WormBase-Caltech Weekly Calls June 2011
June 2, 2011
- 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
- Setting up production environment
- Will have dedicated set of servers
- 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
- (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
- 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 back on normal hardware
- Should be running normally
- Let Juancarlos know otherwise
- 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?