Difference between revisions of "WormBase-Caltech Weekly Calls"
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*Interaction pages - explain what the interaction is based on; provenance/reference | *Interaction pages - explain what the interaction is based on; provenance/reference | ||
*Gene Orienteer shows data, but user has to link out | *Gene Orienteer shows data, but user has to link out | ||
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WormBase IWM souvenir? | WormBase IWM souvenir? | ||
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*Complementary iPads? ;) | *Complementary iPads? ;) | ||
*Antifungal socks? wristbands? | *Antifungal socks? wristbands? | ||
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SPELL | SPELL | ||
*new data doesn't load; problem runnning search engine; can load it on athena, not generalizable problem? | *new data doesn't load; problem runnning search engine; can load it on athena, not generalizable problem? | ||
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*complexity of the application; Linux can run multiple applications; caprica has SVM production and WormMart; understand demand of the application; requirements; development vs running scripts, how often? Efficient use of machines. Have 2 computers, getting a third; for WormMart need power; traffic suddenly increased yesterday; monitor traffic; not much personal experience with server maintenance; cluster needs lots of expertise | *complexity of the application; Linux can run multiple applications; caprica has SVM production and WormMart; understand demand of the application; requirements; development vs running scripts, how often? Efficient use of machines. Have 2 computers, getting a third; for WormMart need power; traffic suddenly increased yesterday; monitor traffic; not much personal experience with server maintenance; cluster needs lots of expertise | ||
*building official sever of SPELL at OICR? Yes | *building official sever of SPELL at OICR? Yes | ||
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WormMart | WormMart |
Revision as of 01:03, 19 February 2011
June 11, 2009
- Discussion of allele-paper connections
- Jolene has a Textpresso-based pipeline for identifying alleles in papers
- Alleles get associated with a paper if there is phenotypic or molecular data
- List of all alleles associated with a paper could possibly be passed on to Sanger for subsequent connection
- Discussion of gene-paper connections
- What criteria should be used for associating genes with papers?
- Currently being associated manually by a curator during first-pass
- Could Textpresso be harnessed for this task?
- There are different evidences attached to gene-paper connections
- Genes associated with a paper via Textpresso searches could be presented to the first-pass curator for approval in the first-pass form
- Need to fix current abstract-gene associating script to include proteins (e.g. PIE-1)
- Incorporate a customized Textpresso query on WormBase object pages so users could look for additional info if they want
- Data type curator could help design a useful query
- Other gene-object connections
- Develop a canned query for all objects that should be associated with the gene page
- Worm Meeting
- Pre-meeting - meeting rooms?
- Pre-meeting - practice talks for WormBase workshop
- Storage for swag - pavillion should be okay
June 18, 2009
- Worm Meeting and Pre-Meeting
- WormBase Help Desk Schedule - set for worm meeting
- Wen may need help carrying boxes of swag
- Do any Sanger or WashU people need rides to UCLA?
- Mary Alvarez is working on finding rooms for the pre-meeting
- Be prepared to report on curation status of your data type and what we might need
- Author contact information on first-pass form
- email goes to the first email address found by Textpresso
- Raymond - we do care where this data comes from
- Erich - can we send it to the designated corresponding author
- first-pass curation could capture the corresponding author
- if the email didn't go to the corresponding author, it may affect our response rate
- two-stage approach proposal
- respond to Bernard - we'll try to find corresponding author in the future and add his name to the comments field for now
- going forward, how best to determine corresponding author?
- keep track of IP address from which the data was sent?
- add text to email saying that authors may include their contact information in the comments box, if they wish
- Raymond will proof-read papers to check on corresponding author designation and email addresses
- Zfin visit - PATO progress, worth looking at
- Erich noted no genome browser - what is the issue?
- Their experience with getting figures from journals might be helpful.
February 10, 2011
- Should we have a Caltech project/site manager? We'll look at the issues to be solved first
- Todd would like to know more about what's going on at Caltech
- What would Todd like to know about? New ideas, data types?
- What can we communicate more effectively to Todd?
- Should we take minutes of Caltech WormBase group meetings and send around?
- Kimberly: helpful (for off site individuals) if we go around the room to talk about what each of us is working on
- Bitbucket use
- How do we see only what pertains to us, individually?
- Paul: good way to document bugs and fixes, problems/solutions
- Bitbucket Wiki - does that capture what people want/need to see?
- Who should Todd follow? What would Todd like to know about?
- Raymond: used for code development/versioning by OICR; may be the best use for Bitbucket
- Should we develop best practices guideline for Bitbucket use?
- Avoid posting topics that are too specific or too vague?
