User:Hiram: Difference between revisions

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<h4>Office phone: 831-459-5871</h4>
'''Office phone: 831-459-5871'''<BR>
Office: room 515 Engineering II
Office: room 515 Engineering II U.C. Santa Cruz<BR>
U.C. Santa Cruz
Email: note the <em>E-mail this user</em> button in the toolbox on the left<BR>


Mailstop: CBSE/ITI
Mailstop: CBSE/ITI, 1156 High Street, Santa Cruz, CA 95064
1156 High Street
Santa Cruz, CA 95064


<h4>Areas of Responsibility</h4>
==Areas of Responsibility==
 
<TABLE BORDER=1>
<TR><TD>Building new browser assemblies</TD>
<TD>"[[wiggle]]" data encoding tracks</TD></TR>
<TR><TD>Correlation functions on the Table browser</TD>
<TD>Source tree organization, browser porting issues, [[browser installation]] setup</TD></TR>
<TR><TD>Wiki installation and evaluation</TD>
<TD>[[Cluster Jobs|Cluster job organization]] and management</TD></TR>
<TR><TD>"[[randomPlacement]]" program for genome location randomization experiments</TD>
<TD>[http://genome-test.soe.ucsc.edu/~hiram/WEBStats/ Web Statistics]</TD></TR>
<TR><TD>Unix expertise</TD>
<TD>[http://jday.sourceforge.net/ Date/Time] functions (local genomewiki Special Pages< [[Special:Jday]] php programming example)</TD></TR>
<TR><TD>Astrophotography</TD>
<TD>Solar Eclipse experience</TD></TR>
</TABLE>
 
==To Do List==
<ul>
<ul>
<li>Building new browser assemblies
<li> test edit</li>
<li>"[[wiggle]]" data encoding tracks
<li> this list is now maintained in the redmine system</li>
<li>Correlation functions on the Table browser
 
<li>Source tree organization and porting issues
<li> big wigs need an equivalent hgWiggle exploration command line tool</li>
<li>Cluster job organization and management
 
<li>Unix expertise
<li> turn on 3-letter searching (done) </li>
<li>Date/Time functions
 
<li>Astrophotography
<li> petMar2 genome build</li>
<li>Solar Eclipse experience
 
<li> sacCer1 nucleosome track</li>
<li> need to get the various CGI binaries immune to custom track db outage</li>
 
<li> trace archive difference display, with Andy(delayed)</li>
<li> integrate blat results into the browser, behave like custom tracks</li>
 
<li> wiki administration (on-going situation)</li>
<li> [[Hiram_Tasks_Done|Tasks Completed]]</li>
<li> remember this, to display gcc default predefines: echo | cpp -dM</li>
</ul>
</ul>


