WormBase-Caltech Weekly Calls
From WormBaseWiki
Previous Years
2015 Meetings
April 2015
April 2, 2015
Adding Species information to nightly geneace dumps
- Michael Paulini is adding Species information for the WBGene IDs in the genes.ace file
- Does anyone want Species information for any of the other files
- For list of files, see: ftp://ftp.sanger.ac.uk/pub/consortia/wormbase/STAFF/mh6/nightly_geneace/
- Data in postgres in table gin_species
WormBase Ontology Browser WS248 online on Dev
- Caveat: the rest of the WormBase data on the Dev site is WS247 (one release behind)
- Would explain some discrepancies
Micropublication form
- Daniela waiting for feedback from Paul's lab
- Will send to Alison Frand and Elissa Hallem at UCLA to get input
Mary Ann's IWM abstract for community annotation
- People can send comment over next day or two
- Will make revisions and send around next week
April 9, 2015
Tazendra
- Had some glitches this week, not sure what the problem is
- /home2 directory is not intended as a primary storage; curators need to back data up
- Paper PDFs stored on /home2 as the primary storage location
- Papers are backed up on Athena (Wen's computer)
- TIF files are stored on CDs
- Main Tazendra hard drive backed up (RAIDed/mirrored), backed up nightly up to ~1 month (or 0.5 month), monthly for a year, but no older versions
Citace data upload
- April 28th, 10am
Community Annotation Forms
- Mary Ann's IWM (poster) abstract includes community annotation forms
- Community annotation form list:
- Micropublication
- Gene Expression form (made 15 years ago); mostly not used; micropublication form could be co-opted
- Gene description form
- "Submit Data" list on WormBase (http://www.wormbase.org/about/userguide/submit_data#0--10)
- Would be good to have a community annotation portal/landing page
- Mary Ann will send around a summary of discussions about community annotation, along with prioritization of forms for curators and Juancarlos
- Relevant curators should consider reviewing existing forms for updates
modSeek
- http://seek.princeton.edu/modSeek/
- Princeton 6th year grad student developed it (leaving within 6 months)
- "Seek" developed for human on microarray and RNAseq data
- 5 model organisms in "modSeek": yeast, worm, fly, mouse, zebrafish
- Pulls in data from Gene Expression Omnibus (GEO)
- Analysis computed from raw data
- Data from SPELL should be reasonably transferred to modSeek
- We need to determine if WormBase data can be updated per release
- Has text mining
- Cross-species comparisons available