WormBase-Caltech Weekly Calls June 2011

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June 2, 2011

Website (Todd)

  • Wrapped up support for all classes (display, etc.)
  • Have one person volunteer to look at potential problems for a particular page?
    • Send e-mail out to curators, etc.
    • People volunteer for a page
    • Reviewers send feedback to Todd/Web Team
    • Google Document for signing up for looking at pages
  • Todd
    • Setting up production environment
    • Will have dedicated set of servers
  • Abby
    • Debugging behavior of web app
    • Stress testing dynamic loading of content
  • Once exposed to worm community at International Meeting, can develop focus groups to enhance/improve features


Computer Security breach

  • Sandbox/Fedora machine hacked
  • Limited infection/compromised machines
  • Raymond and Juancarlos working on it
  • Textpresso-dev affected


Virtual Worm Site

  • Make link on WormBase homepage
  • Announce on homepage
  • Fold into new web site release
  • Will add note to site about how the model may be integrated into WormBase
  • Chris will discuss more detail with Todd at/after International Meeting


Expression pattern OA

  • Juancarlos and Daniela have to fix a couple of things
  • Should be live soon


New Tazendra Login

  • New password
  • Raymond: Assume that once logged into another machine, your keystrokes could be monitored
  • Don't ssh or scp to another machine (or type any passwords) while logged into a machine other than your own
  • Limit off-site access?
  • Setup dedicated machine (with open Port 22) for logging into and then ssh'ing or scp'ing to other machines from
  • Consider security audit (what machines are operating and which ports are open)
  • VPN, should always use VPN if accessing machines from a public WiFi spot


Textpresso-dev

  • (Michael) need to make textpresso-dev more redundant to address need for access
  • Security fixes, etc.
  • Switched off right now (up again a couple hours later -- J)


June 9, 2011

Tazendra reinstallation (Juancarlos)

  • Raymond and Juancarlos working on now
  • Will be running on slower sandbox until next week (slightly noticeable)
  • Hardware will be swapped (fast machine has 4G ram + 4 cores ; slower machine has 2G ram + 2 cores)
  • Shouldn't affect work of curators
  • Curators should make note if Tazendra feels slower than usual and document
  • Ubuntu slower than Fedora for postgres queries, for some reason?
  • Upgrade tazendra more frequently in future?
  • Should restore tazendra up to the point when there was the security breach and go from there


Expression pattern OA is live (Daniela)

  • Working well and ready to use


BioGRID curation coordination (Kimberly)

  • Focusing on Wnt pathway papers
  • Still need to work out some details of curation sharing/prioritization
  • They want to follow up on using Textpresso tools


Aldrin Montana here next week (Karen)

  • Talk to Karen if you want to talk to him
  • Karen can make a schedule


Wiki setup for curation status (Karen)

  • Flagged papers, how many have been taken care of
  • Details of false positive flags
  • Used to take Andrei's flags as gold standards
  • Textpresso/SVM success/fail rates
  • How do the numbers affect the curation pipeline?
  • What is the ultimate goal? Meet needs/wants of users?
  • Full disclosure/transparency to users as to what has or hasn't been curated
  • Generate feedback from user community
  • Paper stats vs. data type stats
  • Difficult to determine the false negative rates without a study
  • Use Textpresso tools to identify SVM false negatives?
  • First need to generate estimates
  • Tell users "We have 90% recall" vs. "We only get 30% recall" for example
  • Would be great to have an automated way to report the numbers/stats
  • Should include criteria for finding/flagging papers?
  • Provide more refined flagging info to author first-pass forms, and authors correct
  • Add info to WBPaper pages including possible data types and what's been curated?
  • This data is useful for NIH reporting


International Meeting Help Desk

  • Do we need a computer for users?
  • Curators will bring their own laptops
  • Wireless internet should be fine


WormBase laptop?

  • Had been discussed previously
  • Most curators ended up getting their own laptop
  • Laptops are relatively cheap these days (~$300?)


Post-International Meeting WormBase meeting

  • Conference room reserved


June 16, 2011

Tazendra

  • Tazendra back on normal hardware
  • Should be running normally
  • Let Juancarlos know otherwise


Scripting requests?

  • Raymond can start taking requests
  • Large-scale data set processing
  • Querying ACeDB


Ask Karen @ wormbase.org account

  • If you need an account for WormBase login, talk to Karen


Interaction meeting review

  • Genetic interaction examples
  • Adding new genetic interaction types tags
  • Separating Physical interaction from interaction model


GSA Go-term markup

  • Automated linking OK; will ignore false negatives
  • Need to discuss with SGD


Karen spoke to Alex Pico @ WikiPathways

  • New tool to click on pathway and navigate, highlight genes, etc.
  • May be able to integrate into pathway widget in WormBase
  • WikiPathways working with Reactome, WikiGenes
  • Incorporate community curation?
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