Difference between revisions of "WormBase-Caltech Weekly Calls"
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Revision as of 17:07, 7 July 2011
2011 Meetings
July 7, 2011
Root Passwords for all machines
- Send to Paul for emergency access
Issue Trackers
- All code in production use in BitBucket or equivalent
- Textpresso - Subversion (code can be shared)
- WormBase - Bitbucket, GitHub (can commit code)
- Todd says Github for code is best
Alex Bishop Help Desk E-mail
- Interolog Finder
- FlyBase will include links soon
- Is WormBase interested connecting to it?
- Can it be sustainably maintained?
- We should make a link under the Tools section of WormBase
- Interolog Finder provides cytoscape files
- Does Cytoscape have a web interface?
Elbrus is currently working stably
- Raymond stabilized Elbrus
- Elbrus is a frankenstein now
- Sanger/EBI taking over the RNAi mappings
- Will discuss with Igor once we determine the remaining issues
- Elbrus still needed for RNAi scripts to generate ACE files
Oliver Hobert correcting expression patterns occasionally
- Ask Oliver to point out what is missing
- Also ask Shawn Lockery
- Cell-specific markers
- Curated as transgenes
- Can link to specific promoters if transgenes present
- Bottom of every transgene page has a link to the static Marker table
- Check on new Beta version of WormBase website
Changing language of e-mail to authors to confirm data
- Non-nematode papers in WormBase via Cecilia?
- Authors sending all papers in their CV
Expression Cluster data curation
- Including GO terms, life stage, etc.
- Link to process pages?
Expression Cartoons
- Attempting to depict expression patterns by separate images for each tissue
- Would be nice to have a consolidated image with the option to expand to see individual tissue images
- Will maintain consolidated and expandable images for each gene as well as each expression pattern for each gene
- Trying to capture "Certain", "Uncertain", and "Partial" curation tags
Molecule curation
- Will need a molecule page on WormBase at some point
- Need a way to handle molecules that do not have a Mesh IDs
- Will replace WBMolecule IDs with Mesh IDs when they become available
- WBMolecule ID will be made a synonym of the molecule name alongside the Mesh ID
- Need to consider how the data will be stored and referred to in the long term (via ACE files etc.)