Difference between revisions of "WormBase-Caltech Weekly Calls"

Revision as of 17:07, 7 July 2011

2009 Meetings

2011 Meetings

February

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.)

@@ Line 12: / Line 12: @@
 [[WormBase-Caltech_Weekly_Calls_May_2011|May]]
+[[WormBase-Caltech_Weekly_Calls_June_2011|June]]
-== 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?

Difference between revisions of "WormBase-Caltech Weekly Calls"

Revision as of 17:07, 7 July 2011

2011 Meetings

July 7, 2011

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