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'' | ||
− | |||
* 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, | |
− | 0900 | + | 0900 Dataflow and backend -Kevin Howe |
− | + | Overview of dataflow | |
+ | Progress/plans for back-end migration | ||
+ | Plans for integrating with Alliance | ||
− | 0945 | + | 0945 Curation -Chris Grove |
− | + | Prioritization of datatypes | |
− | + | How this is impacted by Alliance | |
− | 1030 break | + | 1030 ''break'' |
− | 1100 | + | 1100 Website and service - Todd Harris |
+ | Usage status | ||
DevOps | DevOps | ||
− | |||
Running on datomic | Running on datomic | ||
− | 1130 | + | 1130 Tools and displays |
− | + | WormMine - | |
− | + | Ontology Browsing - Raymond Lee | |
− | + | 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.
Contents
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
- 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 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
- 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