Difference between revisions of "WormBase-Caltech Weekly Calls"
From WormBaseWiki
Jump to navigationJump to searchm |
|||
Line 84: | Line 84: | ||
** What is different in the field? | ** What is different in the field? | ||
** How is data changing? | ** How is data changing? | ||
+ | |||
+ | |||
+ | == October 13, 2011 == | ||
+ | |||
+ | WORM Publiction | ||
+ | *Looks good overall | ||
+ | *Change "library" of papers to "index" | ||
+ | *Putative deadline of November 15th | ||
+ | *Put in more details about the new website? | ||
+ | |||
+ | |||
+ | Paper pipeline | ||
+ | *Need to fix some PubMed IDs | ||
+ | *Over 900 articles in Postgres do not have a PubMed ID; Why? How to fix? | ||
+ | *Could some aspects of the pipeline be accomplished by a non-PhD? | ||
+ | *Supplemental hires? Students? | ||
+ | *What tasks would need to be done? | ||
+ | *Can these tasks be scripted/automated? Community input? | ||
+ | |||
+ | |||
+ | SVM | ||
+ | *Almost all scripts working | ||
+ | *Output of SVM slightly different from Ruihua's results | ||
+ | *Need to resolve the differences | ||
+ | *Data inconsistencies | ||
+ | *Need to spot check the papers to see what the major problems might be | ||
+ | *Yuling ~90% confident in his results | ||
+ | *Get feedback from relevant/interested curator(s) | ||
+ | *One-day CPU/computation time (~30 hours for 70 papers with 9 models) |
Revision as of 18:18, 13 October 2011
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?
October 13, 2011
WORM Publiction
- Looks good overall
- Change "library" of papers to "index"
- Putative deadline of November 15th
- Put in more details about the new website?
Paper pipeline
- Need to fix some PubMed IDs
- Over 900 articles in Postgres do not have a PubMed ID; Why? How to fix?
- Could some aspects of the pipeline be accomplished by a non-PhD?
- Supplemental hires? Students?
- What tasks would need to be done?
- Can these tasks be scripted/automated? Community input?
SVM
- Almost all scripts working
- Output of SVM slightly different from Ruihua's results
- Need to resolve the differences
- Data inconsistencies
- Need to spot check the papers to see what the major problems might be
- Yuling ~90% confident in his results
- Get feedback from relevant/interested curator(s)
- One-day CPU/computation time (~30 hours for 70 papers with 9 models)