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 through the entrance at 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, Marie-Claire Harrison

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 (we grab our own 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 -- Community phenotype curation
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?

Pathways
- GO-CAM, microPublication, Vsualization

Thursday dinner for staff and SAB member

Evening, Thursday July 12

SAB

Advisors

attending

regrets

Oliver Hobert
Julie Ahringer
Andrew Chisholm
Mike Cherry

Agenda

0800 Arrival / coffee

0830 Overview of Project, Funding, The Alliance, Big Picture, Issues, Outreach -- Paul Sternberg

0900 Dataflow and backend: status and plans -- Kevin Howe

0945 Curation: status and plans -- Chris Grove

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 WormBase ParaSite - Faye Rodgers

1150 Ontology Browsing -- Raymond Lee

1200 lunch (Catering, vegan option available)

1300 SAB discussion

1430 Feedback, and Discussion

1630 conclude

2018 Advisory Board Meeting

Contents