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| | [[WormBase-Caltech_Weekly_Calls_August_2011|August]] | | [[WormBase-Caltech_Weekly_Calls_August_2011|August]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_September_2011|September]] |
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| − | == September 1, 2011 ==
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| − | SPELL
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| − | *Raymond and Wen worked on putting on Amazon cloud
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| − | *SPELL running on Amazon cloud
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| − | *What next?
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| − | *Need to be careful about running a cloud instance
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| − | *Elastic IP? No, not yet
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| − | *What are the requirements for SPELL? Free instance is currently sufficient
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| − | *Need more memory for the start-up process
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| − | *Haven't yet figured out a way to do stress tests
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| − | *SPELL does not have many users (~500 queries per month)
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| − | *Free tier available for only 6 months and then gone
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| − | *Need to determine what the build requirements are (needed for every build/release)
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| − | *Only want one copy of it (so we aren't paying twice)
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| − | *Single canonical AMI
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| − | *First step, firgure out build requirements (need more memory during build?) and runtime requirements
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| − | *Free instance 2GB memory (upgraded) for build, 600MB memory OK for runtime
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| − | *What will it take to maintain one of these instances for a year?
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| − | *Double up SPELL queries with the main WormBase instance on the cloud to consolidate?
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| − | *How to more fully incorporate SPELL into WormBase?
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| − | *Integrate SPELL into the new WormBase App? (branding, tracking access)
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| − | *Running under Apache; Ruby-on-Rails
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| − | *Could maintain cloud instance for now and see how it will function (and what it will cost) over the year
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| − | *Better if elastic IP assigned (25 cents/day? Or free once attached to an instance?)
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| − | *Can it run in a micro-instance? Yes
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| − | *$175/year for cpu plus disk space and transfer
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| − | *Switch credit cards (from Raymond's to Caltech)
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| − | *Follow logs to assess likely costs later on
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| − | == September 8, 2011 ==
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| − | NAR Paper
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| − | *Ranjana having Editing trouble
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| − | *Karen will format tomorrow for the bibliography and so will be off Google Docs
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| − | *Paper due at end of October
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| − | *There is discussion of submitting other papers to other journals; Worm?
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| − | *Want consistent presence in Worm? Ad space?
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| − | *Journals: NAR, BMC (Bioinformatics etc.), Worm, Database
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| − | *What content would be appropriate for each journal? Who is the target audience?
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| − | *Ongoing short editorial (or something) in each issue of Worm? "Hints from WormBase"?
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| − | Caltech Internet/Network issues yesterday
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| − | | |
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| − | Aldrin Montana
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| − | *Difficulty installing AMIGO on computers
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| − | *Busy with it until had to go back to school
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| − | | |
| − | | |
| − | RNAi Curation Standard Operating Procedure (SOP)
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| − | *Written on WormBase Wiki under Caltech Documentation > RNAi
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| − | | |
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| − | SVM transition
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| − | *From Ruihua to Yuling
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| − | *Ruihua will meet with Yuling next week to discuss
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| − | *There likely will be issues during the transition
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| − | *Should alert Hinxton/EBI and Wash U
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| − | | |
| − | | |
| − | == September 15, 2011 ==
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| − | | |
| − | | |
| − | Worm Paper?
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| − | *Brainstorming topics/ideas
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| − | *Topics:
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| − | **Overview
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| − | **New Website
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| − | **Expression patterns (image curation and 3D graphics)
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| − | | |
| − | | |
| − | Picture Curation
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| − | *Adrian back at OICR, fixed some picture displays
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| − | *Transgenome
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| − | *Working on import pipeline
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| − | *Contacted Worm Atlas for GFP images
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| − | *Automated permissions request
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| − | **Contacted ZFIN, since they have been using images for years
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| − | **Requested permission for each image, too much work
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| − | **No luck with Wiley, Nature, Science, etc.
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| − | **Maybe collaborate with ZFIN to have greater influence
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| − | *Elsevier gave blanket permission for expression pattern images
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| − | *Nature Publishing Group needs a list of each image that we request permission for
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| − | *Eventually want images other than just expression patterns (e.g. phenotypes)
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| − | *Obviously automated e-mails have less influence/pull
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| − | *Need formal statement of permission from Genetics
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| − | *Elsevier publisher suggested putting a WormBase logo next to article in Science Direct
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| − | **A link can be made which would redirect users to the relevant WormBase paper page
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| − | | |
| − | | |
| − | Expression Cluster
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| − | *Wen finished recuration of expression cluster papers
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| − | *Still have papers IDed from Author First Pass with microarray data
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| − | **Papers don't have microarray data but other expression cluster-related info
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| − | **Authors aren't responding to e-mails
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| − | **Detailed info does not have details for microarray curation. How to handle?
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| − | | |
| − | | |
| − | SVM Transition
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| − | *Ruihua working on code for SVM
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| − | *Yuling still planning to meet with Ruihua
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| − | | |
| − | | |
| − | WormMart
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| − | *OICR back in charge
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| − | *OICR doesn't have access to the server that WormBase is running on (caprica)
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| − | *Paul has usernam/password for root access to server
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| − | *OICR working with BioMart developers
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| − | *New data loader that should improve function
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| − | *Want to give access to BioMart to existing configuration
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| − | *BioMart will implement new data loader and then hand back over to OICR for maintenance
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| − | | |
| − | | |
| − | Genetic Interaction Ontology
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| − | *Almost arrived at concensus with BioGRID (Rose, Andrew)
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| − | *Mike Tyers was happy with the development of the ontology
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| − | *Once complete can be sent to Charlie Boone, Fritz Roth, etc. to review
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| − | | |
| − | | |
| − | Textpresso
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| − | *Textpresso for HIV and for Wnt signalling
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| − | | |
| − | | |
| − | Orcid (Library of Congress)
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| − | *Give each person, website, etc. a unique ID via publications
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| − | *Global scale
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| − | *May be interested in WormBase IDs (proof of concept for Orcid)
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| − | *Pre-populate their system with our data
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| − | *Initial launch will be self registration -> how to catalog people automatically
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| − | | |
| − | | |
| − | GSA GO Linking
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| − | *Going to go ahead with GO term linking for GSA paper abstracts
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| − | *Arun needs to streamline the pipeline to accommodate
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| − | == September 22, 2011 ==
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| − | | |
| − | | |
| − | Computers
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| − | *Three computers in Church 63, Raymond, Yuling have access to all three
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| − | *Backing up files
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| − | *Will turn off/on and check
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| − | *Todd has access as well; need to monitor WormMart during shut down, etc.
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| − | | |
| − | | |
| − | Genetic Interactions Ontology
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| − | *(Chris) Will send around before next meeting to review/discuss
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| − | *Have incorporated some new terms like "over-suppression"
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| − | *Have powerpoint slides to visually depict types of genetic interactions on a phenotype scale
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| − | | |
| − | | |
| − | Picture curation
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| − | *(Daniela) Getting official confirmation of permission for images
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| − | | |
| − | | |
| − | Beta website
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| − | *We should actively report issues: dead ends, errors, missing data
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| − | *Missing AQL and WBQL query pages?
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| − | *Use issue reporter or BitBucket(?)
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| − | | |
| − | | |
| − | Pharyngeal Connectivity Data
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| − | *Working on reconstruction (Raymond)
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| − | *Discuss with Erik Jorgensen
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| − | *Look over cortex paper
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| − | | |
| − | | |
| − | Concise descriptions
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| − | *Tested on sandbox
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| − | *Should be live on tazendra soon
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