- What do we want most to get out of Bitbucket?
- Curation efforts? No
- SAB Meeting
- Not much feedback for literature curators
- User interface stuff took precedence
- Paul: Testing, spot-checking website for errors
- Web issues, e-mails from Gary and Oliver
- WormBase-wide conference call twice per month
- First & third Thursday of the month
- Starting next Thursday (2-17) @ 8:30am PST
- Web redesign meetings on Thursdays will have to be every other week? Do both same day?
- Raymond: WormBase mirrors
- Do we want to implement the Genome Browser for the mirror(s)? If practical
- It seems as though Caltech mirror has been crashing often
- Has the Caltech mirror been working for people lately? Yes, more or less
February 17, 2011
Interaction dumping script
- Spot check table
- Push changes to Git? Yes, to main branch
Interactions automatically downloaded to FTP every release? Yes
- People should check their own curation data
- Users query frequently?
- Can WormMart work instead?
- Ruihua - feature can be added
- Todd - good to have pre-defined queries generated automatically
- Parse/remove predicted interactions (400,000) from others during dump? Yes
- Paul - Wei Wei wants to help with updates - who should she contact at WB?
Ranjana - Solar flares causing static on phone? ;)
Newsletter for new website release? Yes
- Todd - 5 development milestones
- teleconference with Gary Ruvkun's lab next week
- Go live with Beta version in June (@IWM)
- Go live live with new site in September
- Retire old site at end of year
- Need outreach, documentation, screencasts
BioGRID
- WormBase to BioGRID curation
- Issues of mapping interaction types: WB -> BioGRID vs. BioGRID -> WB
- Moving towards using WB interaction types
- Definitions of our interaction types
- Rose will propose to BioGRID community
- Physical interactions - BioGRID has a better format
- break physical interactions away from other interaction types?
- Kimberly can propose changes to model: YH separate from other interactions?
- Physical vs Genetic interactions? keep separate
- We need an interaction ontology, of some sort
- Who should Wei Wei contact, how to coordinate with Hinxton; getting data from FlyBase and SGD?
- Automation?
- Interaction pages - explain what the interaction is based on; provenance/reference
- Gene Orienteer shows data, but user has to link out
WormBase IWM souvenir?
- Computer stress ball? with new site address?
- bouncy ball?
- worm rubber band thing?
- Screen shield?
- Complementary iPads? ;)
- Antifungal socks? wristbands?
SPELL
- new data doesn't load; problem runnning search engine; can load it on athena, not generalizable problem?
- OS was not complete with an update; try again
- two virtual machines working back and forth for support
- how often is SPELL being used? log?; had 6-7 users within two weeks complaining of SPELL problems
- Todd - can send Google analytic tool to put at bottom of page
- Wen - SPELL testing server; official and mirror; want a separate testing server for new releases; mirror on athena (Wen's working machine); Raymond says don't want to attract users to that machine; WB's running SPELL on altair; heavily loaded and has had problems; relying on athena may be problematic
- maybe we need analysis of all of our machines to see big picture; can we consolidate machines; make use of ones we have? If not we can get another machine.
- what type of machine do we need?
- Log of all machines with purchase date and functionality?
- Linux vs Mac curators? athena development machine;
- how much power do the scripts need? can check
- may not be appropriate as official server if main machine goes down
- WB and athena can run SPELL server, but not others. security problems?
- prefer work machine is readily re-bootable; reconfigure software easily without affecting other things that people rely on
- need 10GB space; 4GB memory? SPELL production server; want it stable for outside world; hardware designed for that purpose; farm it out to IMSS?
- complexity of the application; Linux can run multiple applications; caprica has SVM production and WormMart; understand demand of the application; requirements; development vs running scripts, how often? Efficient use of machines. Have 2 computers, getting a third; for WormMart need power; traffic suddenly increased yesterday; monitor traffic; not much personal experience with server maintenance; cluster needs lots of expertise
- building official sever of SPELL at OICR? Yes
WormMart
- with WormMart and WormBase, people just want to know if it's down, just to know to lessen frustration; Official statement from dev team
- WormMart - we give users testing url; can we just change WormBase link to that testing server?
- going to change HTML to update users with most recent information; discuss with Lincoln, 5 datasets on testing server; remaining 3 datasets. if WormMart not working, put a message on main site
- it doesn't look good to have a link to a tool linked from a production server; if we don't trust the data we shouldn't put it up.
- would like to keep the html page as a testing server; could modify page
- if WormMart is working OK but not perfect, that's OK; Comment in the banner
- the html page is a useful tool to get feedback from users