==links to remember==
<TABLE BORDER=1><TR><TD>
[http://meta.wikimedia.org/wiki/Writing_a_new_special_page Writing Special Pages]</TD><TD>
[http://bugzilla.wikimedia.org/show_bug.cgi?id=1924 Restricted Rights]</TD></TR>
<TR><TD>
[http://meta.wikimedia.org/wiki/Page_access_restriction_with_MediaWiki Restrict Patch]</TD><TD>
[http://meta.wikimedia.org/wiki/Hidden_pages Hidden Pages]</TD></TR>
<TR><TD>
[http://meta.wikimedia.org/wiki/Help:Custom_namespaces Custom Namespaces]</TD><TD>
[http://en.wikipedia.org/wiki/Collaborative_software Collaborative Software]</TD></TR>
<TR><TD>
[[NavBarMods|Change Navigation Links]]</TD><TD>
[http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Image link syntax]</TD></TR>
<TR><TD>
[http://en.wikipedia.org/wiki/Criticism_of_Wikipedia Wikipedia Criticism]</TD><TD>
[http://www.fxparlant.net/ConfirmEdit Adding Captcha]</TD></TR>
<TR><TD>
[http://meta.wikimedia.org/wiki/Wikistats Wiki Stats]</TD><TD>
[http://www.wormbase.org/wiki/ Wormbase Wiki]</TD></TR>
<TR><TD>
[http://fr.wikipedia.org/wiki/Utilisateur:Serenity/poll.php Polling]</TD><TD>
[http://en.wikipedia.org/wiki/Wikipedia:Tools/Editing_tools Editing Tools]
</TD></TR>
<TR><TD>
[http://meta.wikimedia.org/wiki/MediaWiki_Bulk_Page_Creator Bulk Page Creator]</TD>
<TD>
[http://www.mediawiki.org/wiki/Manual:Moving_a_wiki Moving a wiki]
</TD></TR>
<TR><TD>
[http://www.musicofnature.com/songsofinsects/ Songs of Insects] songsofinsects.com</TD>
<TD>[http://www.mediawiki.org/wiki/Markup_spec| Markup Spec]</TD>
</TR>
<TR><TD>[http://recaptcha.net/index.html reCaptcha] recaptcha.net</TD>
<TD>[http://www.umasswiki.com/wiki/UMassWiki:Blocking_Spam_In_Mediawiki Blocking Spam]</TD>
</TR>
<TR><TD>[http://content.hccfl.edu/pollock/aunix1/filepermissions.htm File Permissions]</TD>
<TD>&nbsp;</TD>
</TR>
</TABLE>
==Genome Browser Saved Sessions==
<UL>
<LI>Opossum Viewpoint 0
[http://hgw1.soe.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=monDom4_0]
</LI>
<LI>Photo Gateway [http://genome-test.soe.ucsc.edu/~hiram/photoGateway.html]</LI>
</UL>


