Difference between revisions of "2018 Advisory Board Meeting"

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* Michael Paulini -- ''WormBase@Other Resources [ENA UCSC NCBI UniProt EnsEMBL]''
 
* Michael Paulini -- ''WormBase@Other Resources [ENA UCSC NCBI UniProt EnsEMBL]''
 
* Faye Rodgers -- ''The IRIS whipworm annotation project - status and lessons learned''
 
* Faye Rodgers -- ''The IRIS whipworm annotation project - status and lessons learned''
* Matt Russell -- ''Using Datomic for curation data capture (Name server project)''
 
 
* Gary Williams -- ''Curation and analysis of nematode RNASeq data''
 
* Gary Williams -- ''Curation and analysis of nematode RNASeq data''
 
* Chris Grove -- ''Phenotype curation & community phenotype curation, interactions (genetic & physical)''
 
* Chris Grove -- ''Phenotype curation & community phenotype curation, interactions (genetic & physical)''
Line 55: Line 54:
 
* Paulo Nuin
 
* Paulo Nuin
 
* Sibyl Gao -- ''Technology stack modernization for UI and search, Name server UI''
 
* Sibyl Gao -- ''Technology stack modernization for UI and search, Name server UI''
 +
* Matt Russell -- ''Using Datomic for curation data capture (Name server project)''
  
 
=== Discussion session ===
 
=== Discussion session ===
Line 94: Line 94:
  
 
0830 introduction and overview -Paul Sternberg
 
0830 introduction and overview -Paul Sternberg
                Overview of Project, Funding, The Alliance, Big Picture, Issues, Outreach,  
+
                Overview of Project, Funding, The Alliance, Big Picture, Issues, Outreach,  
  
0900 dataflow and backend: status and plans -Kevin Howe
+
0900 Dataflow and backend -Kevin Howe
                Status
+
                Overview of dataflow
 +
                Progress/plans for back-end migration
 +
                Plans for integrating with Alliance
  
0945 curation: status and plans -Chris Grove
+
0945 Curation -Chris Grove
                Prioritization of datatypes
+
                Prioritization of datatypes
                How this is impacted by Alliance
+
                How this is impacted by Alliance
  
1030 break
+
1030 ''break''
  
1100 website: status and plans - Todd Harris
+
1100 Website and service - Todd Harris
 +
                Usage status
 
                 DevOps
 
                 DevOps
                Tools
 
 
                 Running on datomic
 
                 Running on datomic
  
1130 tools and displays;status and plans
+
1130 Tools and displays
                WormMine -
+
                WormMine -
                Ontology Browsing  -Raymond  
+
                Ontology Browsing  - Raymond Lee
                ParaSite - Kevin Howe
+
                ParaSite - Kevin Howe
  
 
1200 lunch
 
1200 lunch

Revision as of 13:34, 27 June 2018

The 2018 edition of the WormBase project meeting / Scientific Advisory Board meeting will take place at OICR on 12/13 July 2018.

Logistics

Attending

  • Hinxton
    • Matt Berriman, Kevin Howe, Michael Paulini, Paul Davis, Gary Williams, Matt Russell, Faye Rodgers
  • Caltech
    • Chris Grove, Kimberly Van Auken, Raymond Lee, Karen Yook, Paul Sternberg, Wen Chen, April Jauhal, Ranjana Kishore, Juancarlos Chan
  • OICR
    • Lincoln Stein, Todd Harris, Adam Wright, Paulo Nuin, Sibyl Gao

Presentation slides, drafts, etc

Project meeting

Agenda (tentative)

  • 0900: Coffee
  • 0930: Lightning talks 1
  • 1045: Break
  • 1100: Lightning talks 2
  • 1215: Lunch
  • 1330: Lightning talks 3
  • 1445: Break
  • 1500: Discussion session
  • 1700 (or whenever): Close

Lightning talks

--5 minutes pe peson with 5 minutes discussion 10 x 20 = ~3.5 hours

  • Paul Davis -- CGC, Variants and Strains
  • Kevin Howe -- Gene structure curation - what/how/why
  • Michael Paulini -- WormBase@Other Resources [ENA UCSC NCBI UniProt EnsEMBL]
  • Faye Rodgers -- The IRIS whipworm annotation project - status and lessons learned
  • Gary Williams -- Curation and analysis of nematode RNASeq data
  • Chris Grove -- Phenotype curation & community phenotype curation, interactions (genetic & physical)
  • Kimberly Van Auken -- gene function annotation using GO
  • Raymond Lee
  • Karen Yook -- making more use of microPublication
  • Wen Chen
  • April Jauhal -- Gene regulation interactions
  • Ranjana Kishore -- Automated gene descriptions and disease models
  • Juancarlos Chan
  • Paul Sternberg -- Transcriptional Regulation, what we need to do
  • Todd Harris -- website status; use and users; associated costs and management; third party projects we support
  • Adam Wright
  • Paulo Nuin
  • Sibyl Gao -- Technology stack modernization for UI and search, Name server UI
  • Matt Russell -- Using Datomic for curation data capture (Name server project)

Discussion session

  • Database migration project
    • Datomic migration status
    • How can we dovetail with the Alliance infrastructure work?
    • Plans for using Datomic in curation(?)
  • What processes/tools should we centralise in the Alliance?
    • Curation tools?
    • WormMine?


Thursday dinner for staff and SAB member

Evening, Thursday July 12

SAB

Advisors

attending

regrets

  • Oliver Hobert
  • Julie Ahringer
  • Andrew Chisholm
  • Mike Cherry
  • John Calarco

Agenda

0800 coffee???

0830 introduction and overview -Paul Sternberg

               Overview of Project, Funding, The Alliance, Big Picture, Issues, Outreach, 

0900 Dataflow and backend -Kevin Howe

               Overview of dataflow
               Progress/plans for back-end migration
               Plans for integrating with Alliance

0945 Curation -Chris Grove

               Prioritization of datatypes
               How this is impacted by Alliance

1030 break

1100 Website and service - Todd Harris

               Usage status
               DevOps
               Running on datomic

1130 Tools and displays

               WormMine -
               Ontology Browsing  - Raymond Lee
               ParaSite - Kevin Howe

1200 lunch

1300 SAB discussion

1430 Feedback, and Discussion

1630 conclude

Dinner for those who are not departing immediately

Evening, Friday, July 13