</TD><TD><br />
'''Click to download the spreadsheet:'''<BR><br />
[http://genomewiki.ucsc.edu/images/0/01/UcscLinks.xls ucscLinks.xls]<br />
<br />
</TD></TR></TABLE><br />
<br />
Careful use of Excel's "copy" and "move" functions should allow the links on this sheet to be used without modification.<br />
<br />
==Customizing the links==<br />
<br />
Postion-based link. The contents of the last cell in the image above are as follows:<br />
<br />
<PRE><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position="&E22&"&dgv=pack&knownGene=pack&omimGene2=pack","ucsc")<br />
</PRE><br />
<br />
Gene-name link. The URL for a link to a gene name is made in this way:<br />
<br />
<pre><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&singleSearch=knownCanonical&position="&E16&"&omimGene2=pack&decipher=pack&snp141=dense","ucsc")<br />
</pre><br />
<br />
Gene details link. A link to the UCSC Genes details page would look like this:<br />
<br />
<pre><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgGene?org=human&db=hg19&hgg_gene="&E16,"ucsc")<br />
</pre><br />
<br />
Add tracks of choice. The position-based link above shows how to create a link that turns on three specific tracks of interest. In this case, these tracks are explicitly turned on:<br />
<br />
Database of Genomic Variants (table: dgv)<br />
UCSC Genes (table: knownGene)<br />
OMIM Genes (table: omimGene2) <br />
<br />
Each track is set to "pack" in the link as follows:<br />
<br />
dgv=pack<br />
knownGene=pack<br />
omimGene2=pack<br />
<br />
Any track that has been open in on your Browser will remain in the view when the new browser window opens. Any track that is on by default must be turned off using:<br />
<br />
<tablename>=hide<br />
<br />
A new track can be added using the tablename and a visibility of choice. e.g.:<br />
<br />
&snp141=dense<br />
<br />
Simply add to the end of the url any other desired <tablename>=visibility, appended to the url by an ampersand (&). The simplest way to learn the name of the table underlying a track is to do a mouseover in a Genome Browser image and read the url at the bottom of the browser page. The table is shown in the url as<br />
<br />
g=tablename<br />
<br />
You can also see the tablename by clicking into an item in the track and then clicking "show table schema" on the next page.<br />
<br />
Visibility options include:<br />
<br />
hide<br />
dense<br />
squish<br />
pack<br />
full</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Assembly_Hubs&diff=22314Assembly Hubs2014-12-05T21:13:04Z<p>Kuhn: /* 2bit file */ added link to source of faToTwoBit</p>
<hr />
<div>==Overview==<br />
<br />
The Assembly Hub function allows you to display your novel genome sequence using the UCSC Genome Browser.<br />
<br />
==Web Server==<br />
<br />
To display your novel genome sequence, use a web server at your institution to supply your files to the UCSC Genome Browser (please note, hosting hub files on HTTP is highly recommended and much more efficient than FTP). You then establish a hierarchy of directories and files to host your novel genome sequence. For example:<br />
<pre><br />
myHub/ - directory to organize your files on this hub<br />
hub.txt – primary reference text file to define the hub, refers to:<br />
genomes.txt – definitions for each genome assembly on this hub<br />
newOrg1/ - directory of files for this specific genome assembly<br />
newOrg1.2bit – ‘2bit’ file constructed from your fasta sequence<br />
description.html – information about this assembly for users<br />
trackDb.txt – definitions for tracks on this genome assembly<br />
groups.txt – definitions for track groups on this assembly<br />
bigWig and bigBed files – data for tracks on this assembly<br />
external track hub data tracks can be displayed on this assembly<br />
</pre><br />
<br />
The URL to reference this hub would be: <nowiki>http://yourLab.yourInstitution.edu/myHub/hub.txt</nowiki><br />
<br />
You can view a working example hierarchy of files at:<br />
[http://genome-test.cse.ucsc.edu/~hiram/hubs/Plants/ Plants]<br />
<br />
==hub.txt==<br />
<br />
The initial file [http://genome-test.cse.ucsc.edu/~hiram/hubs/Plants/hub.txt hub.txt] is the primary URL reference for your assembly hub. The format of the file:<br />
<pre><br />
hub hubName<br />
shortLabel genome<br />
longLabel Comment describing this hub contents<br />
genomesFile genomes.txt<br />
email contactEmail@institution.edu<br />
</pre><br />
<br />
The ''shortLabel'' is the name that will appear in the ''genome'' pull-down menu at the UCSC gateway page. Example: '''Plants'''<br />
<br />
The ''genomesFile'' is a reference to the next definition file in this chain that will describe the assemblies and tracks available<br />
at this hub. Typically '''genomes.txt''' is at the same directory level as this '''hub.txt''', however it can also be a relative path<br />
reference to a different directory level.<br />
<br />
The ''email'' address provides users a contact point for queries related to this assembly hub.<br />
<br />
==genomes.txt==<br />
The [http://genome-test.cse.ucsc.edu/~hiram/hubs/Plants/genomes.txt genomes.txt] file provides the references to the<br />
genome assemblies and tracks available at this assembly hub. The example file indicates the typical contents:<br />
<pre><br />
genome ricCom1<br />
trackDb ricCom1/trackDb.txt<br />
groups ricCom1/groups.txt<br />
description July 2011 Castor bean<br />
twoBitPath ricCom1/ricCom1.2bit<br />
organism Ricinus communis<br />
defaultPos EQ973772:1000000-2000000<br />
orderKey 4800<br />
scientificName Ricinus communis<br />
htmlPath ricCom1/description.html<br />
</pre><br />
<br />
There can be multiple assembly definitions in this single file. Separate these stanzas with blank lines. The references to other files are relative path references. In this example there is a sub-directory here called '''ricCom1''' which contains the files for this specific assembly.<br />
<br />
* The ''genome'' name is the equivalent to the UCSC database name. The genome browser displays this database name in title pages in the genome browser.<br />
* The ''trackDb'' refers to a file which defines the tracks to place on this genome assembly. The format of this file is described in the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html Track Hub] help reference documentation.<br />
* The ''groups'' refers to a file which defines the track groups on this genome browser. Track groups are the sections of related tracks grouped together under the primary genome browser graphics display image.<br />
* The ''description'' will be displayed for user information on the gateway page and most title pages of this genome assembly browser. It is the name displayed in the ''assembly'' pull-down menu on the browser gateway page.<br />
* The ''twoBitPath'' refers to the '''.2bit''' file containing the sequence for this assembly. Typically this file is constructed from the original fasta files for the sequence using the kent program '''faToTwoBit'''<br />
