WormBase-Caltech Weekly Calls

2009 Meetings

2011 Meetings

February

March

April

May

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?

July 7, 2011

Root Passwords for all machines

• Send to Paul for emergency access

Issue Trackers

• All code in production use in BitBucket or equivalent
• Textpresso - Subversion (code can be shared)
• WormBase - Bitbucket, GitHub (can commit code)
• Todd says Github for code is best

Alex Bishop Help Desk E-mail

• Interolog Finder
• FlyBase will include links soon
• Is WormBase interested connecting to it?
• Can it be sustainably maintained?
• We should make a link under the Tools section of WormBase
• Interolog Finder provides cytoscape files
• Does Cytoscape have a web interface?

Elbrus is currently working stably

• Raymond stabilized Elbrus
• Elbrus is a frankenstein now
• Sanger/EBI taking over the RNAi mappings
• Will discuss with Igor once we determine the remaining issues
• Elbrus still needed for RNAi scripts to generate ACE files

Oliver Hobert correcting expression patterns occasionally

• Ask Oliver to point out what is missing
• Also ask Shawn Lockery
• Cell-specific markers
• Curated as transgenes
• Can link to specific promoters if transgenes present
• Bottom of every transgene page has a link to the static Marker table
• Check on new Beta version of WormBase website

Changing language of e-mail to authors to confirm data

• Non-nematode papers in WormBase via Cecilia?
• Authors sending all papers in their CV

Expression Cluster data curation

• Including GO terms, life stage, etc.
• Link to process pages?

Expression Cartoons

• Attempting to depict expression patterns by separate images for each tissue
• Would be nice to have a consolidated image with the option to expand to see individual tissue images
• Will maintain consolidated and expandable images for each gene as well as each expression pattern for each gene
• Trying to capture "Certain", "Uncertain", and "Partial" curation tags

Molecule curation

• Will need a molecule page on WormBase at some point
• Need a way to handle molecules that do not have a Mesh IDs
• Will replace WBMolecule IDs with Mesh IDs when they become available
• WBMolecule ID will be made a synonym of the molecule name alongside the Mesh ID
• Need to consider how the data will be stored and referred to in the long term (via ACE files etc.)