WormBase-Caltech Weekly Calls
From WormBaseWiki
Previous Years
2016 Meetings
April 7, 2016
Tissue-enrichment tool
- Juancarlos and Raymond working on
- How to best integrate this into WormBase?
- Best to have all production code/material in one place, but could set up a proxy if it's already up and running
- Considering we don't know yet how popular the tool will be, the proxy could be a sufficient first step
- Could be a subdomain, e.g. tissueenrichement.wormbase.org, similar to the data submission forms
- Is this adaptable for the other MODs/organisms? Will submit the paper first
Karen's talk at ZFIN
- Talk went well
- some interest with SVM
- Having good discussions about data types and nomenclature
- Have their own reagent mapping pipeline to their genome browser
Daniela starting on gene regulation curation
- Daniela working with Xiaodong to learn the curation process
- Xiaodong's last day, next Friday 16th
April 21, 2016
Author submission forms
- Cell Press generating simple 3-column table asking for reagents
- Likely has a for-profit incentive; we need to push data tables that aid the MODs
- Chris will send around the table for minimum information of phenotype data
- Chris will look into a similar table for interactions
FTP file content changes
- GAFs, for example, get changed
- We need a mechanism/protocol to make notes of changes to file formats, etc.
- We could post timestamp and signature entries to a READ_ME file in each FTP directory for all changes to files
- In addition, we can post on the WB homepage and bog
- Ranjana will email Todd and Kevin to ask about best practices
- Ranjana will then send email to staff once a decision has been made
Micropublications
- Force11 (https://www.force11.org/) Force2016 challenge
- Research communication challenge submission
- Some positive tweets sent around about micropublication
- Some suggestions to use BioCaddie (https://biocaddie.org/)
April 28, 2016
joint mod team meeting (ky)
- ZFIN, SGD, WB: Next Wednesday May 4. All WormBase invited
- Doug Howe will send around the announcement with links to some google docs
- SGD will be supplying video conferencing through Blue Jeans http://bluejeans.com/video-conferencing
- Introductions of each MOD team member and overview of the forum
- Doug, Karen, and possible SGD person will spend 10-15 minutes introducing the respective MOD website, very basic navigation and search.
- will invite all mods
InterMOD (Intermine) call (ky)
- Getting ready for the TAGC conference in July
- Creating a single portal for mining across all MODmine instances
- Current problem is deciding on which homology sets to use, different mods have different source preferences for these homolog sets. e.g. elegans uses Phylome, OrthoDB, Others use Panther, DIOPT. different homolog sets give different results.