WormBase-Caltech Weekly Calls
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Contents
Previous Years
2013 Meetings
September 5, 2013
SPELL
- Wen contacted Matt Hibbs
- Matt will not maintain SPELL in near future
- Undergrad at Caltech to maintain/upgrade (Ruby 2 -> Ruby 3)?
- Connect Matt with undergrad (work study?)
- Cynthia(?) at Caltech may know Ruby (needed for interface)
- Communicate with Mike Cherry / SGD as they use SPELL as well
- Does SGD have a SPELL developer?
- Java experience needed to maintain backend
Expression Clusters
- Wen found that many authors don't publish lists of clustered genes
- We could take in the data
Gene ACE Dumps
- Kimberly took a look at what Michael sent us
- Looked at gene objects specifically
- More in the full Gene ACE that we could make use of than what was included in the 'nightly' dump from Michael
- Could other curators take a look at what could be used/requested from GeneACE?
- Karen and Juancarlos will discuss for variations today
- Examples: CDS to Pseudogene changes, gene-to-variation mappings/pairings
Discussions on Value of Manual Curation
- What would WormBase look like without any manually curated data?
- Can concise descriptions be automated in any way? "This gene encodes ... It is involved in [GO process]..." etc.
- How are the concise description forms working? In progress...
Enhancer curation
- Will upload for WS240
Interaction changes
- Interaction model changed to update genetic interaction terms
- Also, "Electrophoretic Mobility Shift Assay" has been added as a 'Physical Interaction Detection Method'
- Interaction OA and dumper has been updated and is working properly
Historical Genes
- Abby has setup display of historical genes in Overview widgets of relevant objects (Interaction, Expr_pattern, Antibody, Transgene, Process)
- Looks good on staging
Upgrading transgene curation
- Capturing related sequence features and displaying on GBrowse
- Single molecule FISH data: Use case
- Look in GBrowse to see probe sequence vs transgene sequence; find discrepancy in expression patterns
- Tim Schedl would like to see what transgenes have been used for in vitro (purified from worms) experiments (e.g. physical interactions)
- Would like to capture epitope tags like FLAG, MYC, HIS, etc.
- Capturing what does or does not rescue a mutation
- Association with site-of-action data?
