User:Hiram

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

• 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

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

Google calendar embedded

<embedurl>http://www.google.com/calendar/embed?src=hiram%40soe.ucsc.edu&ctz=America/Los_Angeles</embedurl>

Embed a browser shot

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