Hiram Tasks Done

2011 Tasks completed

• move preDraw bigWig fetch into loadItems to avoid open file bigWig file forever(2011-06-22)
• WS220 nematode 9-way alignment on ce10 and browser releases for WormBase(2011-06-13)
• new post-doc training for Max(2011-06-03)
• genomewiki upgraded and moved to new machine(2011-06-02)
• implement cgiApoptosis function to avoid long-running CGI processes(2011-06-01)
• Lizard anoCar2 7-way multiple alignment completed(2011-05-17)
• add fail-safe redundancy checking to the ncbiIncident track construction(2011-05-10)
• new employee training for Matt(2011-05-06)
• Chimp panTro3 12-way multiple alignment completed(2011-05-06)
• mafAddIRows problem resolved, reworking some of the maf files(2011-05-04)
• investigate potential status bar progress meter for custom track loading(2011-04-30)
• Ensembl genes v62 imported(2011-04-20)
• Lizard anoCar2 into the pushQ(2011-04-15)
• turn on account confirmation procedure on genomewiki(2011-04-13)
• rewrite sections of dbTrash cleaner to avoid MySQL show table status(2011-04-11)
• finish 12-way alignment on Chimp panTro3(2011-03-31)
• work up the 29-Mammals tracks in big* files in the genomewiki(2011-03-22)
• clean up and remove all Amazon cloud experiments(2011-03-16)
• apache log analysis to discern country and user profiles for annual reports(2011-03-14)
• Chimp panTro3 browser built and ready for the initial push to the RR(2011-02-25)
• add printVmPeak function to big* utilities to track maximum memory size(2011-02-11)
• implement bigBed automated update track for NCBI Incident database track(2011-02-10)
• writing python script for automatic file upload into genomewiki(2011-02-09)
• consolidate trash cleaners into a single process and fix memory links in refresh saved sessions code(2011-01-27)
• lifting some of the outstanding tracks from hg18 to hg19(2011-01-06)
• finish 8-way conservation for danRer7(2011-01-05)
• BME230 lecture(2011-01-06)
• fixup byte order drawing bug on ppc architecture(2011-01-03)

2010 Tasks completed

• solve mysterious buggy behavior in msa_view aggregate, new program has new options(2010-12-30)
• Neandertal and Denisova tracks lifted to hg19(2011-12-16)
• Zebrafish danRer7 browser in the pushQ(2011-12-10)
• check in the phoneHome function in the browser(2011-11-30)
• recovered lost symLinks on hgwdev /gbdb/ file system(2010-11-19)
• building new trash cleaner script for hgnfs1(2010-11-19)
• building browsers for: ce9, melInc1, melHap1, bruMal1, caeJap3(2010-10-26)
• hg18 vs. hg19 differences plus patches to hg19 tracks added(2010-09-07)
• bug fix in wiggle track display(2010-08-25)
• fixup blastTab business for danRer6(2010-08-11)
• Ensembl v59 genes loaded(2010-08-10)
• developed new custom trash cleaner scripts for hgwdev(2010-08-09)
• completed Amazon AMI image for a public browser release(2010-08-02)
• boot camp training session with Brooke and Vanessa(2010-07-30)
• calJac3 quality track, and mm9 phyloP added to 30-way(2010-07-15)
• attending 3rd annual ISCA meeting, Bethesda MD(2010-06-29)
• source tree makefile cleanup work(2010-06-17)
• GIT transition work, fixup makefiles for a cleaner build(2010-06-18)
• recover Intronerator information(2010-06-17)
• Amazon Seattle bioinformatics meeting(2010-06-08)
• vacation Clovis NM 2010-05-31 - 2010-06-04
• Ensembl v58 gene update(2010-05-28)
• assist Max Haussler to build the Publications track(2010-05-28)
• data transfer bandwidth testing(2010-05-14)
• susScr2 Pig assembly released(2010-05-12)
• genecats presentation, UNIX environment(2010-05-05)
• oryCun2 Rabbit assembly released(2010-04-26)
• Rockville MD NHGRI conference(2010-04-21)
• Ensembl v57 update complete(2010-04-16)
• ailMel1 Panda assembly released(2010-04-16)
• loxAfr3 Elephant assembly released(2010-03-24)
• write up product/scripts/ to manage a mirror site(2010-03-19)
• establish chainNet priority scripting(2010-03-17)
• tetNig2 Tetraodon assembly released(2010-03-12)
• out of office 2010-03-08 thru 2010-03-12
• new employee training(2010-02-25)
• genomewiki on a new machine(2010-02-04)
• attend ISCA conference, Atlanta GA(2010-01-29)
• tetNig2 assembly in the pushQ(2010-01-08)
• BME230 class presentation(2010-01-07)

