Genome Browser Project Tasks		12-May-2010
Prio	Project	Engineer	Dependencies/Status	Resolution Date
1	Neandertal	Angie	DONE	DONE
1	Work w/Todd on trackDb issue	Mark	DONE	DONE
2	2.3_sw_linux.zip BAM support	Angie	In progress	None
2	add ability to link directly to a gene	Angie	None	None
2	BAM loose ends	Angie	In progress	None
2	Missing hg19 tracks (see Donna's list 4/15)	Chin	In progress	None
2	git migration	Galt	In progress	None
2	danRer6 comp genomics tracks	Galt	In progress	None
2-Q	Convert net/chain tracks to composites	Hiram	IN QA	None
2-Q	UCSC Genes -- mm9	Jim	In QA	None
2	refactor -- separate track name/table	Jim	In progress	None
2	Multiple wiggles on same track	Jim	In progress	None
2	hgTracks right click	Larry	Partly done -- dependency on other UI mods	??
2	Gencode analysis work	MarkD	Ongoing	None
2	GenBank support	MarkD	Ongoing	None
2	htdocs cleanup	MarkD	In progress	None
2	GenBank v3	MarkD	Stalled	None
2	RO1 with Karchin lab	MarkD	In progress	None
2-Q	hg18 Retrogenes	Robert	In QA	None
2	hgTracks reorder	Tim	In progress	None
2	Support for Larry's right click functionality	Tim	None	None
2	hgTracks scroll right/left 1x	Tim	Dependency on completion of drag reorder	??
2	New exoniphy track for hg19	Adam/MelissaH	DONE	DONE
2	Extend BAM track handler to paired entries	Angie	DONE	DONE
2	GWAS catalog track	Angie	DONE	DONE
2	Lowe lab tRNA tracks	Fan	DONE	DONE
2	zv8 browser	Galt	DONE	DONE
2	Automate ordering of paired aligns for QA	Hiram	DONE	DONE
2	Lingering issues w/UCSC Genes on hg19	Jim	DONE	DONE
2	wiggle track view limits	Jim	DONE	DONE
2	TrackDb.ra improvements	Jim, Hiram	DONE	DONE
2	CCDS/GENCODE reading frame conservation	MarkD	DONE	DONE
3-Q	DGV	Angie	In QA	None
3	dbSNP 131 for hg19	Angie	Waiting for files	??
3	dbSNP 130/131 - non-human orgs	Angie	In progress	None
3	Work w/Ensembl to sort out hg18/19 lift diffs	Angie	In Ensembl's court -- done?	??
3	BAC/Fosmids - hg19	Angie/Pieter	Pieter DeJong (CHORI) will do	None
3	BAM support to liftOver	Brian	None	None
3	Update human proteins annotations to hg19	Brian	None	None
3	Add vertical bar to GB image to hilite locus	Brian	Requested by ENCODEers via Kate
3	Fix D link bug on hgTracksUi	Brian	See email	None
3	Anopheles genome update	Chin	See email	None
3	New sheep browser	Chin	In progress	None
3	Add RGD pathways to UCSC genes (&GS?)	Fan	In progress	None
3	Illumina update (new data set)	Fan	None	None
3	Shift rat to RGD gene set	Fan	In progress	None
3	Link to CB pathways from KG details page	Fan	None	None
3	DECIPHER	Fan	Waiting for OK from contributor	??
3	GAD track - hg19	Fan	None	None
3	Illumina tracks for hg19 (CytoSNP-12 array)	Fan	None	None
3	Affy tracks for dm3	Fan	Requested on mailing list	None
3	Add KEGG column to GS	Galt	None	None
3	Add Compugen probes to zfish	Galt	See email from 10/27	None
3	Worm cons update for modENCODE	Hiram
3	GNF microarray data problems	Hiram	Should reassign to Andy if he can handle	soon?
3	Investigate putting bigWig in cloud	Hiram	In progress	None
3	Weird link on rat KG page	Hiram	None	None
3	Human nucleosome data - Fire lab	Hiram	In their court -- bigBed/Wig may be solution	?
3	Graceful CT failure when DB server is down	Hiram	None	None
3	GS use trackVersion for Ensembl outlinks	Hiram	None	None
3	Single nucleosome positions - sacCer1	Hiram	Mailing list request (Vishy Iyer)	None
3	gc5Base bug w/small display window	Hiram	Reported by Katrina	None
3	Pig browser	Hiram	In QA	None
3	New cat assembly	Hiram/Chin	In QA	None
3	anoCar2 browser	Hiram/Chin	Waiting for GenBank	?
3	new chicken assembly	Hiram/Chin	Waiting for GenBank	?
