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| | [[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]] | | [[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]] |
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| − | ==February 10, 2011==
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| − | *Should we have a Caltech project/site manager? We'll look at the issues to be solved first
| + | ==2011 Meetings== |
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| − | *Todd would like to know more about what's going on at Caltech
| + | [[WormBase-Caltech_Weekly_Calls_February_2011|February]] |
| − | **What would Todd like to know about? New ideas, data types?
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| − | **What can we communicate more effectively to Todd?
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| − | *Should we take minutes of Caltech WormBase group meetings and send around?
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| − | *Kimberly: helpful (for off site individuals) if we go around the room to talk about what each of us is working on
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| − | *Bitbucket use
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| − | **How do we see only what pertains to us, individually?
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| − | **Paul: good way to document bugs and fixes, problems/solutions
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| − | **Bitbucket Wiki - does that capture what people want/need to see?
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| − | **Who should Todd follow? What would Todd like to know about?
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| − | **Raymond: used for code development/versioning by OICR; may be the best use for Bitbucket
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| − | **Should we develop best practices guideline for Bitbucket use?
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| − | ***Avoid posting topics that are too specific or too vague?
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| − | ***What do we want most to get out of Bitbucket?
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| − | **Curation efforts? No
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| − | *SAB Meeting
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| − | **Not much feedback for literature curators
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| − | **User interface stuff took precedence
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| − | **Paul: Testing, spot-checking website for errors
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| − | **Web issues, e-mails from Gary and Oliver
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| − | *WormBase-wide conference call twice per month
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| − | **First & third Thursday of the month
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| − | **Starting next Thursday (2-17) @ 8:30am PST
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| − | **Web redesign meetings on Thursdays will have to be every other week? Do both same day?
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| − | *Raymond: WormBase mirrors
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| − | **Do we want to implement the Genome Browser for the mirror(s)? If practical
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| − | **It seems as though Caltech mirror has been crashing often
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| − | **Has the Caltech mirror been working for people lately? Yes, more or less
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| − | == February 17, 2011 ==
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| − | Interaction dumping script
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| − | *Spot check table
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| − | *Push changes to Git? Yes, to main branch
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| − | Interactions automatically downloaded to FTP every release? Yes
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| − | *People should check their own curation data
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| − | *Users query frequently?
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| − | *Can WormMart work instead?
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| − | *Ruihua - feature can be added
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| − | *Todd - good to have pre-defined queries generated automatically
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| − | *Parse/remove predicted interactions (400,000) from others during dump? Yes
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| − | *Paul - Wei Wei wants to help with updates - who should she contact at WB?
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| − | Ranjana - Solar flares causing static on phone? ;)
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| − | Newsletter for new website release? Yes
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| − | *Todd - 5 development milestones
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| − | **teleconference with Gary Ruvkun's lab next week
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| − | **Go live with Beta version in June (@IWM)
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| − | **Go live live with new site in September
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| − | **Retire old site at end of year
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| − | **Need outreach, documentation, screencasts
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| − | BioGRID
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| − | *WormBase to BioGRID curation
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| − | *Issues of mapping interaction types: WB -> BioGRID vs. BioGRID -> WB
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| − | *Moving towards using WB interaction types
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| − | *Definitions of our interaction types
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| − | *Rose will propose to BioGRID community
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| − | *Physical interactions - BioGRID has a better format
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| − | **break physical interactions away from other interaction types?
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| − | **Kimberly can propose changes to model: YH separate from other interactions?
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| − | **Physical vs Genetic interactions? keep separate
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| − | *We need an interaction ontology, of some sort
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| − | *Who should Wei Wei contact, how to coordinate with Hinxton; getting data from FlyBase and SGD?
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| − | **Automation?
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| − | *Interaction pages - explain what the interaction is based on; provenance/reference
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| − | *Gene Orienteer shows data, but user has to link out
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| − | WormBase IWM souvenir?
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| − | *Computer stress ball? with new site address?
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| − | *bouncy ball?
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| − | *worm rubber band thing?
