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<H4>Welcome to the UCSC Genome Wiki Site</H4>
=== Welcome to the Public Support UCSC Genome Browser Wiki ===


Please feel free to organize your collaborations
This wiki site provides a forum for sharing information about the [http://genome.ucsc.edu/ UCSC Genome Browser], a web-based tool that provides a fast, easy way to display a specific region of a genome assembly, along with dozens of aligned annotation tracks. The browser features data from a large collection of vertebrates, model organisms, and selected invertebrate genomes.  
and exchange tips and tricks for
[http://genome.ucsc.edu/ genome browser] usage.
We are looking forward to the development here
of interesting projects and a store of information
useful to a variety of audiences.


See also [[Help:Contents]]
In addition to offering general information about the browser on this site, we'd also like to share tips and tricks for more advanced users, information for mirror sites and developers, and discussions of the underlying data sets and experimental protocols. Please feel free to use this wiki to organize your collaborations and exchange ideas about Genome Browser usage. Our intent is to develop a collection of interesting projects and a store of information useful to a variety of audiences.


Since this wiki site is based on the same software operated
Before editing this wiki, please create an account by clicking on the "Log in/create account" link at the top of the page. For information about editing wiki pages, see also the [[Help:Contents]] link for specific information about this wiki, or for a more extensive discussion of page editing, the Wikipedia guidelines on [http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page How to edit a page]. For navigation and organization assistance within this Wiki, use the [[Special:Categories|Categories]] link in the navigation panel on the left.
at [http://en.wikipedia.org/wiki/Main_Page Wikipedia,] the
help pages there on editing are useful and appropriate to
editing pages here.  For example,
[http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page How to edit a page.]


== Custom Tracks ==
== Get help ==


How to create a custom track [http://genome.cse.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks]
The UCSC Genome Browser Support Team is available to answer questions by contacting one of the support forums:


== Genome Analysis ==
* Post to the Public Help Forum: Email genome@soe.ucsc.edu​ or search the [https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome Public Archives]
* Post to the Mirror Help Forum: Email genome-mirror@soe.ucsc.edu or search the [https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-mirror Mirror Archives​]
* Confidential/private help: Email genome-www@soe.ucsc.edu


Phylogenetic origin of human SGSH introns [[Ancestral_introns:_SGSH]]
Also see related pages on the UCSC Genome Browser site:


== Implementation Notes ==
* [http://genome.ucsc.edu/contacts.html Contact Us]
* [http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html Browser Documentation]


[[Implementation_Notes]] describe some of the down-and-dirty details that QAers often ask developers about... or that they get an earful about when they ask simple questions!
== UCSC Genome Browser Announcements List ==


<h2> Entering Math </h2>
Subscribing to this list provides occasional email alerts for new data & software.


To display math equations, you can use TeX formatting:
* Subscribe: Email genome-announce+subscribe@soe.ucsc.edu
* Unsubscribe: Email genome-announce+unsubscribe@soe.ucsc.edu


<math>
Also see related pages on the UCSC Genome Browser site:
\sqrt{2}\approx 1.4
</math>


See also: [http://meta.wikimedia.org/wiki/Help:Formula Math Markup]
* [http://genome.ucsc.edu/goldenPath/releaseLog.html  Release Log]
* [[Genome_Browser_Software_Features|Tri-weekly New Software Summaries]]
* [http://genome.ucsc.edu/goldenPath/newsarch.html News Archives]
* [http://genome.ucsc.edu/training/index.html Training]


<h2> administration information </h2>
== Join us on social media ==


Wiki software successfully installed.
Join us on Social Media!


Please see [http://meta.wikipedia.org/wiki/MediaWiki_i18n documentation on customizing the interface]
* [https://www.facebook.com/ucscGenomeBrowser Facebook]
and the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide User's Guide] for usage and configuration help.
* [http://www.twitter.com/GenomeBrowser Twitter]
* [http://genome.ucsc.edu/blog/ Wordpress Blog]
* [http://www.youtube.com/channel/UCQnUJepyNOw0p8s2otX4RYQ YouTube]


You must log in to edit pages. Create a new account if have not done so to write articles.
== Using genome.ucsc.edu ==
* [[Learn about the Browser|Learn more about the browser]]
* [http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks How to create a custom track]
* [[Browser_installation|Minimal browser install]]
* [[Browser Mirrors|Maintaining Browser mirrors]]
* [[Browser Installation| Installing Browser Mirror]]


