WormBase-Caltech Weekly Calls April 2013
April 4, 2013
- Abstracts for posters (6 posters total)
- WormBase booth with desks and poster space
- How is the space going to be configured?
- Will there be enough space?
- Projector? Need space to project
- Standing tables instead of desks
IWM Promotional ideas
- Recycle ideas/items
- See what we have in stock
- Temporary tattoos?
- SPlit cost with GSA?
- Triangular worm pick/pencil grip
Expression pattern, personal communication
- Can we include expression patterns from WormBook?
- Original report from paper by Chris Li et al
- Conflicting neuropeptide expression pattern from Oliver Hobert & Cori Bargmann in WormBook
- How do we handle? Can we put description in WormBase?
- Normally we don't curate from reviews
- Best to contact Chris Li, check with her about expression pattern
- Amend/Edit expression pattern as appropriate
Function, Human Disease poster
- "Gene Function & Dysfunction"
- Concise description
- GO terms
- Phenotypes (RNAi- and variation-based)
- Anatomy: Site of Action and Anatomy Function
- Handling large number of variations in OA
- Generating list of variations likely to be attributed with phenotypes
- Table maker vs Scripts?
- Variation data from GeneAce, how frequently updated? Real time?
- Get new variations from Variation Name Server, not GeneAce
- Is it worth trying to get daily updates?
- Name Server: get Variation & Gene info from
- Propose adding the Variation-Gene connections to Name Server
- Can we (Caltech) mirror/copy GeneAce locally? Fire wall issues
- Store MySQL databases on the cloud? Bypass fire walls? Maybe for long term plan
April 11, 2013
- Deadline tomorrow
- Topics to place posters under? Database, biological topics?
- What's the status?
- Karen made a Google doc, but asked us to hold off on filling out info until she talks to Mary Alvarez
Upload coming up
- Wen preparing mid-build
- Wen pushing Citace Minus fixes
Dead gene handling
- Historical_gene tag has been added to appropriate models
- Chris will work with Juancarlos to sort out OA dumping scripts for Gene_regulation and Interaction OAs
- Chris will work with web team to sort out web display issues
- Chris will write up a template describing all the changes that need to be made
- Raymond setup FTP directory for Wen
- If anyone wants an FTP folder, we can do that
- Would exist on caltech.wormbase.org on Canopus
- Spica: WS237 was having problems
- Couple of issues with Spica: older hardware, using older operating system (Red Hat)
- ACEDB software problem
- Possible but difficult to upgrade ACEDB software
- Not yet resolved issue with XACE or AcePerl, but AceDiff is resolved
- WS237 had a data problem
- Raymond re-installed WS database
- Mac issues: key mapping (e.g. Alt+F4)
- Solution? Use virtual machine?
- VMWare has Fusion; apparently works fairly well
- Mac users could install, for example, Ubuntu with Fusion and run ACEDB on Ubuntu
- Raymond is confident in providing support for this approach
- Running ACEDB remotely is possible, but probably not a long-term, robust, or sustainable solution
- Note: ACEDB needs to be built from source; binary images don't work
April 25, 2013
- Posters and talk(s)
- We may not be able to get booth space to accommodate all (6) posters AND a projection screen
- Todd and Chris will discuss with Anne Marie Mahoney
- Need better upload/release schedule
- Add more events: Citace testing?
- Strict vs flexible timeline?
- Proposed timeline on Time Glider app: Karen's proposal
WormBase You Tube Channel
- Abby and Todd looking into this now
- Macs running OSX Lion or higher have a good screen capture functionality with Quicktime (for free)
- We can prepare videos with content for the upcoming workshops
Capturing curation pipeline documentation on GitHub WormBase curation repository
- Store scripts for OA dumping scripts, for example
- Can keep links to relevant Wiki pages
- Curators should be the ultimate manager of scripts, working with Juancarlos to make any required changes
- Karen will work out a procedure for "Gitifying" her curation pipelines and will share what worked with other curators