WormBase-Caltech Weekly Calls September 2011
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September 1, 2011
SPELL
- Raymond and Wen worked on putting on Amazon cloud
- SPELL running on Amazon cloud
- What next?
- Need to be careful about running a cloud instance
- Elastic IP? No, not yet
- What are the requirements for SPELL? Free instance is currently sufficient
- Need more memory for the start-up process
- Haven't yet figured out a way to do stress tests
- SPELL does not have many users (~500 queries per month)
- Free tier available for only 6 months and then gone
- Need to determine what the build requirements are (needed for every build/release)
- Only want one copy of it (so we aren't paying twice)
- Single canonical AMI
- First step, firgure out build requirements (need more memory during build?) and runtime requirements
- Free instance 2GB memory (upgraded) for build, 600MB memory OK for runtime
- What will it take to maintain one of these instances for a year?
- Double up SPELL queries with the main WormBase instance on the cloud to consolidate?
- How to more fully incorporate SPELL into WormBase?
- Integrate SPELL into the new WormBase App? (branding, tracking access)
- Running under Apache; Ruby-on-Rails
- Could maintain cloud instance for now and see how it will function (and what it will cost) over the year
- Better if elastic IP assigned (25 cents/day? Or free once attached to an instance?)
- Can it run in a micro-instance? Yes
- $175/year for cpu plus disk space and transfer
- Switch credit cards (from Raymond's to Caltech)
- Follow logs to assess likely costs later on
September 8, 2011
NAR Paper
- Ranjana having Editing trouble
- Karen will format tomorrow for the bibliography and so will be off Google Docs
- Paper due at end of October
- There is discussion of submitting other papers to other journals; Worm?
- Want consistent presence in Worm? Ad space?
- Journals: NAR, BMC (Bioinformatics etc.), Worm, Database
- What content would be appropriate for each journal? Who is the target audience?
- Ongoing short editorial (or something) in each issue of Worm? "Hints from WormBase"?
Caltech Internet/Network issues yesterday
Aldrin Montana
- Difficulty installing AMIGO on computers
- Busy with it until had to go back to school
RNAi Curation Standard Operating Procedure (SOP)
- Written on WormBase Wiki under Caltech Documentation > RNAi
SVM transition
- From Ruihua to Yuling
- Ruihua will meet with Yuling next week to discuss
- There likely will be issues during the transition
- Should alert Hinxton/EBI and Wash U
September 15, 2011
Worm Paper?
- Brainstorming topics/ideas
- Topics:
- Overview
- New Website
- Expression patterns (image curation and 3D graphics)
Picture Curation
- Adrian back at OICR, fixed some picture displays
- Transgenome
- Working on import pipeline
- Contacted Worm Atlas for GFP images
- Automated permissions request
- Contacted ZFIN, since they have been using images for years
- Requested permission for each image, too much work
- No luck with Wiley, Nature, Science, etc.
- Maybe collaborate with ZFIN to have greater influence
- Elsevier gave blanket permission for expression pattern images
- Nature Publishing Group needs a list of each image that we request permission for
- Eventually want images other than just expression patterns (e.g. phenotypes)
- Obviously automated e-mails have less influence/pull
- Need formal statement of permission from Genetics
- Elsevier publisher suggested putting a WormBase logo next to article in Science Direct
- A link can be made which would redirect users to the relevant WormBase paper page
Expression Cluster
- Wen finished recuration of expression cluster papers
- Still have papers IDed from Author First Pass with microarray data
- Papers don't have microarray data but other expression cluster-related info
- Authors aren't responding to e-mails
- Detailed info does not have details for microarray curation. How to handle?
SVM Transition
- Ruihua working on code for SVM
- Yuling still planning to meet with Ruihua
WormMart
- OICR back in charge
- OICR doesn't have access to the server that WormBase is running on (caprica)
- Paul has usernam/password for root access to server
- OICR working with BioMart developers
- New data loader that should improve function
- Want to give access to BioMart to existing configuration
- BioMart will implement new data loader and then hand back over to OICR for maintenance
Genetic Interaction Ontology
- Almost arrived at concensus with BioGRID (Rose, Andrew)
- Mike Tyers was happy with the development of the ontology
- Once complete can be sent to Charlie Boone, Fritz Roth, etc. to review
Textpresso
- Textpresso for HIV and for Wnt signalling
Orcid (Library of Congress)
- Give each person, website, etc. a unique ID via publications
- Global scale
- May be interested in WormBase IDs (proof of concept for Orcid)
- Pre-populate their system with our data
- Initial launch will be self registration -> how to catalog people automatically
GSA GO Linking
- Going to go ahead with GO term linking for GSA paper abstracts
- Arun needs to streamline the pipeline to accommodate
September 22, 2011
Computers
- Three computers in Church 63, Raymond, Yuling have access to all three
- Backing up files
- Will turn off/on and check
- Todd has access as well; need to monitor WormMart during shut down, etc.
Genetic Interactions Ontology
- (Chris) Will send around before next meeting to review/discuss
- Have incorporated some new terms like "over-suppression"
- Have powerpoint slides to visually depict types of genetic interactions on a phenotype scale
Picture curation
- (Daniela) Getting official confirmation of permission for images
Beta website
- We should actively report issues: dead ends, errors, missing data
- Missing AQL and WBQL query pages?
- Use issue reporter or BitBucket(?)
Pharyngeal Connectivity Data
- Working on reconstruction (Raymond)
- Discuss with Erik Jorgensen
- Look over cortex paper
Concise descriptions
- Tested on sandbox
- Should be live on tazendra soon
September 29, 2011
SVMs
- Manuscript version available soon
- Updating code, processing
Home Page for Ontology Annotator
- OntologyAnnotator.org is available
- List all interfaces on left, description on right
- Could be linked to sandbox
- $12 per year for domain name (one option)
- GoDaddy (cheaper), Network Solutions (more expensive)
- IMSS? (caltech.edu/ontology_annotator)
Genetic Interaction Ontology
- Google Doc available
- Powerpoint slide explanations
- Try to curate:
- Expected phenotype (free-text)
- Individual phenotypes (values? free-text?)
- Remark details (free-text)