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

Location

• Enter OICR from the West Tower 5th floor (where the receptionist is located).
• Meeting room: West Tower 6-11 and 6-12 (The rooms by the stairs on the the 6th floor, upstairs from the Receptionist)

Ontario Institute for Cancer Research
MaRS Centre
661 University Avenue, Suite 510
Toronto, Ontario
Canada, M5G 0A3

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: Overview; Community; Architecture -- Todd Harris

1115 The Datomic-to-Catalyst website -- Sibyl Gao

1125 The Datomic architecture and devops at WormBase -- Adam Wright

1135 WormMine -- Paulo Nuin

1140 Tools and displays

               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