2009 Tasks completed

• trackDb chainNet composite transition(2009-12-30)
• trackDb reorg maintenance(2009-12-18)
• genome assembly training class, 4 days(2009-12-16)
• hg19 46-way multiple alignment done(2009-11-20)
• MySQL transition from v4 to v5(2009-09-09)
• Running Amazon Cloud instances
• CPR and First Aid training(2009-08-18)
• Ensembl v55 update complete(2009-07-20)
• UCSC genes build for hg19(2009-06-30)
• canFamPoodle1 chains and nets on canFam2(2009-06-30)
• wikiTrack function turned on for the RR system(2009-06-24)
• Attending Amazon Web Services presentation with Mike(2009-06-16)
• implement composite chain/net tracks for hg19(2009-06-15)
• Baboon papHam1 browser built(2009-05-15)
• BAC Ends, STS markers, and cytoband tracks done for hg19(2009-05-15)
• Create translation system for UCSC contigs to Ensembl coordinates(2009-05-07)
• Human hg19/GRCh37 browser built and released(2009-04-27)
• Amazon Cloud Computing investigated, browser image created, hg18 data snapshots(2009-04-21)
• CD ROM backup copy of genomewiki created for Tom(2009-03-27)
• MHC complex multiple alignment created for the RECON group work(2009-03-20)
• fixed up net and chain tracks to work as a single composite(2009-03-19)
• updated Yeast browser sacCer2 released(2009-03-10)
• mirror site hgdownload file cleanup(2009-03-03)
• new custom track machine started up to expand 500 Gb disk limit(2009-02-14)
• Ensembl v52 update complete(2009-01-23)
• 44-way conservation track on hg18(released 2009-01-23)
• Added FOX2 adaptor-trimmed CLIPseq track to hg17,hg18(2009-01-09)
• out of disk space situation for the custom tracks(2009-01-09)
• BME230 class presentation(2009-01-08)