<h4>To Do List</h4>
==Publications==
<ul>
<ul>
<li> Coveraget track on Hg18 (trying to figure this out)
<LI> 2010-10-09
<li> Attempting to finish off monDom4 (needs Hg18 mapped proteins)
[http://nar.oxfordjournals.org/content/early/2010/10/30/nar.gkq1017.abstract ENCODE whole-genome data in the UCSC genome browser (2011 update)]<BR>
<li> microRNA targets tracks (waiting for submittor review)
    Brian J. Raney, Melissa S. Cline, Kate R. Rosenbloom, Timothy R. Dreszer, Katrina Learned, Galt P. Barber, Laurence R. Meyer, Cricket A. Sloan, Venkat S. Malladi, Krishna M. Roskin, Bernard B. Suh, Angie S. Hinrichs, Hiram Clawson, Ann S. Zweig, Vanessa Kirkup, Pauline A. Fujita, Brooke Rhead, Kayla E. Smith, Andy Pohl, Robert M. Kuhn, Donna Karolchik, David Haussler, and W. James Kent<BR>
<li> mm8 panTro2 alignments (panTro2 being rebuilt)
  (2010) <I>Nucleic Acids Research</I> October 2010 <B>10.1093/nar/gkq1017</B><BR>
<li> rework multiz when mm8/panTro2 done
      PMID: 21037257
<li> panTro2 monDom4 alignments (panTro2 being rebuilt)
<LI> 2010-10-18
<li> mm8 self chain/net (DONE 2006-03-24)
[http://nar.oxfordjournals.org/content/early/2010/10/18/nar.gkq963.abstract The UCSC Genome Browser database: update 2011]<BR>
<li> monDom4 human proteins mapping (trying to get Hg18 set of proteins)
Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ.<BR>
<li> monDom4 self chain/net (chaining on kolossus, takes too long)
  (2010) <I>Nucleic Acids Research</I> October 2010 <B>10.1093/nar/gkq963</B><BR>
<li> wiki administration (on-going situation)
      PMID: 20959295
<LI> 2009-10-09
[http://nar.oxfordjournals.org/content/38/suppl_1/D613.abstract The UCSC Genome Browser database: update 2010]<BR>
Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ.<BR>
  (2009) <I>Nucleic Acids Research</I> October 2009 <B>Vol. 38, Database issue D613-D619</B><BR>
      PMID: 19906737
<LI> 2007-06-14
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2212820/ Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project]<BR>
ENCODE Project Consortium, Birney E, et. al.<BR>
    (2007) <I>Nature</I> June 2007 <B>14;447(7146):799-816.</B><BR>
      PMID: 17571346
<LI> 2006-12-13
[http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D663 The ENCODE Project at UC Santa Cruz]<BR>
        Daryl J. Thomas, Kate R. Rosenbloom, Hiram Clawson, Angie S. Hinrichs, Heather Trumbower, Brian J. Raney, Donna Karolchik, Galt P. Barber, Rachel A. Harte, Jennifer Hillman-Jackson, Robert M. Kuhn, Brooke L. Rhead, Kayla E. Smith, Archana Thakkapallayil, Ann S. Zweig, The ENCODE Project Consortium, David Haussler and W. James Kent<BR>
    (2006) <I>Nucleic Acids Research</I> January 2007 <B>Vol. 35, Database issue D663-D667</B><BR>
        PMID: 17166863
<LI> 2006-11-16
[http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D668 The UCSC genome browser database: update 2007]<BR>
        R. M. Kuhn, D. Karolchik, A. S. Zweig, H. Trumbower, D. J. Thomas, A. Thakkapallayil, C. W. Sugnet, M. Stanke, K. E. Smith, A. Siepel,2 K. R. Rosenbloom, B. Rhead, B. J. Raney, A. Pohl, J. S. Pedersen, F. Hsu, A. S. Hinrichs, R. A. Harte, M. Diekhans, H. Clawson, G. Bejerano, G. P. Barber, R. Baertsch, D. Haussler,1 and W. J. Kent<BR>
    (2006) <I>Nucleic Acids Research</I> January 2007 <B>Vol. 35, Database issue D668-D673</B><BR>
        PMID: 17142222
<LI> 2006-07-14
[http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0020086 Intronic alternative splicing regulators identified by comparative genomics in nematodes]<BR>
        Kabat JL, Barberan-Soler S, McKenna P, Clawson H, Farrer T, Zahler AM, Stormo G<BR>
        (2006) <I>PLoS Computational Biology</I> 14 July 2006 <B>2(7):e86</B><BR>
        PMID: 16839192
</LI>
<LI> 2006-05-01
[http://bioinformatics.oxfordjournals.org/cgi/reprint/22/9/1036 The UCSC Known Genes]<BR>
        Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D<BR>
        (2006) <I>Bioinformatics</I> 01 May 2006 <B>22(9):1036-46</B><BR>
        PMID: 16500937
</LI>
<LI> 2006-01-01
[http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D590" The UCSC Genome Browser Database: update 2006]<BR>
        Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H,
        Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM,
        Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE,
        Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ,
        Weirauch M, Zweig AS, Haussler D, Kent WJ<BR>
        (2006) <I>Nucleic Acids Research</I> 01 Jan 2006 <B>34(Database issue):D590-8</B><BR>
        PMID: 16381938
</LI>
<LI> 2005-08-25
[http://www.genome.org/cgi/content/full/15/8/1034" Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes]<BR>
        Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K,
        Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK,
        Gibbs RA, Kent WJ, Miller W, Haussler D<BR>
        (2005) <I>Genome Research</I> 15 Aug 2005 <B>(8):1034-50</B><BR>
        PMID 16024819
</LI>
<LI> 2005-05-15
[http://www.genome.org/cgi/content/full/15/5/737" Exploring relationships and mining data with the UCSC Gene Sorter]<BR>
        Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D<BR>
        (2005) <I>Genome Research</I> 15 May 2005 <B>(5):737-41</B><BR>
        PMID 15867434
</LI>
<LI> 2004-10-22
[http://www.sciencemag.org/cgi/content/full/306/5696/636 The ENCODE (ENCyclopedia Of DNA Elements) Project]<BR>
        The Encode Project Consortium<BR>
        (2004) <I>Science</I> 22 Oct 2004 <B>306(5696):636-40</B>
</LI>
<LI> 2004-04-14
[http://www.genome.org/cgi/content/full/14/4/708" Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner]<BR>
        Mathieu Blanchette, W. James Kent, Cathy Riemer,
        Laura Elnitski, Arian F.A. Smit, Krishna M. Roskin,
        Robert Baertsch, Kate Rosenbloom, Hiram Clawson,
        Eric D. Green, David Haussler and Webb Miller<BR>
        (2004) <I> Genome Research </I> 14 April 2004 <B>(4):708-715</B>
        <I> ISSN 1088-9051 </I><BR>
        PMID 15060014
</LI>
<LI> 2004-04-01
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=15057822&dopt=Abstract" Genome sequence of the Brown Norway rat yields insights into mammalian evolution]<BR>
        Rat Genome Sequenceing Project Consortium
        (2004) <I> Nature </I> 01 April 2004 <B>428(6982):493-521</B><BR>
        PMID 15057822
</LI>
</ul>
</ul>


