User:Hiram: Difference between revisions
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<h4>To Do List</h4> | <h4>To Do List</h4> | ||
<ul> | <ul> | ||
<li> | <li> vega gene updates to hg18 and mm9</li> | ||
<li> Wiki Track Implementation (move from prototype to production)</li> | <li> Wiki Track Implementation (move from prototype to production)</li> | ||
<li> update C. elegans, C. remanei, P. pacificus and C. japonica when WS190 is out</li> | <li> update C. elegans, C. remanei, P. pacificus and C. japonica when WS190 is out</li> | ||
<li> Mouse transcriptome data from LICR (C. Iseli)(what is this ?)</li> | <li> Mouse transcriptome data from LICR (C. Iseli)(what is this ?)</li> | ||
<li> sync upstream updates w/GenBank updates (what is this ?)</li> | <li> sync upstream updates w/GenBank updates (what is this ?)</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> MAF as custom track work with Kate</li> | <li> MAF as custom track work with Kate</li> | ||
<li> Allow local caching of popular custom tracks</li> | <li> Allow local caching of popular custom tracks</li> | ||
<li> Venter and Watson genomes multiple alignment with Brian and Mark</li> | <li> Venter and Watson genomes multiple alignment with Brian and Mark</li> | ||
| Line 40: | Line 37: | ||
<li> implement a "my favorite positions" list function</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> 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:Done|Tasks Completed]]</li> | ||
Revision as of 17:46, 6 May 2008
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
- vega gene updates to hg18 and mm9
- Wiki Track Implementation (move from prototype to production)
- update C. elegans, C. remanei, P. pacificus and C. japonica when WS190 is out
- Mouse transcriptome data from LICR (C. Iseli)(what is this ?)
- sync upstream updates w/GenBank updates (what is this ?)
- need to get the various CGI binaries immune to custom track db outage
- MAF as custom track work with Kate
- Allow local caching of popular custom tracks
- Venter and Watson genomes multiple alignment with Brian and Mark
- trace archive difference display, with Andy(delayed)
- integrate blat results into the browser, behave like custom tracks
- implement a "my favorite positions" list function
- fix gateway page so it does not lose track of position when switching assemblies
- wiki administration (on-going situation)
- Tasks Completed
links to remember
Genome Browser Saved Sessions
Publications
- 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
<embedurl>http://www.google.com/calendar/embed?src=hiramlogs%40gmail.com&ctz=America/Los_Angeles{width=800}{height=600}</embedurl>
Embed a browser shot
<embedurl> http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=RIPs {width=1000}{height=600} </embedurl>