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| − | *Screen shield?
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| − | *Complementary iPads? ;)
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| − | *Antifungal socks? wristbands?
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| − | SPELL
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| − | *new data doesn't load; problem runnning search engine; can load it on athena, not generalizable problem?
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| − | *OS was not complete with an update; try again
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| − | *two virtual machines working back and forth for support
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| − | *how often is SPELL being used? log?; had 6-7 users within two weeks complaining of SPELL problems
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| − | *Todd - can send Google analytic tool to put at bottom of page
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| − | *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
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| − | *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.
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| − | *what type of machine do we need?
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| − | *Log of all machines with purchase date and functionality?
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| − | *Linux vs Mac curators? athena development machine;
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| − | *how much power do the scripts need? can check
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| − | *may not be appropriate as official server if main machine goes down
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| − | *WB and athena can run SPELL server, but not others. security problems?
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| − | *prefer work machine is readily re-bootable; reconfigure software easily without affecting other things that people rely on
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| − | *need 10GB space; 4GB memory? SPELL production server; want it stable for outside world; hardware designed for that purpose; farm it out to IMSS?
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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
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| − | *building official sever of SPELL at OICR? Yes
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| − | WormMart
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| − | *with WormMart and WormBase, people just want to know if it's down, just to know to lessen frustration; Official statement from dev team
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| − | *WormMart - we give users testing url; can we just change WormBase link to that testing server?
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| − | *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
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| − | *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.
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| − | *would like to keep the html page as a testing server; could modify page
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| − | *if WormMart is working OK but not perfect, that's OK; Comment in the banner
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| − | *the html page is a useful tool to get feedback from users
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| − | == February 24, 2011 ==
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| − | CIT Computer Survey - done
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| − | CD/DVD burner not working (Wen)
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| − | Build Scripts:
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| − | *run @ OICR
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| − | *dynamic/static files
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| − | *problem: no one takes care of them
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| − | *curators should claim them and take care of them
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| − | **Gene interaction dump script claimed by Raymond and Xiaodong
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| − | **256 interaction objects empty (should not be); emptied during build?
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| − | *Monitor usage with new site
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| − | *Files (like FASTA, GFF) should be immediately available to users
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| − | *Page that links to the scripts (FTP)
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| − | *Need to define what we should have (common datasets)
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| − | **Example: Table with all genes, RNAi phenotype, genetic phenotype, etc.
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| − | **How many genes have been knocked out by RNAi?, etc.
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| − | **Metrics table on each species: #genes, #chromosomes, etc.
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| − | *Curators think about what data should be available
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| − | *Modifying existing script is easier than making new one
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| − | *Gary Williams already generates RNAi-phenotype-gene connections?
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| − | Snehal work half-time at WormBase?
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| − | *Will interview
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| − | *UI testing?
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| − | *Curation? GO? Phenotype?
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| − | *Start April 15th - 8 months? (Sept.) maybe longer
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| − | *Focus on particular papers?
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| − | Physical Interaction model
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| − | *Have been discussing with Rose at BioGRID
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| − | *Y2H, CoIPs, Pull downs, etc.
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| − | *Store physical interactions in WB outside of GO curation
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| − | *Data model
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| − | **YH model vs Interaction model
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| − | **Physical interaction tag in current interaction model unused
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| − | **Generalize YH model -> physical interaction model
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| − | **Add experiment types
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| − | **Issue: what do we do with existing physical interaction tag in interaction model?
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| − | **Split out different interaction types into individual classes?
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| − | **Separate into physical, genetic, predicted classes? Textpresso?
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| − | **Create separate classes for each experimental type? (Y2H, CoIP, etc.)
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| − | **XREF Interaction to Physical interaction, Genetic interaction
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| − | **Goal is for cleanliness and completeness
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| − | **How to capture experimental-specific info in curation and database?
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| − | **Suppress Y2H import from BioGRID?
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| − | **Keep interaction models as they are?
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| − | **All curators: Review interaction models to see what they want on the curation end
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