WormBase-Caltech Weekly Calls

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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.)

July 14, 2011

Concise descriptions

• OA being developed for concise descriptions
• Wiki page for concise descriptions
• User Community involvement - individual user curation/annotation

Diseases

• Managing disease relevance tags in appropriate models
• Relating human disease genes to C. elegans orthologous genes
• Developing an integrated view for users to browse human disease relevance
• Manual vs Automated curation processes

Worm Breeder's Gazette mass e-mails

• Users complained about e-mails going to old e-mail addresses
• Will only e-mail the most current e-mail on a user's profile

GitHub

• WormBase curation repository
• Should Juancarlos put postgres (and other) cgi's there?
• Make a separate Tazendra repository?
• Generate symbolic links for flat files (non-code)?
• Are we limited in the number of repositories we can have? Cost-dependent
• We could pay more for more repositories; is it worth it?