WormBase-Caltech Weekly Calls

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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/)