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.
Contents
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
