Issues-9/24/2013
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Tuesday Sept 24th, 2pm, HL35
WS239 / Current Development
- Pre-caching has begun
State of the Staging branch
Closed issues about to move to Master (Sept)
These closed issues will be moving to production soon. Take a quick look and make sure we're not pushing any big mistakes.
Note: Most GBrowse fixes were reverted and pushed back to WS240 together with GFF3 support
- #737 - modENCODE track height - JB
- #794 - PCR page update overlapping gene - JW
- #983 - Other_name search - AC
- #1006 - link outs blastp - AC
- #1082 - transposon family summary pages - JW
- #1114 - start_not_found/stop_not_found - JW
- #1365 - Variation summary - JB
- #1430 - Historical_gene - AC
- #1511 - remove links to non-curated species strains - JW
- #1629 - execute individual test - JB
- #1644 - Error messages Sequence/Clone page - AC
- #1677 - Webpage links case sensitive - AC
- #1693 - phenotype legend filter - JW
- #1694 - Natural isolates - AC
- #1725 - Expr overview error on staging - AC
- #1726 - Transgene page - AC
- #1727 - Transgene reporter - AC
- GFF databases, full name - JB, AC
- Searching fix - add cutoff - AC
Open issues on staging
These need to be closed before we merge to master.
- JD: #1603 - Pseudogene page
- JD: #1709 - protein history
Other development
Issues (not on staging)
- #741- lineage browser - JW
- usable, wokring with Chris on final product
- #1602 - sequence summary - JW
- GFF research
- #603 - Movies on expression pattern page - JW
- try as sibling
- #662 - Variation display - JW
- researching
- GFF databases
- Various other issues - JB
Intermine Dev (JW)
- Due Sept 27th
- Generated sources/datafiles for FASTA and GFF3 for all species
- loaded all FASTA
- ran into error loading GFF3s
- expanded data mappings for all classes loaded
- gene/cds/tanscript/phen/exp clus/exp pattern/var/anatomy term/life stage
- none of these loaded
- gene/cds/tanscript/phen/exp clus/exp pattern/var/anatomy term/life stage
- Next: add RNA
- adding orthologies
- as it's own category
- deadline might be pushed back to Sept 4
Visualisations (JB)
- on hold
WS240 Development
GFF3
GBrowse - JB
- GBrowse on dev
- Fixed landmarks
- fixed hieght of non-coding/coding genes
- fixed showing diff labels/desc for genomic featues
- KH - working on redo-ing type and source assignments in GFF3
- looking into alternative:
- types - sequence ontology types
- source always WormBase
- might add GFF3 attribute to denote spec attr of feature
- Testing things like this now
- looking into alternative:
- cannot search genomic features
- worked after lunch!