WormBase-Caltech Weekly Calls
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2011 Meetings
October 6, 2011
SVM
- SVM Manuscript in process of resubmission
- Messy procedures in place; needs to be cleaned up
- Yuling able to get pipeline running from beginning to the end
- May take longer than previously expected to get up and running
- FlyBase has code running for SVM
- Yuling should contact FlyBase to make sure they're OK, once he has WormBase SVM working
- SGD would like to incorporate SVM into they're database
- Yuri would work on SGD SVM, ultimately
Physical interaction model
- Close to done
- Once model approved, work on:
- Converting BioGRID file to the ACE model
- Convert existing YH data into new model
Image curation
- Need to establish legal process for acquiring images
- Contact Caltech Office of the General Counsel for approval
WORM Paper
- Karen working on it
- Need a clearer/new plan
Expression pattern display
- Showing composite images with the option to see greater detail
- Separate out detail images according to Qualifier tags (Certain, Uncertain, Partial)
- Render oblique angles of cells/tissues to show 3D features/morphology of anatomy objects and, possibly, animations
- "Real" images should always take precedence to "virtual" images
- May talk to John Murray or Bill Mohler for confocal images of embryos
Worm Method (Worm Book)
- Any new web pages for C. elegans researchers, send to Raymond
- URL-finder for neuroscience (Yuling)
Textpresso
- Working on Fly Textpresso site (and others)
- Rose Oughtred would like Wnt Textpresso tools
- PDF tools (URL extractor)
- SVM re-working
- Arun working on GSA editor
Grants
- Need to think about next grant in a couple of months (winter); due in October 2012? 30 pages, short?
- Focus on writing papers (anatomy function, WORM, virtual worm, etc.)
- Focus on human-relevance
- Need Gantt charts and quarterly statements of progress
- Stats
- Where are we with each data type
- Status of website
- Automation
- What is different in the field?
- How is data changing?
