WormBase-Caltech Weekly Calls
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Contents
Previous Years
2017 Meetings
August 3, 2017
WB grant
- Progress (maintenance stuff) can be written as of last grant cycle
- Current projects and report the steady state
CRISPR alleles
- Some authors not reporting CRISPR alleles with standard nomenclature
- Some in Paul's lab creating same knockin with same name (should be distinct). Mary Ann to update nomenclature guidelines.
- Some (e.g. Bruce Bowerman) knock-in GFP in frame and use RNAi against GFP to knockdown endogenous gene
- RNAi mapping pipeline not setup to handle this
- Could maybe use endogenous sequence near insertion site (not ideal, for off-target effects)
- Maybe best, once new ?Phenotype_experiment model is in place, to just refer to perturbed gene
Ontology Browser
- Has been less stable lately; Raymond has needed to restart machine
- Being served from Dell server (in Braun building)
August 10, 2017
WormBase grant
- Neuronal wiring with Scott Emmons? Maybe not for this round
- Transcription regulatory networks? Is a priority
- Paul will assemble existing parts and send around for review
Entity markup
- In silico entity linking project needs link checking
- There is a brief summary table outlining the link URLs and predicted quality
- Could Cecilia check links?
- New interface will come out in a few months; if anyone starts now, they'll have to relearn when the new interface comes out
- Eventually markup should be job of authors during the process of writing. Need an authoring tool
Sequence features
- Should we have a standard human readable names for sequence features?
- Should we consolidate several features associated with the same gene when displaying in network views?
- Is there an automated way to give them public names?
- Maybe name automatically, but then allow manual overwriting
- Use gene name when experimentally demonstrated connection
- Needs to be automated, rule-based
- Could name based on neighboring gene(s)
Person lineage graph
- Running off of Datomic
Docker container system
- Potentially very useful for WB web services
Consider content for NAR paper
- Send ideas to Raymond