* The ''organism'' string is displayed along with the ''description'' on most title pages in the genome browser. Adjust your names in ''organism'' and ''description'' until they are appropriate. This example is very close to what the genome browser normally displays. This ''organism'' name is the name that appears in the ''genome'' pull-down menu on the browser gateway page.<br />
* The ''defaultPos'' specifies the default position the genome browser will open when a user first views this assembly. This is usually selected to highlight a popular gene or region of interest in the genome assembly.<br />
* The ''orderKey'' is used with other genome definitions at this hub to order the pull-down menu ordering the ''genome'' pull-down menu.<br />
* The ''htmlPath'' refers to an html file that is used on the gateway page to display information about the assembly.<br />
<br />
==2bit file==<br />
The '''.2bit''' file is constructed from the fasta sequence for the assembly. The ''kent'' source program ''faToTwoBit'' is used to construct this file. Download the progrem from the [http://hgdownload.soe.ucsc.edu/admin/exe/ downloads] section of the Browser. <br />
For example:<br />
faToTwoBit ricCom1.fa ricCom1.2bit<br />
<br />
Use the ''twoBitInfo'' to verify the sequences in this assembly and create a ''chrom.sizes'' file which is not used in the hub, but is useful in later processing to<br />
construct the ''big*'' files:<br />
twoBitInfo ricCom1.2bit stdout | sort -k2rn > ricCom1.chrom.sizes<br />
<br />
The ''.2bit'' commands can function with the ''.2bit'' file at a URL:<br />
twoBitInfo -udcDir=. <nowiki>http://genome-test.cse.ucsc.edu/~hiram/hubs/Plants/ricCom1/ricCom1.2bit</nowiki> stdout | sort -k2nr > ricCom1.chrom.sizes<br />
<br />
Sequence can be extracted from the ''.2bit'' file with the ''twoBitToFa'' command, for example:<br />
twoBitToFa -seq=chrCp -udcDir=. <nowiki>http://genome-test.cse.ucsc.edu/~hiram/hubs/Plants/ricCom1/ricCom1.2bit</nowiki> stdout > ricCom1.chrCp.fa<br />
<br />
==groups.txt==<br />
<br />
The [http://genome-test.cse.ucsc.edu/~hiram/hubs/Plants/ricCom1/groups.txt groups.txt] file defines the grouping of track controls under the primary genome browser image display. The example referenced here has the usual definitions as found in the UCSC Genome Browser.<br />
<br />
Each group is defined, for example the '''Mapping''' group:<br />
<pre><br />
name map<br />
label Mapping<br />
priority 2<br />
defaultIsClosed 0<br />
</pre><br />
<br />
* The ''name'' is used in the ''trackDb.txt'' track definition ''group'', to assign a particular track to this group.<br />
* The ''label'' is displayed on the genome browser as the title of this group of track controls<br />
* The ''priority'' orders this track group with the other track groups<br />
* The ''defaultIsClosed'' determines if this track group is expanded or closed by default. Values to use are '''0''' or '''1'''<br />
<br />
==Building Tracks==<br />
<br />
It helps to have a cluster super computer to process the genomes to construct tracks. It can be done for small genomes<br />
on single computers that have multiple cores. The process for each track is unique. Please note the continuing<br />
document: [[Browser Track Construction]] for a discussion of constructing tracks for your assembly hub.<br />
<br />
<br />
[[Category:Technical FAQ]]<br />
[[Category:Assembly/Track Hubs]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Spreadsheet_links_to_Genome_Browser_views&diff=22311Spreadsheet links to Genome Browser views2014-12-05T04:25:09Z<p>Kuhn: /* Customizing the links */ added hoe to make a link to UCSC Genes details page</p>
<hr />
<div>Many users of the Genome Browser gather data of their own in Excel spreadsheets and would like to create links to the Browser using data in the spreadsheet. For example, a clinical geneticist may have lists of regions or genes for a patient that are duplicated or deleted, as determined by comparative genomic hybridization (CGH). These regions can be the source information for a browser view allowing access to each region with a single click.<br />
<br />
<TABLE><TR><TD><br />
[[Image:ucscLinks.gif]]<br />
<br />
</TD><TD><br />
'''Click to download the spreadsheet:'''<BR><br />
[http://genomewiki.ucsc.edu/images/0/01/UcscLinks.xls ucscLinks.xls]<br />
<br />
</TD></TR></TABLE><br />
<br />
Careful use of Excel's "copy" and "move" functions should allow the links on this sheet to be used without modification.<br />
<br />
==Customizing the links==<br />
<br />
The contents of the last cell in the image above (cell G22 in the actual spreadsheet) are as follows:<br />
<br />
<PRE><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position="&E22&"&dgv=pack&knownGene=pack&omimGene2=pack","ucsc")<br />
</PRE><br />
<br />
The gene-name URL is made in this way:<br />
<br />
<pre><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&singleSearch=knownCanonical&position="&E16&"&omimGene2=pack&decipher=pack&snp131=dense","ucsc")<br />
</pre><br />
<br />
A link to the UCSC Genes details page would look like this:<br />
<br />
<pre><br />
=HYPERLINK("http://genome.ucsc.edu/cgi-bin/hgGene?org=human&db=hg19&hgg_gene="&E16,"ucsc")<br />
</pre><br />
<br />
This example shows how to create a link that turns on specific tracks of interest. In this case, three tracks are explicitly turned on:<br />
<br />
Database of Genomic Variants (table: dgv)<br />
UCSC Genes (table: knownGene)<br />
OMIM Genes (table: omimGene) <br />
<br />
Each track is set to "pack" in the link as follows:<br />
<br />
dgv=pack<br />
knownGene=pack<br />
omimGene2=pack<br />
<br />
Any track that has been open in on your Browser will remain in the view when the new browser window opens.<br />
<br />
A new track can be added using the tableName and a visibility of choice. e.g.:<br />
<br />
&snp131=dense<br />
<br />
Simply add to the end of the url any other desired tableName=visibility, appended to the url by an ampersand (&). The simplest way to learn the name of the table underlying a track is to do a mouseover in a Genome Browser image and read the url at the bottom of the browser page. The table is shown in the url as<br />
<br />
g=tableName<br />
<br />
You can also see the tableName by clicking into an item in the track and then clicking "show table schema" on the next page.<br />
<br />
Visibility options include:<br />
<br />
hide<br />
dense<br />
squish<br />
pack<br />
full</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=ABRF2010_Tutorial&diff=22282ABRF2010 Tutorial2014-11-21T18:39:47Z<p>Kuhn: old link was usurped by something irrelvant</p>
<hr />
<div>Presented by Angie Hinrichs and Robert Kuhn March 20, 2010 as part of the workshop <em>Tools to Facilitate Management, Analysis and Visualization of 2nd Generation Sequencing Data</em> at [http://www.abrf.org/ ABRF 2010].<br />
<br />
== Intro: Basic Genome Browser navigation==<br />
<br />
Here we will explore the Genome Browser to get familiar with moving around the landscape and load a simple Custom Track<br />
<br />
===Navigation -- find a gene===<br />
<br />
There are several ways to get started. We will start with a clean "cart", select a genome assembly and enter a gene name.<br />
<br />
====Steps====<br />
<br />