3	New marmoset assembly	Hiram/Chin	In QA	None
3	TB output data limit on BigBed	Jim	In progress	None
3	Finish all.joiner links for new UCSC Genes	Jim	In progress	None
3	Composite custom track	Jim	In progress	None
3	Riken CAGE data - human/mouse	Kate	In progress	None
3	Supertrack bug	Kate	See email	None
3	Track search tool	Larry	May give to Brian, depending on Larry's hours	None
3	Add expand/collapse all sections - hgGene	Larry	Requested by Mark	None
2	DAS work to support Gencode	MarkD	In progress - onging work with Ensembl	None
3	Add PAR visualization to GB	MarkD	In progress	None
3	Fix probs w/track desc. in GenBank aligns	MarkD	In progress	None
3	TCGA file formats & gene models	MarkD	In progress	None
3	Reconstruction support	MarkD	In progress	None
3	Add clear button to PCR program	Melissa	See email - 10/30/09	None
3	hg18/19 mapability	Rachel	In progress	None
3-Q	Burge RNA-seq data -- hg18/19	Rachel	In QA - B queue	None
3	Segmental Dups track -- hg19, mm9	Rachel	Waiting for possible data update from lab	?
3	Fix subtrack bug in ext. case/color options	Tim	None	None
3	Fix cons details pg bug w/cons elements box	Tim	Reported by Kayla	None
3-D	Microarray display bug	Brian	DONE	DONE
3-D	NIA Gene Index -- mm9	Fan	DONE	DONE
3-D	Illumina tracks for hg19 (Jen Stone)	Fan	DONE	DONE
3-D	Aplysia browser	Galt	DONE	DONE
3-D	Rabbit browser	Hiram	DONE	DONE
3-D	Vega Genes auto update	Hiram/Rachel	DONE	DONE
3-D	Panda browser	Hiram	DONE	DONE
3-D	New tetraodon assembly	Hiram	DONE	DONE
3-D	HINV data - hg19	Hiram/Chin	DONE	DONE
3-D	Elephant browser	Hiram	DONE	DONE
3-D	Remove human refSeqs from panTro2 refGene	MarkD	DONE	DONE
4	Improve SNP functional annotation	Angie	None	None
4	Extend CT persistence in hgSessions	Angie	On RR -- in monitoring phase til ~Mar 09	None
4	Add configurable numbers to lines - Get DNA	Angie	None	None
4	hgSession - mirrors	Angie	None	None
4	Xeno mRNA alignment-in-window display	Angie	None	None
4	Add kluster power-saving features to parasol	Galt	None	None
4	Display Rfam structures in browser	Jakob	None	None
4	keepAlive	Mark	None	None
5	Transcriptome browser (PB II)	Jim	None	None
5	Remember pos info for all assemblies on hgGateway	Kate	None	None
	RNA structures on details page		from Jakob, requested by Bob
	hg19 polyA track?
	Integrate Epigenomics roadmap data		See Jim email 1/20/10
	Add registration to GB mirror/downloads?
	Add defaults button on config page
	track search mechanism
	galGal4
	TB Sel. Flds -- show kgRef as well as knownG.		requested by Bob 3/16 email
	start=end gives error in CT		reported by Mark 10/29
	Microarray incompatibility issues with TB	Andy		None
	extended case/color bug - cons track		see email from Donna
	variant call format
x	adopt/run Sean Eddy pipeline - UCSC Genes
x	Add Todd's RNA plfold track to GB		Requested by David	None
	conversion tool: big* <-> SAM/BAM		Angie
	get DNA for other species		Brian 7/31
	Venter genome feature request		Jen 7/31
	problem with TB GFF format export		Jen 8/4
	assist QA w/automation (Brooke's list)
	Ensembl nav bar link on other species		Hiram 8/5
	hg18 -- no HARs nor ultras		Angie -- David sez only if we can lift
	broken links on ENCODE Gencode track		Pauline 8/10
	synch data view scaling/vert viewing range		Requested by David via Pauline
	sort sessions by date		Requested by Kayla
x	miRNAs & targets in the browser		Requested at SAB
	add thin bar betw primers - isPCR brwsr dsply		Requested by user
	failed searches return to default page		Requested by Bob & others - see email
	TB problem connecting tbls across DBs		Requested by Bob - see email from Ann
	zv8 geneset
	export UCSC Genes to GS from GB window		Requested by Bob
	export gene list from chrom interval		Jim sez ~1 day to implement
	add ability to streamline/narrow seach		Suggestions by Bob/Angie - email 12/10
	evofold secondary structure image		Requested by Bob - see email
	isPCR batch mode		Requested by Bob
	Page to run simplify script to time blat submissions		Requested by OH
	Reflect CT query in CT header		Requested by OH
	PicTar track - hg18, mm9?	Hiram	Hiram contacted Niklaus, update from R. Bauer - may be waiting a while for new data	?
	Track control rendering performance
3	Suppress auto-display of default trks - session		Requested by Brian et al.
3	Better integration of Blat results into hgTracks		None	None
3	Multi-fasta output from TB	(formerly Brian's)	None	None
3	New AGP-level cat release from Jim Mullikin	????	Wait for 8X	Date?
3	Incorporate Webb's SNP ancestral alleles	????	None	None
3	SNP details pg - switch genes list to KG, include mult. genes & intergenic	????	None	None
3	Update SNP recomb rates - HapMap phs I->II	????	None - have data,  need ~1 wk to process	None
3	Show conservation for nonsynon SNPs	????	Need MarkD input	?
3	Enable restriction enzyme retrieval - hgTables	????	?	?
3	Microarray data shown as graph	????	?	?
3	Restrict search to certain genomic region	????	?	?
3	Separate microarray data from KG details pg	????	None	None
3	platypus cDNA from 454 sequencer	????
4	Add zfish data - GIS	???	Having difficulties obtaining data	?
4	danRer5 "known genes"	???	None	None
4	Upgrade GFF parsing	???	Requested by Mark	None
4	Custom LD-formatted tracks	???	Request from ASHG
4	SIB alt-splice track -- extended case/color	???	Requested on mailing list. Jim sez several dys
5	TB mods - microarray track tissue info	????	Suggested by Andy	None
5	Genome Graphs mods frm Ross Lazarus	????
5	CTs with LD structure	????	Requested on mailing list
5	Venter et al. genomes (net, liftOver)	????	Design discussion? Use Kidd method?	None
	dasToGff program		REMOVED	None
	yellow = in QA
	blue = done
	lavender = unprioritized/unassigned