User:Hiram: Difference between revisions

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<TD>[[Cluster Jobs|Cluster job organization]] and management</TD></TR>
<TD>[[Cluster Jobs|Cluster job organization]] and management</TD></TR>
<TR><TD>"[[randomPlacement]]" program for genome location randomization experiments</TD>
<TR><TD>"[[randomPlacement]]" program for genome location randomization experiments</TD>
<TD>[http://genome-test.cse.ucsc.edu/~hiram/WEBStats/ Web Statistics]</TD></TR>
<TD>[http://genome-test.soe.ucsc.edu/~hiram/WEBStats/ Web Statistics]</TD></TR>
<TR><TD>Unix expertise</TD>
<TR><TD>Unix expertise</TD>
<TD>[http://jday.sourceforge.net/ Date/Time] functions (local genomewiki Special Pages< [[Special:Jday]] php programming example)</TD></TR>
<TD>[http://jday.sourceforge.net/ Date/Time] functions (local genomewiki Special Pages< [[Special:Jday]] php programming example)</TD></TR>
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==To Do List==
==To Do List==
<ul>
<ul>
<li> human nucleosome data from Fire lab</li>
<li> test edit</li>
<li> petMar2 genome build to update the automation tools to the hive layout</li>
<li> this list is now maintained in the redmine system</li>
<li> rn5 genome browser build</li>
 
<li> 44-way multiz on hg18</li>
<li> big wigs need an equivalent hgWiggle exploration command line tool</li>
<li> make hgGateway indicate problems when databases are not present or otherwise unavailable</li>
 
<li> turn on 3-letter searching (done) </li>
 
<li> petMar2 genome build</li>
 
<li> sacCer1 nucleosome track</li>
<li> sacCer1 nucleosome track</li>
<li> Wiki Track Implementation (move from prototype to production)</li>
<li> sync upstream updates w/GenBank updates</li>
<li> need to get the various CGI binaries immune to custom track db outage</li>
<li> need to get the various CGI binaries immune to custom track db outage</li>
<li> Allow local caching of popular custom tracks</li>
 
<li> Venter and Watson genomes multiple alignment with Brian and Mark</li>
<li> trace archive difference display, with Andy(delayed)</li>
<li> trace archive difference display, with Andy(delayed)</li>
<li> integrate blat results into the browser, behave like custom tracks</li>
<li> integrate blat results into the browser, behave like custom tracks</li>
<li> implement a "my favorite positions" list function</li>
 
<li> fix gateway page so it does not lose track of position when switching assemblies</li>
<li> wiki administration (on-going situation)</li>
<li> wiki administration (on-going situation)</li>
<li> [[Hiram:Done|Tasks Completed]]</li>
<li> [[Hiram_Tasks_Done|Tasks Completed]]</li>
<li> remember this, to display gcc default predefines: echo | cpp -dM</li>
</ul>
</ul>


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</TR>
</TR>
<TR><TD>[http://recaptcha.net/index.html reCaptcha] recaptcha.net</TD>
<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>
<TD>&nbsp;</TD>
</TR>
</TR>
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<UL>
<UL>
<LI>Opossum Viewpoint 0  
<LI>Opossum Viewpoint 0  
[http://hgw1.cse.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=monDom4_0]
[http://hgw1.soe.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=monDom4_0]
</LI>
</LI>
<LI>Photo Gateway [http://genome-test.cse.ucsc.edu/~hiram/photoGateway.html]</LI>
<LI>Photo Gateway [http://genome-test.soe.ucsc.edu/~hiram/photoGateway.html]</LI>
</UL>
</UL>


==Publications==
==Publications==
<ul>
<ul>
<LI> 2010-10-09
[http://nar.oxfordjournals.org/content/early/2010/10/30/nar.gkq1017.abstract ENCODE whole-genome data in the UCSC genome browser (2011 update)]<BR>
    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>
  (2010) <I>Nucleic Acids Research</I> October 2010 <B>10.1093/nar/gkq1017</B><BR>
      PMID: 21037257
<LI> 2010-10-18
[http://nar.oxfordjournals.org/content/early/2010/10/18/nar.gkq963.abstract The UCSC Genome Browser database: update 2011]<BR>
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>
  (2010) <I>Nucleic Acids Research</I> October 2010 <B>10.1093/nar/gkq963</B><BR>
      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
<LI> 2006-12-13
[http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D663 The ENCODE Project at UC Santa Cruz]<BR>
[http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D663 The ENCODE Project at UC Santa Cruz]<BR>
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==Testing Extensions==
==Testing Extensions==
<embedurl>http://www.google.com/calendar/embed?src=hiramlogs%40gmail.com&ctz=America/Los_Angeles</embedurl>
 
<h4>Check the [[WindowMasker|Cite extension]]</h4>
<h4>Check the [[Balloon Extension|balloon extension]]</h4>


<h4>Embed a browser shot</h4>
<h4>Embed a browser shot</h4>
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{scrolling=auto}
{scrolling=auto}
</embedurl>
</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"