# Go to http://genome.ucsc.edu and hit the button "Genome Browser at the upper left in the blue bar.<br />
# Click here to reset (below the pulldown menus). This puts us all at the same place.<br />
# Select assembly hg18 (has richer annotations than the newer hg19, which is still being populated with data sets).<br />
# In the "gene" box, slowly type "PIGP." You will see the choices of gene names appear in the pulldown as you type.<br />
# Got to the gene, PIGP, by hitting the "jump" button.<br />
<br />
===Navigation -- zooming, panning and controlling data tracks===<br />
<br />
To get around in the browser view, you can move to any continuously variable region of your choosing.<br />
<br />
====Steps====<br />
<br />
# Above the browser image, hit the "zoom out 3x" button to see the region around the gene.<br />
# Data in the various "tracks" are drawn from separate tables in the browser database.<br />
# Note the spikes of conserved sequence among the species in the Conservation track.<br />
# Position your cursor at the top of the image in the scale bar above one of the exons. Hold down the mouse button and drag the mouse right or left to highlight the exon. Release the button to expand the exon to full screen.<br />
# We'll turn off some of the default tracks to simplify the view. As we are concerned about next-gen sequencing in this workshop, we'll turn off the Array track. Near the bottom of the browser image, find the track, "SNP Genotyping Arrays" and click the little minibutton to the left side of the track.<br />
# On the configuration page, we could turn on/off any of the subtracks. Select "hide" from the pulldown and Submit. Each data track has configuration options accessible via the little button.<br />
# Below the image, in the track controls, find these tracks and select "hide": RefGene, Human mRNAs, Spliced ESTs, Repeat Masker. Select "Refresh" from any blue bar. <br />
# The UCSC Genes Track, SNPs, and Conservation are still displayed. Note the little chevron arrows on UCSC Gene, PIGP, showing that it is transcribed from the negative strand. Click it to see rich information about the gene.<br />
# Return to the browser via the link the blue bar at the top.<br />
<br />
===Custom Tracks -- add your own data===<br />
<br />
We will load a simple Custom Track to see how user-supplied data can be added to the data already in the browser.<br />
<br />
====Steps====<br />
<br />
# Below the browser image, select "add custom tracks."<br />
# In the upper box, type (or paste):<br />
track name="test custom track" visibility=pack<br />
chr21 10000000 10050000<br />
chr21 10025000 10100000<br />
<br />
This is BED 3 format: chrom, chromStart, chromEnd<br />
# Select "Submit."<br />
# At the browser, select "zoom out 10x"<br />
<br />
<br />
== Tutorial: Viewing sequencing data in the UCSC Genome Browser ==<br />
<br />
This page serves as a step-by-step guide to the demo of UCSC Genome Browser tools presented at the workshop. Earlier in the workshop, Charlie Nicolet shared some sequencing and analysis results on chromosome 21 for ChIP-Seq of RNA polymerase II to HeLa cells. Thanks to Charlie for allowing us to post copies of his data and use them as a basis for this tutorial.<br />
<br />
In case internet fails at the workshop, slides will be used ([[Image:ABRF2010 UCSC NGS.ppt]] | [[Image:ABRF2010 UCSC NGS.pdf]]).<br />
<br />
=== Genome Graphs with .sgr data ===<br />
<br />
Some of the result files from the ChIPSeq toolset that Charlie Nicolet showed us earlier are in the .sgr format, i.e. tab-separated text that specifies chromosome, position and a numeric signal value. This format can be uploaded to UCSC's Genome Graphs tool for genome-at-a-glance view of the data. <br />
<br />
====Steps====<br />
<br />
# In a new web browser window or tab, go to '''<nowiki>http://genome.ucsc.edu/</nowiki>''' .<br />
# On the left side of the page, there is a blue sidebar. Click on "Genome Graphs", the 7th link from the top of the sidebar.<br />
# In the assembly menu, change the selection to "Mar. 2006 (NCBI36/hg18)".<br />
# Click the upload button. <br />
# In the input labeled "name of data set", type or paste "redbin". <br />
# Paste this URL: '''<nowiki>http://genome-test.cse.ucsc.edu/ABRF2010/chr21_extended.txt_redbin.sgr</nowiki>''' in the box labeled "Paste URLs or data", and click submit.<br />
# You should see confirmation screen; click OK to return to the Genome Graphs display.<br />
# Now you should see a layout of human chromosomes. Genome Graphs doesn't show the data until you select it. In the graph menu on the left, change "--nothing--" to "redbin 1". Now the data appear -- in this case, for chr21 only. <br />
[[Image:ABRF2010_ggData.png|border|link=http://genome.ucsc.edu/cgi-bin/hgGenome?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=ABRF2010_GG|catch up]] <br />
<br />
If you don't see blue data appearing over chromosome 21, go to http://genome.ucsc.edu/cgi-bin/hgGenome?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=ABRF2010_GG to catch up.<br />
<br />
Now we will use Genome Graphs to navigate to the Genome Browser.<br />
# Click on a peak to jump to the Genome Browser, displaying a 1,000,000-base region of the genome corresponding to the location you clicked in Genome Graphs.<br />
# Note the track at the top labeled "redbin 1" on the left and "User Supplied Track 1" above -- that is the data shown in Genome Graphs. Click on the top label "User Supplied Track 1" to make the peaks taller and more visible. In general, peaks correspond to upstream regions of genes, which makes sense for RNA polymerase II ChIP-seq.<br />
[[Image:ABRF2010 redbin 1.png|border|link=http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=ABRF2010_redbin_1|catch up]]<br />
<br />
If you don't see the above, go to http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=ABRF2010_redbin_1 to catch up.<br />
<br />
=== Transforming .sgr into bedGraph for Genome Browser viewing ===<br />
<br />
The Genome Browser can draw a somewhat nicer display of .sgr data, if we do a simple transform of the .sgr data into a similar format called bedGraph. bedGraph has both start and end genomic coordinates, so scores can be drawn over regions as opposed to single bases. Here is a command that translates .sgr to bedGraph, expanding each data point to cover a 30-base region:<br />
<br />
perl -wpe '@w=split("\t"); $_ = "$w[0]\t" . ($w[1]-1) . "\t" . ($w[1]+29) . "\t$w[2]";' \<br />
chr21_extended.txt_redbin.sgr > redbin.bed<br />
<br />
If you would like to show only datapoints above a certain threshold, say 5, you can make the command slightly more complicated:<br />
<br />
perl -wpe '@w=split("\t"); $_ = "$w[0]\t" . ($w[1]-1) . "\t" . ($w[1]+29) . "\t$w[2]"; \<br />
if ($w[2] < 15) {$_ = "";}' \<br />
chr21_extended.txt_redbin.sgr > redbinGt15.bed<br />
<br />
This line can be added to the beginning of redbinGt15.bed, in order to add labels to the track display and configure default appearance (see http://genome.ucsc.edu/goldenPath/help/bedgraph.html for more information about settings). A line break is used for readability here, but must be removed if you are going to edit this track line into a file:<br />