<h4>links to remember</h4>
==Testing Extensions==
[http://bugzilla.wikimedia.org/show_bug.cgi?id=1924 Restricted Rights]<BR>
 
[http://meta.wikimedia.org/wiki/Hidden_pages Hidden Pages]<BR>
<h4>Check the [[WindowMasker|Cite extension]]</h4>
[http://meta.wikimedia.org/wiki/Help:Custom_namespaces Custom Namespaces]<BR>
<h4>Check the [[Balloon Extension|balloon extension]]</h4>
[http://en.wikipedia.org/wiki/Collaborative_software Collaborative Software]
 
<h4>Embed a browser shot</h4>
<embedurl>
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=RIPs
{scrolling=auto}
</embedurl>
 
<h4>using wikimedia commons links</h4>
[[File:Stratford CA Main St view east.jpeg|left|thumb|Stratford CA Main St view east]]

Latest revision as of 07:16, 1 September 2018

Office phone: 831-459-5871
Office: room 515 Engineering II U.C. Santa Cruz
Email: note the E-mail this user button in the toolbox on the left

Mailstop: CBSE/ITI, 1156 High Street, Santa Cruz, CA 95064

Areas of Responsibility

Building new browser assemblies "wiggle" data encoding tracks
Correlation functions on the Table browser Source tree organization, browser porting issues, browser installation setup
Wiki installation and evaluation Cluster job organization and management
"randomPlacement" program for genome location randomization experiments Web Statistics
Unix expertise Date/Time functions (local genomewiki Special Pages< Special:Jday php programming example)
Astrophotography Solar Eclipse experience

To Do List

  • test edit
  • this list is now maintained in the redmine system
  • big wigs need an equivalent hgWiggle exploration command line tool
  • turn on 3-letter searching (done)
  • petMar2 genome build
  • sacCer1 nucleosome track
  • need to get the various CGI binaries immune to custom track db outage
  • trace archive difference display, with Andy(delayed)
  • integrate blat results into the browser, behave like custom tracks
  • wiki administration (on-going situation)
  • Tasks Completed
  • remember this, to display gcc default predefines: echo | cpp -dM

links to remember

Writing Special Pages Restricted Rights
Restrict Patch Hidden Pages
Custom Namespaces Collaborative Software
Change Navigation Links Image link syntax
Wikipedia Criticism Adding Captcha
Wiki Stats Wormbase Wiki
Polling

Editing Tools

Bulk Page Creator

Moving a wiki

Songs of Insects songsofinsects.com Markup Spec
reCaptcha recaptcha.net Blocking Spam
File Permissions  

Genome Browser Saved Sessions

  • Opossum Viewpoint 0 [1]
  • Photo Gateway [2]