I'm wondering what it takes to change the navigation links.  Possibly it takes a more
* [[:Category:User Developed Scripts| User Developed Scripts]] - helpful hints from the user community
powerful account than I have.  This may be a good thing.  Here's an example of
a wiki taken over by spambots: http://dbc.rubyforge.org/wiki/wiki.pl?Getting_Started
  -Jim Kent


You need to have '''admin''' rights to change navigation links. I can take care of that for you. Let me know what you want as a top level navigation link and on that link you can have more links that regular users can edit. -Chester
== Genome Browser in a Box (GBiB) ==
* [[GBiB: From download to BLAT at assembly hubs]]
* [[GBiB: Deploying on VMWare ESXi]]


Wikipedia has had experience with [http://en.wikipedia.org/wiki/Wikibot Wikibots] including the problem of [http://meta.wikimedia.org/wiki/Vandalbot Vandelbots,] there
== Genome Biology ==
may be some experience there that would be useful.
* Genome Analysis - Phylogenetic origin of human SGSH introns [[Ancestral_introns:_SGSH]]


== Browser Development ==
* [[:Category:Technical_FAQ|Technical FAQ Category]] - list of technical discussions
* [[ENCODE Project at UCSC]]
* [[Automation]] of genome assembly database builds
* [[Custom track database]] implementation
* [[Track metadata handling]] - discussion of design for expanded search/display, especially for ENCODE
* [[Known genes III]] - design and discussion of next generation known genes track
* [[Medical Sequencing Data|Medical sequencing data]] - discussion for design of next generation medical sequence data organization
* [[Web Services & Javascript]] - design and discussion of a genome browser architecture for the 2010's and maybe 2009....
* [[Implementation_Notes]] describe some of the down-and-dirty details that QA engineers often ask developers about... or that they get an earful about when they ask simple questions!


[[Image:G-Wiki.jpg]]
 
----
== Science and Justice ==
* [[Genomics and Justice Meeting at UC Santa Cruz, May 17-18, 2007]]
* [https://scijust.ucsc.edu/ Science and Justice] at UCSC.
* [[Ethics in the News]]
 
== Administrative Information ==
 
You must log in '''and''' confirm your email address to edit pages. To create an account, click the "Log in/create account" link at the top of the page, then confirm your email address via the "Preferences" link. '''Please note:''' all content you create in genomewiki is public content and cannot be removed since it is always in the history of a page even if it is deleted after creation.
 
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[[Category:Wiki Administration]]

Latest revision as of 21:15, 26 February 2019

Welcome to the Public Support UCSC Genome Browser Wiki

This wiki site provides a forum for sharing information about the UCSC Genome Browser, a web-based tool that provides a fast, easy way to display a specific region of a genome assembly, along with dozens of aligned annotation tracks. The browser features data from a large collection of vertebrates, model organisms, and selected invertebrate genomes.

In addition to offering general information about the browser on this site, we'd also like to share tips and tricks for more advanced users, information for mirror sites and developers, and discussions of the underlying data sets and experimental protocols. Please feel free to use this wiki to organize your collaborations and exchange ideas about Genome Browser usage. Our intent is to develop a collection of interesting projects and a store of information useful to a variety of audiences.

Before editing this wiki, please create an account by clicking on the "Log in/create account" link at the top of the page. For information about editing wiki pages, see also the Help:Contents link for specific information about this wiki, or for a more extensive discussion of page editing, the Wikipedia guidelines on How to edit a page. For navigation and organization assistance within this Wiki, use the Categories link in the navigation panel on the left.

Get help

The UCSC Genome Browser Support Team is available to answer questions by contacting one of the support forums:

  • Post to the Public Help Forum: Email genome@soe.ucsc.edu​ or search the Public Archives
  • Post to the Mirror Help Forum: Email genome-mirror@soe.ucsc.edu or search the Mirror Archives​
  • Confidential/private help: Email genome-www@soe.ucsc.edu

Also see related pages on the UCSC Genome Browser site:

UCSC Genome Browser Announcements List

Subscribing to this list provides occasional email alerts for new data & software. 

* Subscribe: Email genome-announce+subscribe@soe.ucsc.edu 
* Unsubscribe: Email genome-announce+unsubscribe@soe.ucsc.edu

Also see related pages on the UCSC Genome Browser site:

Join us on social media

Join us on Social Media!

Using genome.ucsc.edu

Genome Browser in a Box (GBiB)

Genome Biology

Browser Development


Science and Justice

Administrative Information

You must log in and confirm your email address to edit pages. To create an account, click the "Log in/create account" link at the top of the page, then confirm your email address via the "Preferences" link. Please note: all content you create in genomewiki is public content and cannot be removed since it is always in the history of a page even if it is deleted after creation.

<google></google>

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