WormBase-Caltech Weekly Calls September 2011

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)