Publications

  • 2010-10-09 ENCODE whole-genome data in the UCSC genome browser (2011 update)
    Brian J. Raney, Melissa S. Cline, Kate R. Rosenbloom, Timothy R. Dreszer, Katrina Learned, Galt P. Barber, Laurence R. Meyer, Cricket A. Sloan, Venkat S. Malladi, Krishna M. Roskin, Bernard B. Suh, Angie S. Hinrichs, Hiram Clawson, Ann S. Zweig, Vanessa Kirkup, Pauline A. Fujita, Brooke Rhead, Kayla E. Smith, Andy Pohl, Robert M. Kuhn, Donna Karolchik, David Haussler, and W. James Kent
    (2010) Nucleic Acids Research October 2010 10.1093/nar/gkq1017
    PMID: 21037257
  • 2010-10-18 The UCSC Genome Browser database: update 2011
    Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ.
    (2010) Nucleic Acids Research October 2010 10.1093/nar/gkq963
    PMID: 20959295
  • 2009-10-09 The UCSC Genome Browser database: update 2010
    Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ.
    (2009) Nucleic Acids Research October 2009 Vol. 38, Database issue D613-D619
    PMID: 19906737
  • 2007-06-14 Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    ENCODE Project Consortium, Birney E, et. al.
    (2007) Nature June 2007 14;447(7146):799-816.
    PMID: 17571346
  • 2006-12-13 The ENCODE Project at UC Santa Cruz
    Daryl J. Thomas, Kate R. Rosenbloom, Hiram Clawson, Angie S. Hinrichs, Heather Trumbower, Brian J. Raney, Donna Karolchik, Galt P. Barber, Rachel A. Harte, Jennifer Hillman-Jackson, Robert M. Kuhn, Brooke L. Rhead, Kayla E. Smith, Archana Thakkapallayil, Ann S. Zweig, The ENCODE Project Consortium, David Haussler and W. James Kent
    (2006) Nucleic Acids Research January 2007 Vol. 35, Database issue D663-D667
    PMID: 17166863
  • 2006-11-16 The UCSC genome browser database: update 2007
    R. M. Kuhn, D. Karolchik, A. S. Zweig, H. Trumbower, D. J. Thomas, A. Thakkapallayil, C. W. Sugnet, M. Stanke, K. E. Smith, A. Siepel,2 K. R. Rosenbloom, B. Rhead, B. J. Raney, A. Pohl, J. S. Pedersen, F. Hsu, A. S. Hinrichs, R. A. Harte, M. Diekhans, H. Clawson, G. Bejerano, G. P. Barber, R. Baertsch, D. Haussler,1 and W. J. Kent
    (2006) Nucleic Acids Research January 2007 Vol. 35, Database issue D668-D673
    PMID: 17142222
  • 2006-07-14 Intronic alternative splicing regulators identified by comparative genomics in nematodes
    Kabat JL, Barberan-Soler S, McKenna P, Clawson H, Farrer T, Zahler AM, Stormo G
    (2006) PLoS Computational Biology 14 July 2006 2(7):e86
    PMID: 16839192
  • 2006-05-01 The UCSC Known Genes
    Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D
    (2006) Bioinformatics 01 May 2006 22(9):1036-46
    PMID: 16500937
  • 2006-01-01 " The UCSC Genome Browser Database: update 2006
    Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ
    (2006) Nucleic Acids Research 01 Jan 2006 34(Database issue):D590-8
    PMID: 16381938
  • 2005-08-25 " Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D
    (2005) Genome Research 15 Aug 2005 (8):1034-50
    PMID 16024819
  • 2005-05-15 " Exploring relationships and mining data with the UCSC Gene Sorter
    Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D
    (2005) Genome Research 15 May 2005 (5):737-41
    PMID 15867434
  • 2004-10-22 The ENCODE (ENCyclopedia Of DNA Elements) Project
    The Encode Project Consortium
    (2004) Science 22 Oct 2004 306(5696):636-40
  • 2004-04-14 " Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
    Mathieu Blanchette, W. James Kent, Cathy Riemer, Laura Elnitski, Arian F.A. Smit, Krishna M. Roskin, Robert Baertsch, Kate Rosenbloom, Hiram Clawson, Eric D. Green, David Haussler and Webb Miller
    (2004) Genome Research 14 April 2004 (4):708-715 ISSN 1088-9051
    PMID 15060014
  • 2004-04-01 " Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Rat Genome Sequenceing Project Consortium (2004) Nature 01 April 2004 428(6982):493-521
    PMID 15057822

Testing Extensions

Check the Cite extension

Check the balloon extension

Embed a browser shot

<embedurl> http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=RIPs {scrolling=auto} </embedurl>

using wikimedia commons links

Stratford CA Main St view east
Retrieved from "https://genomewiki.ucsc.edu/index.php?title=User:Hiram&oldid=24950"