Difference between revisions of "WormBase-Caltech Weekly Calls"

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* Some positive tweets sent around about micropublication
 
* Some positive tweets sent around about micropublication
 
* Some suggestions to use BioCaddie (https://biocaddie.org/)
 
* Some suggestions to use BioCaddie (https://biocaddie.org/)
 +
 +
==April 28, 2016==
 +
===joint mod team meeting===
 +
*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, SGD person will spend 10 minutes introducing the respective MOD website, very basic navigation and search.
 +
 +
===InterMOD (Intermine) call===
 +
*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.

Revision as of 18:01, 28 April 2016

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings


2016 Meetings

January

February

March


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

April 28, 2016

joint mod team meeting

  • 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, SGD person will spend 10 minutes introducing the respective MOD website, very basic navigation and search.

InterMOD (Intermine) call

  • 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.