<br />
track name=redbinGt15 description="redbin items with score >= 15, expanded to 30 bases" \<br />
type=bedGraph viewLimits=0:100 autoScale=off maxHeightPixels=128:20:11<br />
<br />
The file has been saved here: http://genome-test.cse.ucsc.edu/ABRF2010/redbinGt15.bed .<br />
<br />
====Steps====<br />
<br />
# In the Genome Browser, click the "manage custom tracks" button below the image.<br />
# Click on "add custom tracks"<br />
# Paste these two lines into the box labeled "Paste URLs or data" and click submit:<br />
'''<nowiki>http://genome-test.cse.ucsc.edu/ABRF2010/redbinGt15.bed</nowiki>'''<br />
'''browser position chr21:42,886,797-43,886,796'''<br />
# You should see a confirmation page like this (''image'')<br />
# To go to the genome browser, you can click on "Genome Browser" in the top blue bar, or click on "chr21" in the Pos column of the table showing your custom tracks, or on the "go to genome browser" button. Note: in the absence of a "browser position" line, only the top blue bar link will return you to the position you were looking at before.<br />
# Now the new custom track shows grayscale representations of the score. You can click on the track title ("redbin items with score > 15") to expand the display to bar graph, which should look a lot like the "redbin 1" track created in Genome Graphs. <br />
<br />
[[Image:ABRF2010_redbinGt15.png|border|link=http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=ABRF2010_redbinGt15|catch up]]<br />
<br />
If you don't see two tracks labeled "redbin 1" and "redbinGt15" over the UCSC Genes track, go to http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=ABRF2010_redbinGt15 to catch up.<br />
<br />
=== Comparing with UCSC-hosted data ===<br />
Now we will take a look at some ChIP-seq data from the ENCODE project. The "Yale TFBS" track in the Regulation section combines ChIP-seq data from several labs, and it happens to include data for RNA polymerase II ("Pol2") in HeLa-S3 cells, like Charlie Nicolet's chr21 data. We can visually compare the two datasets to see how well they correspond.<br />
<br />
====Steps====<br />
<br />
# In the Genome Browser, scroll down below the image to the Regulation section. Click the "+" button on the left side of the blue "Regulation" header to expand.<br />
# Click on the link titled "Yale TFBS". This will take you to the track controls.<br />
# In the large table under "Select subtracks by cell line and factor", <br />
# Hit the "-" button in upper left corner to deselect all subtracks. Note that HeLa-S3 cell line is in 3rd column of checkboxes.<br />
# Scroll down to factor Pol2. select the 3rd check box. Only HeLa/Pol2 is selected for display.<br />
# Scroll back up to the top of the page. Change visibility to "full" and click submit.<br />
# In the Genome Browser, HeLa/Pol2 peaks and signal appear below "Spliced ESTs". <br />
<br />
The intervening tracks make it a little difficult to compare the ENCODE data with Charlie's, so we will adjust the display to see only the tracks we want to compare. <br />
# Click the "hide all" button under the image.<br />
# In the Custom Tracks section below the image, change the visibilities of redbin 1 and redbinGt15 to "full".<br />
# In the Genes and Gene Prediciton Tracks section, change the visibility of UCSC Genes to "dense".<br />
# In the Regulation section, change the visibility of Yale TFBS to "full".<br />
# Click the "refresh" button on any blue section header.<br />
<br />
[[Image:ABRF2010_TFBS.png|border|link=http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=ABRF2010_TFBS|catch up]]<br />
<br />
If you don't see a clear correspondence between the track on the bottom and the tracks on the top, go to http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=ABRF2010_TFBS to catch up.<br />
<br />
=== Viewing alignments in BAM format ===<br />
<br />
Charlie Nicolet has shared the ELAND export file that accompanies chr21_extended.txt, [http://genome-test.cse.ucsc.edu/ABRF2010/chr21_export.txt chr21_export.txt]. This can be transformed into [http://samtools.sourceforge.net/ BAM] for viewing in the UCSC Genome Browser. The [http://samtools.sourceforge.net/ samtools] package includes a script that converts ELAND export files into SAM (the text version of BAM). Export files often have fasta names instead of sequence names, e.g. "chr21.fa" instead of "chr21", so the ".fa" must be removed:<br />
<br />
export2sam.pl --read1=chr21_export.txt \<br />
| perl -wpe 's/(chr.*)\.fa/$1/' \<br />
> chr21.sam<br />
<br />
Edit chr21.sam to add these header lines at the beginning (note: the words must be separated by tab characters, not spaces):<br />
<br />
@HD VN:1.0 GO:none SO:coordinate<br />
@SQ SN:chr21 LN:46944323<br />
<br />
Note that current versions of samtools do not require the @SQ fields, you can also add the -t option to the "samtools view" command below and specify a chromSizes.txt file in that command (from the chromInfo table, e.g. using the fetchChromSizes script).<br />
<br />
Use samtools to convert SAM to BAM, sort the BAM, and index the sorted BAM (see http://genome.ucsc.edu/goldenPath/help/bam.html for more info):<br />
<br />
samtools view -bSo chr21.unsorted.bam chr21.sam<br />
samtools sort chr21.unsorted.bam chr21<br />
samtools index chr21.bam<br />
<br />
Now the sorted chr21.bam and its index file chr21.bam.bai must be put on a web server (ftp, http, or https). For example, if you create files my.bam and my.bam.bai, and you have a personal web directory <nowiki>http://my.edu/mylab/~me/</nowiki>, you can copy or link the files to <nowiki>http://my.edu/mylab/~me/my.bam</nowiki> and <nowiki>http://mylab/~me/my.bam.bai</nowiki>. Then you would use only the first URL (<nowiki>http://my.edu/mylab/~me/my.bam</nowiki>) in a track definition line like the one below. For this example, we will use <nowiki>http://genome-test.cse.ucsc.edu/ABRF2010/chr21.bam</nowiki> .<br />
<br />
====Steps====<br />
<br />
# In the Genome Browser, click the "manage custom tracks" buttom below the image. <br />
# Click the "add custom tracks" button. <br />
# Paste this text into the box:<br />
'''track name=chr21_export type=bam bigDataUrl=<nowiki>http://genome-test.cse.ucsc.edu/ABRF2010/chr21.bam</nowiki> visibility=pack'''<br />
# Click submit. Click "Genome Browser" in the blue top bar. Now you should see an almost-solid dark blue bar with a few dark red stripes, labeled "chr21_export" above and to the left. <br />
[[Image:ABRF2010_chr21_export_1MB.png|border|link=http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=ABRF2010_chr21_export_1MB|catch up]]<br />
<br />
If you don't see the above, got to http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=ABRF2010_chr21_export_1MB to catch up. There are so many alignments in this 1MB window that the items can't be drawn individually -- the image would become too tall. Let's view a smaller genomic region to get a better look at the alignments.<br />