2008 Tasks completed

• change default pixWidth from 620 to 800(2008-12-18)
• preparing BME230 lecture slides(2008-12-17)
• Ensembl v51 update complete, but never released(2008-12-03)
• verifying rn4 rn5 mm8 mm9 blastz lastz differences(2008-11-26)
• rn5 Rat Rnor4.0 browser built to check this build(2008-11-13)
• oryLat2 medaka browser update completed(2008-11-07)
• gorGor1 Gorilla browser built on genome-test(2008-10-27)
• start on 44-way conservation track for hg18(2008-10-14)
• tried to add Atlas3 MOE430v2 chipset track, ran into problems(2008-10-09)
• hive filesystem migration fixups(2008-09-24)
• upgraded mediawiki software to version 1.13.0(2008-09-19)
• lift nucleosome data from ce4 to ce6(released 2008-09-10)
• update gnf Atlas data to MOE 302v2 chipset(pushQ 2008-09-09)
• genomewiki upgrade to v1.13.0(2008-09-19)
• Medaka broken chrUn fixed, oryLat2 in the pushQ(2008-09-08)
• reviewing the new distributed DB scheme(2008-09-03)
• Ensembl v50 update complete(2008-08-11)
• genecats presentation, ISMB summary(2007-08-06)
• presentation given at ISMB 2008 Toronto (2008-07-19,23)
• WS190 C. elegans ce6 browser released(2008-07-22)
• C. japonica caeJap1 browser released (2008-06-26)
• elegans ce6 WS190 genes chained tblastn track ready to go on cb3, caeRem3, caePb2, caeJap1, priPac1 (2008-06-26)
• elegans ce6 WS190 placed in pushQ (2008-06-20)
• remanei caeRem3 and brenneri caePb2 genome updates released (2008-06-20)
• lamprey petMar1 and lancelet braFlo1 released (2008-06-10)
• Vega genes updated on Hg18 and Mm9 (2008-06-04)
• Transcriptome tracks released on Ce4 and Mm9 (2008-05-29)
• wiki track completed and in pushQ (2008-05-23)
• 25mer track released on Ce4 from the Fire Lab (2008-05-06)
• lamprey petMar1 and lancelet braFlo1 in pushQ(2008-05-01)
• marmoset genome calJac1 released(2008-04-23)
• ensGene v49 update for bosTau3(2008-04-22)
• Nucleosome tracks on ce4 released(2008-04-18)
• Ensembl gene update to v49 done(2008-04-08)
• cow genome bosTau4 released(2008-04-07)
• quick build of C. japonica caeJap1(2008-04-06)
• new hire training(2008-03-25 - 2008-04-11)
• geneId on bosTau3 released (2008-04-01)
• Orangutan genome ponAbe2 released(2008-03-10)
• genecats presentation ensGene Updates(2008-03-05)
• Ensembl gene updates automatic process script done(2008-03-03)
• employment interviews finished(2008-02-28)
• Ensembl browser training(2008-01-28)
• Marmoset calJac1 in the pushQ(2008-01-25)
• training Aaron Wenger in browser building (Lampry petMar1)(2008-01-18)
• added missing BAC END to RP23-473N24(2008-01-09)

2007 Tasks completed

• rebuilt a number of upstream maf files due to mafFrags problems(2007-12-21)
• loaded SGP and geneid gene tracks on bosTau3, felCat3, equCab1, rheMac2 and rn4(2007-12-20)
• ran the self blastz on Hg18 with a chain minScore of 2000(2007-12-19)
• Orangutan ponAbe2 assembly submitted to pushQ(2007-12-12)
• Mouse Mm9 30-way multiz track completed(2007-11-07)
• Mouse Mm9 to Mm8 liftOver (dropUnder) alignment completed(2007-11-07)
• TargetScan miRNA track released(2007-01-02)
• Affy Exon array tracks released for Hg18 and Mm8(2007-10-25)
• UCSC Gene tracks released to the public browser(2007-10-11)
• 29 blastz runs done for Mm9 30-way alignment, starting multiz(2007-10-04)
• UCSC Gene build on Mm9 completed(2007-09-24)
• regPotential7X tracks reloaded on hg17 and hg18 to fix a data outage(2007-09-07)
• starting series of 29 blastz runs against mm9 for 30-way alignment(2007-09-01)
• mouse mm9 browser released(2007-08-22)
• preparing Mm9 multiple alignment to track 30-way mm9 multiple alignment progress(2007-08-20)
• cleanup proliferation of redundant blastz binaries for kluster runs(2007-08-17)
• research MACHTYPE difficulty for kluster jobs, perl sees MACHTYPE differently(2007-08-26)
• reload regPotential7X tracks on hg17 and hg18(2007-08-03)
• nematode browsers ce4, cb3, caeRem2, caePb1, priPac1 released(2007-08-02)
• created gapToLift tool to assist with mm9 assembly(2007-07-24)
• re-loaded tfbsCons track in hg18(2007-07-20)
• wiki track prototype now working to annotate genes on hg18(2007-06-27)
• fix broken captcha login function on the genomewiki (php code)(2007-06-07)
• lizard browser anoCar1 released(2007-05-17)
• assisted with the release of the horse equCab1 release(2007-05-14)
• allow table browser to dump actual SQL table for bedGraph data(2007-05-08)
• fixup configure page to make re-order option appear upon click (javascript)(2007-05-08)
• fixup Internet Explorer bug when it was sending custom track files from directories on the Windows box that had spaces in the name(2007-05-08)
• reviewed chapter 9 of Peter's book(2007-05-05)
• five worm browsers submitted to pushQ(2007-05-01)
• Medaka oryLat1 browser released(2007-04-27)
• Fugu Fr2 browser released(2007-04-11)
• custom track database turned on 2007-04-10 at 16:30 PDT
• pre-release mouse mm9 browser built on genome-test(2007-04-07)
• assisted with the completion of the Stickleback browser (multiz8way)(2007-03-28)
• Lanclet (braFlo1) browser built on genome-test (not released)(2007-03-28)
• table browser batch coordinate upload feature (==regions)(2007-03-20)
• long standing bug fixed in linefile routines(2007-03-08)
• Started Lizard browser(2007-02-16)
• Finished off Fugu and Medaka browsers(2007-02-15)
• Assisted in the completion of the Stickleback browser(2007-02-09)
• Loaded Geneid data into Cat browser(2007-02-05)
• experimented with download procedure for medical sequencing traces from NCBI(2007-01-31)
• Completed one-week training for Cory from the Bejerano lab building Fugu Fr2 browser(2007-01-26)
• Completed 8-way conservation track on Stickleback browser(2007-01-17)

