WormBase-Caltech Weekly Calls
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- 1 Previous Years
- 2 2017 Meetings
- 2.1 August 3, 2017
- 2.2 August 10, 2017
August 3, 2017
- Progress (maintenance stuff) can be written as of last grant cycle
- Current projects and report the steady state
- 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
- Has been less stable lately; Raymond has needed to restart machine
- Being served from Dell server (in Braun building)
August 10, 2017
- 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
- InSilico entity linking project requires curator link checking - for missing links as well as for faulty links - bad links are already an issue when ambiguities exist and this will grow as an issue when we start marking up multiple mod entities in the same paper
- There is a brief summary table outlining the link URLs and predicted quality - this is a useful feature of the current system set up by Arun, we are creating the same type of feature in the new inteface
- 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 - this can be made - there needs to be more discussion between wormbase, and insilico if this is going to be part of the insilico phase II or not
- 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
- Progress made in development, direct lineage running off of Datomic. All of it will need to be completed before it can go into production.
Docker container system
- Potentially very useful for WB web services
Consider content for NAR paper
- Send ideas to Raymond
- Input for the WB grant?
- Could discuss microreviews
- Automated descriptions good for genes with little info
- Human-written descriptions good for genes with lots of info; don't change too frequently
- Some have suggested including protein domain info