Hiram Tasks Done

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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>