2006 Tasks completed

• genomewiki announced to the browser community (2006-11-13)
• Clone Coverage track reloaded on hg18 to be more correct (2006-11-06)
• Turned on Matt's tfbsCons track on hg18 (2006-10-09)
• Now returning error messages from the custom track db loaders (2006-10-09)
• added denseOnly, squishOnly, packOnly, fullOnly trackDb.ra options (2006-09-26)
• limited hgTracks to gif image of 32,000 pixels high (2006-09-26)
• STS markers track reworked to remove errors (2006-09-19)
• Opossum monDom4 browser released (2006-08-08)
• added annotation and frame data to monDom4 7-way conservation (2006-08-01)
• fixed bug in custom track where unusual characters caused problems (2006-07-26)
• integrated dbRIP data track into hg17 browser (2006-07-14)
• measured timings of using custom track database (2006-07-07)
• loaded (again) UW/Reg QCP DNaseI Sens Encode track Hg17 (2006-07-05)
• Ensembl gene tracks loaded on Mm8 and MonDom4 (2006-06-22)
• reworked trash file usage to segregate into sub-directories (2006-06-19)
• added data size limit to wiggle custom tracks 300Mb <2006-06-19)
• loaded Map Contigs (ctgPos table) track on Mm8 (2006-06-15)
• loaded UW/Reg QCP DNaseI Sens Encode track Hg17 (2006-06-15)
• loaded regPotential7X tracks on Hg18, Hg17, Mm8 and Mm7 (2006-06-15)
• loaded Uppsala ChIP Butyrate Encode track Hg17 (2006-06-14)
• loaded SGP GENES track on Mm8 (2006-06-12)
• bug fixed in custom track input, first line comment in pasted text (2006-06-09)
• liftOvers for mm5 and mm6 to mm8 (2006-06-05)
• custom track database function complete (2006-06-02)
• mm8 mouse genome browser released (2006-05-10)
• monDom4 pushQ entries completed (2006-05-08)
• quality track loaded on monDom4 (2006-04-28)
• cytoBand track loaded on Mm8 (2006-04-28)
• blastz completed for danRer4 (2006-04-28)
• example special page programming example completed (2006-04-28)
• reworked mm8.multiz17way to use panTro2 and xenTro2 (2006-04-25)
• liftOver files done for Mm8 to Mm7 and Mm7 to Mm8 (2006-04-24)
• loaded geneid predictions from imim.es on hg18 (2006-04-21)
• monDom4 self chain (2006-04-19)
• picTar microRNA targets tracks (DONE 2006-04-19)
• mm8 panTro2 alignments (DONE 2006-04-19)
• Chain and Net Hg17<->Mm8 for Krish (DONE 2006-04-19)
• Coverage track on Hg18 (DONE 2006-04-04)
• mm8 self chain/net (DONE 2006-03-24)<.li>