# Click and drag on the base position track to select a window around the couple largest peaks. (''If it doesn't work for you, paste '''chr21:43,169,278-43,191,176''' into the position box and click "jump".'')<br />
# Now we are viewing about 22,000 bases covering two peaks, and there are still so many alignments that the track is forced into "squish" display mode: items are shown at half-height and read names are suppressed. Let's zoom in again, to the right side of the left peak ''(or jump to position '''chr21:43,172,778-43,173,354''').<br />
# Even when viewing 577 bases, there is still quite a pileup of read alignments to view. The read names take up a lot of room, so let's hide them. Click on the light blue bar to the left of the chr21_export track, to go to track controls.<br />
# There is a checkbox to the right of "Display read names" -- click to clear the checkbox, and then click submit.<br />
# Mismatches appear as light red tickmarks. They are a bit easier to see if the items are drawn in grayscale, so again click on the light blue bar on the left to return to track controls.<br />
# Under "additional coloring modes", select "Use gray for [alignment quality]", and click submit.<br />
# Note the trend for mismatches to appear more often in alignments with lower quality, and also the relative frequency of lower-quality reads at the edge of the peak. <br />
[[Image:ABRF2010 chr21 export grayQual.png|border|link=|catch up]]<br />
<br />
If you don't see the above, go to http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=ABRF2010_chr21_export_grayQual to catch up.<br />
# Zoom in once again to focus on the region with the most mismatching items ('''chr21:43,172,834-43,172,931'''). Now we see the exact mismatches between reference and read bases.<br />
# Let's take a look at base qualities. Once again, click the light blue bar on the left to return to track controls.<br />
# Change the selection to "Use gray for [base qualities]", and click submit. Some of the mismatches, but not all, almost disappear due to the light shades used for low quality bases. <br />
[[Image:ABRF2010 chr21 export baseQual.png|border|link=http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=ABRF2010_chr21_export_baseQual|catch up]]<br />
<br />
If you don't see the above, go to http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=ABRF2010_chr21_export_baseQual to catch up.<br />
<br />
====Extra: Finding variants in alignment display====<br />
In some regions, stacks of red tickmarks (mismatches) indicate HeLa variants with respect to the reference genome assembly. Here are several examples. <br />
<br />
# Paste '''chr21:37,366,724-37,366,992''' into the position box and click "jump".<br />
# To compare with variants in dbSNP, scroll down to the Variation section and change the visibility of SNPs (130) to pack. Click "refresh" on any blue section header.<br />
# The SNP track appears at the bottom of the image. SNPs classified "coding non-synonymous" by dbSNP are colored red. ''(If you don't see that, click '''<nowiki>http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=ABRF2010_chr21_export_SNPs</nowiki>''' to catch up.)''<br />
# To see a variant not in dbSNP, paste '''chr21:37,367,831-37,367,845'''.<br />
# To see a heterozygous variant adjacent to a dbSNP 3-base indel, paste '''chr21:37,367,478-37,367,492'''.<br />
# This 110-base region contains three know variations from the reference assembly: '''chr21:37,366,860-37,366,969'''.<br />
<br />
== Where to learn more ==<br />
* [http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html Help] link in blue top bar of any page<br />
* [http://genome.ucsc.edu/FAQ/ FAQ] (Frequently asked questions)<br />
* mailto:genome@soe.ucsc.edu and list archives<br />
* [[Main_Page|http://genomewiki.ucsc.edu/]] (this site)<br />
* [http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml OpenHelix] offers free tutorials and reference card PDFs.<br />
<br />
[[Category:Browser Linked]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Generic_Makefile&diff=22279Generic Makefile2014-11-20T20:55:16Z<p>Kuhn: </p>
<hr />
<div><pre><br />
include ${KENT}/src/inc/common.mk<br />
<br />
CFLAGS=-I ${KENT}/src/inc -I ${KENT}/src/hg/inc <br />
L += -lm ${MYSQLLIBS}<br />
MYLIBDIR = ${KENT}/src/lib/${MACHTYPE}<br />
MYLIBS = ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a <br />
<br />
O = ${PROG}.o ../lib/bedUtil.o<br />
<br />
${PROG}: $O ${MYLIBS} <br />
${CC} ${COPT} ${CFLAGS} -o ${HOME}/bin/${MACHTYPE}/${PROG} $O ${MYLIBS} $L<br />
strip ${HOME}/bin/${MACHTYPE}/${PROG}<br />
<br />
clean:<br />
rm *.o<br />
rm core<br />
<br />
</pre><br />
<br />
Make sure that the four indented lines are indented with tabs, otherwise the file will not work.<br />
<br />
See also: the <em>newProg</em> command in the kent source tree. It will generate not only a generic Makefile but also the generic structure of a kent source utility.<br />
<br />
Please note, it is convenient to use the {curlyBraces} instead of (parens) for variables, since the lines can then be cut and pasted into a command line when need be. They work the same way in a Makefile, but not on a command line.<br />
<br />
[[Category:Browser Development]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=22264Other genome browsers2014-10-25T22:57:46Z<p>Kuhn: /* UCSC Genome mirror sites */ added Australian mirror</p>
<hr />
<div><br />
== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
<br />
This mirror is maintained by the Browser staff.<br />
<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome.hmgc.mcw.edu/ Medical College of Wisconsin]. Milwaukee, WI<br />
<br />
* [http://genome-mirror.bscb.cornell.edu/ Cornell University]. Ithaca, NY<br />
<br />
* [http://moma.ki.au.dk/genome-mirror/ Aarhus University]. The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
* [https://ucsc.genome.edu.au/ Genomics Virtual Lab]. QFAB mirror in Australia.<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway?clade=plant&org=Glycine+max&db=0 soybean] and others at UCLA.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, University College, Cork, Ireland.<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly Assembly Hub] mechanism.<br />
<br />
If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=22263Other genome browsers2014-10-25T22:54:58Z<p>Kuhn: /* Browsers Using Non-UCSC Software */ added pointer to Assembly Hub User Guide</p>
<hr />
<div><br />
== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
<br />
This mirror is maintained by the Browser staff.<br />
<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome.hmgc.mcw.edu/ Medical College of Wisconsin] Milwaukee, WI<br />
<br />
* [http://genome-mirror.bscb.cornell.edu/ Cornell University] Ithaca, NY<br />
<br />
* [http://moma.ki.au.dk/genome-mirror/ Aarhus University] The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway?clade=plant&org=Glycine+max&db=0 soybean] and others at UCLA.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, University College, Cork, Ireland.<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly Assembly Hub] mechanism.<br />
<br />
If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=22262Other genome browsers2014-10-25T22:36:17Z<p>Kuhn: /* Locations using UCSC software on other organisms (or people) or additional content on our organisms */</p>
<hr />
<div><br />
== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
<br />
This mirror is maintained by the Browser staff.<br />
<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome.hmgc.mcw.edu/ Medical College of Wisconsin] Milwaukee, WI<br />
<br />
* [http://genome-mirror.bscb.cornell.edu/ Cornell University] Ithaca, NY<br />
<br />
* [http://moma.ki.au.dk/genome-mirror/ Aarhus University] The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway?clade=plant&org=Glycine+max&db=0 soybean] and others at UCLA.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, University College, Cork, Ireland.<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Obscure_But_Useful_Browser_Features&diff=22208Obscure But Useful Browser Features2014-10-13T16:56:03Z<p>Kuhn: </p>
<hr />
<div>You may be able to speed up the browser display dramatically <br />
by turning off the<br />
track control buttons under the graphic display. Some WEB browsers (in particular, <br />
Mac Safari) seem<br />
to take forever figuring out how to arrange all those buttons. Go to<br />
the "Configure" page, and turn off the item:<br />
''Show track controls under main graphic'' or use the 'collapse all' button to collapse the track groups.<br />
<br />
Also on the Configure page, find the Next Item and Next exon arrows buttons. They help for navigating<br />
along a chromosome and add little arrows on the edge of the screen. They do not show up in PDF images<br />
made from the page.<br />
<br />
The base position ruler track has some fascinating track controls to add titles<br />
and position information to the tracks gif image. An excellent aid for preparing<br />
presentation slides.<br />
<br />
The small grey buttons or bars (a.k.a. mini-buttons or mini-bars) at the very left edge of the browser gif tracks display will open a page where you can adjust various parameters that control the display of the track.<br />
This is also the same function entered if you click on the text<br />
label above the track visibility control drop down list (hide, dense, pack, etc...).<br />
<br />
The small arrow left arrow ---> or right arrow <--- displayed when the base position<br />
track is set to full visibility mode to the left of the track in the margin where<br />
track labels usually are, is used to reverse the direction of nucleotide display<br />
when the viewpoint is close enough. Thus you can view either the forward strand<br />
bases, or the reverse strand bases. Click directly on the arrow itself to reverse<br />
the display. The display always displays the 5' of the forward strand to the<br />
left in the tracks display.<br />
<br />
The chain- and net- tracks are colored by chromosome. Keeping this in mind, you can easily spot<br />
locations of synteny, e.g., two features that are far apart but share the same color.<br />
<br />
=-=-=-=-=-<br />
<br />
This is not really browser-related but I don't know any other place to put it:<br />
In firefox, create a bookmark with the keyword hg19 and use the following url:<br />
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=%s (as you can see, position is replaced with %s). When you type "hg19 dach" into the firefox url bar and press return, this will directly jump to the gene...I'm using this all the time now, also for genecards and pubmed. (max)<br />
<br />
hg19 is tedious to type so I make the keyword simply h for homSap and then type in the gene name eg h prnp. that makes it easy to move around to orthologs in various species, using d for canFam etc with firefox bookmark http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=canFam2&position=%s<br />
<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Obscure_But_Useful_Browser_Features&diff=22207Obscure But Useful Browser Features2014-10-13T16:55:41Z<p>Kuhn: </p>
<hr />
<div>You may be able to speed up the browser display dramatically <br />
by turning off the<br />
track control buttons under the graphic display. Some WEB browsers (in particular, <br />
Mac Safari) seem<br />
to take forever figuring out how to arrange all those buttons. Go to<br />
the "Configure" page, and turn off the item:<br />
''Show track controls under main graphic'' or use the 'collapse all' button to collapse the track groups.<br />
<br />
Also on the Configure page, find the Next Item and Next exon arrows buttons. They help for navigating<br />
along a chromosome and add little arrows on the edge of the screen. They do not show up in PDF images<br />
made from the page.<br />
<br />
The base position ruler track has some fascinating track controls to add titles<br />
and position information to the tracks gif image. An excellent aid for preparing<br />
presentation slides.<br />
<br />
The small grey buttons or bars (a.k.a. mini-buttons or mini-bars) at the very left edge of the browser gif tracks display will open a page where you can adjust various parameters that control the display of the track.<br />
This is also the same function entered if you click on the text<br />
label above the track visibility control drop down list (hide, dense, pack, etc...).<br />
<br />
The small arrow left arrow ---> or right arrow <--- displayed when the base position<br />
track is set to full visibility mode to the left of the track in the margin where<br />
track labels usually are, is used to reverse the direction of nucleotide display<br />
when the viewpoint is close enough. Thus you can view either the forward strand<br />
bases, or the reverse strand bases. Click directly on the arrow itself to reverse<br />
the display. The display always displays the 5' of the forward strand to the<br />
left in the tracks display.<br />
<br />
The chain- and net- tracks are colored by chromosome. Keeping this in mind, you can easily spot<br />
locations of synteny, e.g., two features that are far apart but share the same color.<br />
<br />
=-=-=-=-=-<br />
<br />
This is not really browser-related but I don't know any other place to put it:<br />
In firefox, create a bookmark with the keyword hg19 and use the following url:<br />
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=%s (as you can see, position is replaced with %s). When you type "hg18 dach" into the firefox url bar and press return, this will directly jump to the gene...I'm using this all the time now, also for genecards and pubmed. (max)<br />
<br />
hg18 is tedious to type so I make the keyword simply h for homSap and then type in the gene name eg h prnp. that makes it easy to move around to orthologs in various species, using d for canFam etc with firefox bookmark http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=canFam2&position=%s<br />
<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Obscure_But_Useful_Browser_Features&diff=22206Obscure But Useful Browser Features2014-10-13T16:54:06Z<p>Kuhn: </p>
<hr />
<div>You may be able to speed up the browser display dramatically <br />
by turning off the<br />
track control buttons under the graphic display. Some WEB browsers (in particular, <br />
Mac Safari) seem<br />
to take forever figuring out how to arrange all those buttons. Go to<br />
the "Configure" page, and turn off the item:<br />
