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| − | ==June 11, 2009== | + | = Previous Years = |
| − | *Discussion of allele-paper connections
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| − | **Jolene has a Textpresso-based pipeline for identifying alleles in papers
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| − | **Alleles get associated with a paper if there is phenotypic or molecular data
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| − | **List of all alleles associated with a paper could possibly be passed on to Sanger for subsequent connection
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| | | | |
| − | *Discussion of gene-paper connections
| + | [[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]] |
| − | **What criteria should be used for associating genes with papers?
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| − | **Currently being associated manually by a curator during first-pass
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| − | **Could Textpresso be harnessed for this task?
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| − | **There are different evidences attached to gene-paper connections
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| − | **Genes associated with a paper via Textpresso searches could be presented to the first-pass curator for approval in the first-pass form
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| − | **Need to fix current abstract-gene associating script to include proteins (e.g. PIE-1)
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| | | | |
| − | *Incorporate a customized Textpresso query on WormBase object pages so users could look for additional info if they want
| + | [[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]] |
| − | **Data type curator could help design a useful query
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| | | | |
| − | *Other gene-object connections
| + | [[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]] |
| − | **Develop a canned query for all objects that should be associated with the gene page
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| | | | |
| − | *Worm Meeting
| + | [[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]] |
| − | **Pre-meeting - meeting rooms?
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| − | **Pre-meeting - practice talks for WormBase workshop
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| − | **Storage for swag - pavillion should be okay
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| | | | |
| − | ==June 18, 2009==
| + | [[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]] |
| | | | |
| − | *Worm Meeting and Pre-Meeting
| + | [[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]] |
| − | **WormBase Help Desk Schedule - set for worm meeting
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| − | **Wen may need help carrying boxes of swag
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| − | **Do any Sanger or WashU people need rides to UCLA?
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| − | **Mary Alvarez is working on finding rooms for the pre-meeting
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| − | **Be prepared to report on curation status of your data type and what we might need
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| | | | |
| − | *Author contact information on first-pass form
| + | [[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]] |
| − | **email goes to the first email address found by Textpresso
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| − | **Raymond - we do care where this data comes from
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| − | **Erich - can we send it to the designated corresponding author
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| − | **first-pass curation could capture the corresponding author
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| − | **if the email didn't go to the corresponding author, it may affect our response rate
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| − | **two-stage approach proposal
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| − | ***respond to Bernard - we'll try to find corresponding author in the future and add his name to the comments field for now
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| − | ***going forward, how best to determine corresponding author?
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| − | ***keep track of IP address from which the data was sent?
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| − | ***add text to email saying that authors may include their contact information in the comments box, if they wish
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| − | ***Raymond will proof-read papers to check on corresponding author designation and email addresses
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| | | | |
| − | *Zfin visit - PATO progress, worth looking at
| + | [[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]] |
| − | **Erich noted no genome browser - what is the issue?
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| − | **Their experience with getting figures from journals might be helpful.
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| | | | |
| | + | [[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]] |
| | | | |
| − | ==February 10, 2011==
| + | [[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]] |
| | | | |
| − | *Should we have a Caltech project/site manager? We'll look at the issues to be solved first
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| | | | |
| − | *Todd would like to know more about what's going on at Caltech
| + | GoToMeeting link: https://www.gotomeet.me/wormbase1 |
| − | **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?
| + | = 2020 Meetings = |
| | | | |
| − | *Kimberly: helpful (for off site individuals) if we go around the room to talk about what each of us is working on
| + | [[WormBase-Caltech_Weekly_Calls_January_2020|January]] |
| | | | |
| − | *Bitbucket use
| + | [[WormBase-Caltech_Weekly_Calls_February_2020|February]] |
| − | **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
| + | [[WormBase-Caltech_Weekly_Calls_March_2020|March]] |
| − | **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
| + | [[WormBase-Caltech_Weekly_Calls_April_2020|April]] |
| − | **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
| + | [[WormBase-Caltech_Weekly_Calls_May_2020|May]] |
| − | **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 == | + | == June 4, 2020 == |
| | | | |
| − | Interaction dumping script
| + | === Citace (tentative) upload === |
| − | *Spot check table | + | * CIT curators upload to citace on Tuesday, July 7th, 10am Pacific |
| − | *Push changes to Git? Yes, to main branch | + | * Citace upload to Hinxton on Friday, July 10th |
| | | | |
| | + | === Caltech reopening === |
| | + | * Paul looking to get plan approved |
| | + | * People that want to come to campus need to watch training video |
| | + | * Masks available in Paul's lab |
| | + | * Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room |
| | + | ** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart |
| | + | * Need to coordinate, maybe make a Google calendar to do so (also Slack) |
| | + | * Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form |
| | + | * Also, need to submit who you were in contact with for contact tracing |
| | + | * Form is used all week, and hold on to it until asked to be submitted |
| | + | * If someone goes in to the office, they could print several forms for people to pick up in WB offices |
| | | | |
| − | Interactions automatically downloaded to FTP every release? Yes
| + | === Nameserver === |
| − | *People should check their own curation data | + | * Nameserver was down |
| − | *Users query frequently? | + | * CIT curators would still like to have a single form to interact with |
| − | *Can WormMart work instead? | + | * Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea |
| − | *Ruihua - feature can be added | + | * Still putting genotype and all info for a strain in the reason/why field in the nameserver |
| − | *Todd - good to have pre-defined queries generated automatically | + | * We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out |
| − | *Parse/remove predicted interactions (400,000) from others during dump? Yes | + | * Hinxton is pulling in CGC strains, how often? |
| − | *Paul - Wei Wei wants to help with updates - who should she contact at WB? | + | * Caltech could possibly get a block of IDs |
| | | | |
| − | | + | === Alliance SimpleMine === |
| − | Ranjana - Solar flares causing static on phone? ;)
| + | * Any updates? 3.1 feature freeze is tomorrow |
| − | | + | * Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call |
| − | | |
| − | 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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| − | *
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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 | |
| − | *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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