2018 Advisory Board Meeting

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, Ranjana Kishore, Juancarlos Chan

• OICR
  • Lincoln Stein, Todd Harris, Adam Wright, Paulo Nuin, Sibyl Gao

Presentation slides, drafts, etc

• • https://drive.google.com/drive/folders/161gEkCTxIAy22iVm1gRWmhYu_yhavMf6
  • Login with WormBase account to edit.

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 per person with 5 minutes discussion 10 x 20 = ~3.5 hours

• Paul Davis -- CGC, Variants and Strains
• Kevin Howe -- WormBase -> AGR dataflow
• Michael Paulini -- WormBase Data @ 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 and GO-CAM modeling; new AFP (Author First Pass) pipeline
• Raymond Lee -- ontology tools etc.
• Karen Yook -- making more use of microPublication
• Daniela Raciti (Wen Chen) -- expression pattern
• Wen Chen -- microarray, expression cluster, SPELL, SimpleMine
• Ranjana Kishore -- Automated gene descriptions and disease models
• Juancarlos Chan -- curation forms
• 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 -- New REST API and modernizing production deployment with Docker and AWS services
• 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

• Valerie Wood - PomBase
• Mary Shimoyama - RGD
• Ann Rougvie
• Brian Oliver
• Gary Bader
• Brent Derry
• Mei Zhen

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