WormBase-Caltech Weekly Calls

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

January

February

March

April

May

June

July

August

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

• Gold-standard enhancers from Margie's list of papers
• Xiaodong 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 sequences or 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?

In silico phylogenetic tree data

• No current appropriate home for it in WormBase
• Wen and Karen working on how to house the data
• Data should go on Process pages

Process curation and associations

• Can we automatically infer associations to a process by, for example, a gene's mutant phenotype?
• What automatic connections can be made to processes?
• Do we 'hardcode' phenotype-to-process connections?
• Interaction widget with Cytoscape now functional on Process pages (on staging)

September 12, 2013

RNAi movies

• RNAi.org movies need referencing
• May require adding a Database tag to the ?Movie model
• We may be able to add the RNAi.org movie URL to the Movie object Remark field
• Chris will work it out with Todd

Crispr-CAS9 Genome Editing methods

• Will add to the Reagents page (will be under the Resources menu, not there on live site currently)
• URL is: http://www.wormbase.org/resources/reagents
  • Curators can edit or create new widgets if logged in

GeneACE Nightly Dump

• Do people use the Laboratory or Clone info/tags?

AMIGO 2

• Raymond establishing a WormBase development environment that Juancarlos can use
• Troubleshooting installation of Perl libraries
• Also, working to Establish a development environment for the WormBase Ontology Browser server
  • With our own server we can supply WormBase-specific ontologies