''Show track controls under main graphic'' or use the 'collapse all' button to collapse the track groups.<br />
<br />
Also on the Configure page, find the Next Item and Next exon arrows buttons. They help for navigating<br />
along a chromosome and add little arrows on the edge of the screen. They do not show up in PDF images<br />
made from the page.<br />
<br />
The base position ruler track has some fascinating track controls to add titles<br />
and position information to the tracks gif image. An excellent aid for preparing<br />
presentation slides.<br />
<br />
The small grey buttons or bars (a.k.a. mini-buttons or mini-bars) at the very left edge of the browser gif tracks display will open a page where you can adjust various parameters that control the display of the track.<br />
This is also the same function entered if you click on the text<br />
label above the track visibility control drop down list (hide, dense, pack, etc...).<br />
<br />
The small arrow left arrow ---> or right arrow <--- displayed when the base position<br />
track is set to full visibility mode to the left of the track in the margin where<br />
track labels usually are, is used to reverse the direction of nucleotide display<br />
when the viewpoint is close enough. Thus you can view either the forward strand<br />
bases, or the reverse strand bases. Click directly on the arrow itself to reverse<br />
the display. The display always displays the 5' of the forward strand to the<br />
left in the tracks display.<br />
<br />
The chain- and net- tracks are coloured by chromosome. Keeping this in mind, you can easily spot<br />
locations of synteny, e.g., two features that are far apart but share the same colour.<br />
<br />
=-=-=-=-=-<br />
<br />
This is not really browser-related but I don't know any other place to put it:<br />
In firefox, create a bookmark with the keyword hg18 and use the following url:<br />
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=%s (as you can see, position is replaced with %s). When you type "hg18 dach" into the firefox url bar and press return, this will directly jump to the gene...I'm using this all the time now, also for genecards and pubmed. (max)<br />
<br />
hg18 is tedious to type so I make the keyword simply h for homSap and then type in the gene name eg h prnp. that makes it easy to move around to orthologs in various species, using d for canFam etc with firefox bookmark http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=canFam2&position=%s<br />
<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=22108Other genome browsers2014-09-26T18:49:13Z<p>Kuhn: /* Locations using UCSC software on other organisms (or people) or additional content on our organisms */ added GWIPS proteins Browser from Ireland</p>
<hr />
<div><br />
== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
<br />
This mirror is maintained by the Browser staff.<br />
<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome.hmgc.mcw.edu/ Medical College of Wisconsin] Milwaukee, WI<br />
<br />
* [http://genome-mirror.bscb.cornell.edu/ Cornell University] Ithaca, NY<br />
<br />
* [http://moma.ki.au.dk/genome-mirror/ Aarhus University] The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway?clade=plant&org=Glycine+max&db=0 soybean] and others at UCLA.<br />
<br />
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, University College, Cork, Ireland.<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=22042Other genome browsers2014-08-23T22:28:13Z<p>Kuhn: /* Locations using UCSC software on other organisms (or people) or additional content on our organisms */ text edits and added some new mirrors</p>
<hr />
<div><br />
== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
<br />
This mirror is maintained by the Browser staff.<br />
<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome.hmgc.mcw.edu/ Medical College of Wisconsin] Milwaukee, WI<br />
<br />
* [http://genome-mirror.bscb.cornell.edu/ Cornell University] Ithaca, NY<br />
<br />
* [http://moma.ki.au.dk/genome-mirror/ Aarhus University] The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).<br />
<br />
* [http://128.227.123.35:8889/cgi-bin/hgGateway?hgsid=326&clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.<br />
<br />
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway?hgsid=38871&clade=plant&org=Glycine+max&db=0 soybean] and others at UCLA.<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Other_genome_browsers&diff=22041Other genome browsers2014-08-23T20:49:14Z<p>Kuhn: /* Locations using UCSC software on other organisms (or people) or additional content on our organisms */</p>
<hr />
<div><br />
== Official UCSC Genome mirror site ==<br />
<br />
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.<br />
<br />
This mirror is maintained by the Browser staff.<br />
<br />
<br />
== UCSC Genome mirror sites ==<br />
<br />
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.<br />
<br />
* [http://genome.hmgc.mcw.edu/ Medical College of Wisconsin] Milwaukee, WI<br />
<br />
* [http://genome-mirror.bscb.cornell.edu/ Cornell University] Ithaca, NY<br />
<br />
* [http://moma.ki.au.dk/genome-mirror/ Aarhus University] The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark<br />
<br />
<br />
== Locations using UCSC software on other organisms (or people) or additional content on our organisms ==<br />
Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).<br />
<br />
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill<br />
<br />
* [http://genome.ccbr.utoronto.ca/ Cannabis sativa] at U Toronto<br />
<br />
* [http://aedes.caltech.edu/cgi-bin/hgGateway Aedes aegypti] and two other mosquitoes at CalTech<br />
<br />
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC<br />
<br />
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, C. intestinalis and other orgs. (seems to have been retired or moved)<br />
<br />
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly contained in the Track Data Hubs at UCSC.<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting D. melanogaster and some plants<br />
<br />
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.<br />
<br />
* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> Butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).<br />
<br />
== Browsers Using Non-UCSC Software==<br />
<br />
The UCSC Genome Browser is primarily funded to host vertebrate genomes. If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.<br />
<br />
=== Animal Browsers ===<br />
<br />
* [http://www.1000genomes.org 1000 Genomes] A Deep Catalog of Human Genetic Variation<br />
<br />
* [http://159.226.118.44/cgi-bin/hgGateway NONCODE] genome browser. UCSC browser with special tracks for non-coding annotations.<br />
<br />
* [http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Jim Watson] genome browser at CSHL<br />
<br />
* [http://www.jcvi.org/research/huref/ Craig Venter] genome data release<br />
<br />
* [http://falcon.roswellpark.org:9090/cgi-bin/hgGateway?org=Human&db=hg17 dbRIP - Retroposon Insertions] Roswell Park Cancer Institute, MD<br />
<br />
* [http://pipeline.lbl.gov/cgi-bin/vistatrack?db=hg17&position=chr1:995532-995632 Vista] Lawrence Berkeley Lab, CA<br />
<br />
* [http://lgd.abcc.ncifcrf.gov/ GARFIELD] cat genome browser, Federick, MD<br />
<br />
* [http://panda.genomics.org.cn/page/panda/index.jsp Panda genome resources]<br />
<br />
* C. intestinalis: [http://genome.smith.man.ac.uk UCSC-based], [http://ghost.zool.kyoto-u.ac.jp/indexr1.html Gbrowse]<br />
<br />
* [http://genome.jgi-psf.org/euk_home.html The JGI-browser for various species:] Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...<br />
<br />
* [http://www.bio2rdf.org/ Bio2Rdf] Semantic web atlas of postgenomic knowledge about human and mouse<br />
<br />
* [http://aaegypti.vectorbase.org/Genome/Home/ Aedes aegypti] mosquito<br />
<br />
* [http://silkworm.genomics.org.cn/ Silkworm] Bombyx mori, China<br />
<br />
* [http://www.animalgenome.org/ NRSP-8] National Animal Genome Research Program - Bioinformatics Coordination Program<br />
<br />
=== Plant Browsers ===<br />
<br />
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])<br />
<br />
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA<br />
<br />
* [http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9&hgsid=876/ Arabidopsis] genome browser at Dartmouth.<br />
<br />
* [http://atensembl.arabidopsis.info/index.html Arabidopsis] arabidopsis.info Ensembl-based genome browser<br />
<br />
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas Genome Browser] hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster<br />
<br />
* [http://www.gramene.org/ gramene.org] many rice genomes and other grasses<br />
<br />
* [http://rice.plantbiology.msu.edu/ Rice Genome Annotation Project] hosts [http://rice.plantbiology.msu.edu/cgi-bin/gbrowse Oryza sativa browser]<br />
<br />
* [http://www.ricemap.org/ Rice-Map]<br />
<br />
* [http://www.genome.arizona.edu/fpc/rice/gbrowse/ RICE FPC Genome Browser] from the Arizona Genomics Institute (AGI)<br />
<br />
* [http://www.maizesequence.org/ Zea mays] Maize Genome Sequencing Project<br />
<br />
=== Fungi/Yeast Browsers ===<br />
<br />
* [http://www.yeastgenome.org/ Saccharomyces cerevisiae] database and [http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ genome browser] from SGD/Stanford University<br />
<br />
* [http://pombe.nci.nih.gov/genome/ S. pombe] (fission yeast) at NCI, NIH<br />
<br />
=== Other ===<br />
* [http://archaea.ucsc.edu/ Archaea browser] from the [http://lowelab.ucsc.edu/ Lowe Lab] at UCSC<br />
<br />
* [http://bacteria.ensembl.org/index.html EnsemblBacteria]<br />
<br />
* [http://protists.ensembl.org/index.html EnsemblProtists] <br />
<br />
* [http://www.genoscope.cns.fr/externe/Francais/Projets/Projet_FN/ Paramecium tetraurelia] Genoscope, France<br />
<br />
* [http://jpgv.fli-leibniz.de/cgi/index.pl JPGV] Jena Prokaryotic Genome Browser<br />
<br />
==See Also==<br />
[[Other_wiki_sites|Related Wikis]]<br />
<br />
[[Category:Wiki Administration]]<br />
[[Category:Technical FAQ]]</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=File:UcscLinks.xls&diff=22017File:UcscLinks.xls2014-08-17T14:39:36Z<p>Kuhn: uploaded a new version of &quot;File:UcscLinks.xls&quot;: small adjustment</p>
<hr />
<div>spreadsheet to create links that open Genome Browser views when a user types in a variety of entries, including genomic coordinates, gene names or chromosome bands.</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=File:UcscLinks.xls&diff=22016File:UcscLinks.xls2014-08-17T14:33:38Z<p>Kuhn: uploaded a new version of &quot;File:UcscLinks.xls&quot;: update Excel file to include links to hg38 and latest dbSnp version for hg19 (snp138).</p>
<hr />
<div>spreadsheet to create links that open Genome Browser views when a user types in a variety of entries, including genomic coordinates, gene names or chromosome bands.</div>Kuhnhttps://genomewiki.ucsc.edu/index.php?title=Genome_Browser_Session_Gallery&diff=21622Genome Browser Session Gallery2013-11-06T16:42:35Z<p>Kuhn: </p>
<hr />
<div>{| class="wikitable" border="0"|-<br />
|-<br />
|<br />
== ENCODE Tier 1 Cell Lines ==<br />
[[Image:EncodeKent1.gif|800px|thumb|none|Tier 1 cell lines]]<br />
[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kuhn&hgS_otherUserSessionName=hg18_encodeKent1 Launch Browser] <br />
<br />
Basic ENCODE data on the Tier 1 cell lines GM128 (a lymphoid<br />
cell line) and K562 (a myeloid line). This track collection includes:<br />
* RNA-seq, which shows the level of expression of the gene EWSR1<br />
* the histone mark H3K4Me3, which is associated with promoters<br />
* DNAseI hypersensitivity, which is associated with regulatory regions in general<br />
* ChIP-seq, which shows levels of occupancy by the transcription factor c-Fos<br />
<br />
(Contributed by Jim Kent.)<br />
<br />
<br />
|-<br />
|<br />
<br />
== Premature Stop in Reference Assembly ==<br />
<br />
[[Image:EncodeKent2.gif|800px|thumb|none|Premature stop in reference assembly]]<br />
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[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kuhn&hgS_otherUserSessionName=hg18_encodeKent2 Launch Browser] <br />
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A premature stop codon that is found in the reference genome and about half of people of European descent. The UCSC Genes track is forced to skip the codon.<br />
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(Contributed by Jim Kent.)<br />
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== Multiple Histone Marks ==<br />
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[[Image:EncodeKent3.gif|800px|thumb|none|Multiple histone marks.]]<br />
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[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kuhn&hgS_otherUserSessionName=hg18_encodeKent3 Launch Browser] <br />
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Histone ChIP-seq data on two ENCODE Tier 1 cell lines. <br />
H3K4me1 is associated with enhancers and (to an extent) with promoters. <br />
H3K4me3 is associated with promoters, and H3K36me3 is associated with transcribed regions.<br />
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(Contributed by Jim Kent.)<br />
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<!-- Commented out til reg tracks are released<br />
== Session from Ross Hardison ==<br />
[[Image:EncodeHardison1.gif|800px|thumb|none]]<br />
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[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Rosshardison&hgS_otherUserSessionName=8q24_9kb_KateR Launch Browser] -- dang. this session no longer exists.<br />
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(Contributed by Ross Hardison.)<br />
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== Template ==<br />
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[[Image:image.jpg|600px|thumb|none|text below image]]<br />
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[http://urlToSession Launch Browser] <br />
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Description of scenario.<br />
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Contributed by .<br />
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|}</div>Kuhn