Difference between revisions of "2018 Advisory Board Meeting"

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= Logistics =
 
= 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)
 +
 +
<pre>
 +
Ontario Institute for Cancer Research
 +
MaRS Centre
 +
661 University Avenue, Suite 510
 +
Toronto, Ontario
 +
Canada, M5G 0A3
 +
</pre>
  
 
== Attending ==
 
== Attending ==
Line 9: Line 22:
  
 
* Caltech
 
* Caltech
** Chris Grove, Kimberly Van Auken, Raymond Lee, Karen Yook, Paul Sternberg, Wen Chen, April Jauhal, Ranjana Kishore, Juancarlos Chan
+
** Chris Grove, Kimberly Van Auken, Raymond Lee, Karen Yook, Paul Sternberg, Wen Chen, Ranjana Kishore, Juancarlos Chan, Marie-Claire Harrison
  
 
* OICR
 
* OICR
Line 25: Line 38:
 
* 1045: ''Break''
 
* 1045: ''Break''
 
* 1100: Lightning talks 2
 
* 1100: Lightning talks 2
* 1215: ''Lunch''
+
* 1215: ''Lunch'' (we grab our own lunch)
 
* 1330: Lightning talks 3
 
* 1330: Lightning talks 3
 
* 1445: ''Break''
 
* 1445: ''Break''
Line 33: Line 46:
 
=== Lightning talks ===
 
=== Lightning talks ===
  
--5 minutes pe peson with 5 minutes discussion
+
--5 minutes per person with 5 minutes discussion
 
10 x 20 = ~3.5 hours
 
10 x 20 = ~3.5 hours
 
   
 
   
 
* Paul Davis -- ''CGC, Variants and Strains''
 
* Paul Davis -- ''CGC, Variants and Strains''
* Kevin Howe -- ''Gene structure curation - what/how/why''
+
* Kevin Howe -- ''WormBase -> AGR dataflow''
* Michael Paulini -- ''WormBase@Other Resources [ENA UCSC NCBI UniProt EnsEMBL]''
+
* Michael Paulini -- ''WormBase Data @ 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 -- ''Community phenotype curation''
* Kimberly Van Auken -- ''gene function annotation using GO'', "new AFP (Author First Pass) pipeline"
+
* Kimberly Van Auken -- ''gene function annotation using GO and GO-CAM modeling''; ''new AFP (Author First Pass) pipeline''
 
* Raymond Lee -- ontology tools etc.
 
* Raymond Lee -- ontology tools etc.
 
* Karen Yook  --  ''making more use of microPublication''
 
* Karen Yook  --  ''making more use of microPublication''
* Wen Chen -- RNA-seq
+
* Daniela Raciti (Wen Chen) -- ''expression pattern''
* April Jauhal -- ''Gene regulation interactions''
+
* Wen Chen -- ''microarray, expression cluster, SPELL, SimpleMine''
* Ranjana Kishore -- ''Automated gene descriptions and disease models''
+
* Ranjana Kishore -- ''Automated gene descriptions, Disease models''
 
* Juancarlos Chan -- curation forms
 
* Juancarlos Chan -- curation forms
 
* Paul Sternberg  -- ''Transcriptional Regulation, what we need to do''
 
* 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''
+
* Todd Harris -- ''The Four Ages of WormBase''
* Adam Wright
+
* Adam Wright -- ''New REST API and modernizing production deployment with Docker and AWS services''
 
* Paulo Nuin
 
* Paulo Nuin
* Sibyl Gao -- ''Technology stack modernization for UI and search, Name server UI''
+
* Sibyl Gao -- ''Website updates and plans;, Name server UI''
 
* Matt Russell -- ''Using Datomic for curation data capture (Name server project)''
 
* Matt Russell -- ''Using Datomic for curation data capture (Name server project)''
  
Line 67: Line 80:
 
** WormMine?
 
** WormMine?
  
 +
*Pathways
 +
**GO-CAM, microPublication, Vsualization
  
 
= Thursday dinner for staff and SAB member =
 
= Thursday dinner for staff and SAB member =
 
Evening, Thursday July 12
 
Evening, Thursday July 12
 +
6pm at Reds Midtown Tavern (Gerrard and Yonge).
 +
 +
382 Yonge Street, Unit 6
 +
Toronto ON M5B 1S8
  
 
= SAB  =  
 
= SAB  =  
Line 81: Line 100:
 
* [https://wormbase.org/resources/person/WBPerson137 Brent Derry]
 
* [https://wormbase.org/resources/person/WBPerson137 Brent Derry]
 
* [https://www.wormbase.org/resources/person/WBPerson720 Mei Zhen]
 
* [https://www.wormbase.org/resources/person/WBPerson720 Mei Zhen]
 +
* [https://wormbase.org/resources/person/WBPerson6500 John Calarco]
  
 
=== regrets ===
 
=== regrets ===
Line 87: Line 107:
 
* Andrew Chisholm
 
* Andrew Chisholm
 
* Mike Cherry
 
* Mike Cherry
* [https://wormbase.org/resources/person/WBPerson6500 John Calarco]
 
  
 
== Agenda ==
 
== Agenda ==
  
0800 coffee???
+
'''0800''' Arrival / coffee  
 +
 
 +
'''0830''' Overview of Project, Funding, The Alliance, Big Picture, Issues, Outreach -- ''Paul Sternberg''
 +
 
 +
                        questions:     
 +
                        What new data types (and data) are coming soon? (e.g. single cell sequencing, metabolomics, nerual ciruits)
 +
                        How can we better serve our communities?
 +
                        How can we do better outreach?
 +
                        How can we better relate C. elegans knowledge to human genetics and health.
 +
                        How can we improve our community input to curation?
 +
                        How do best take advantage of current flux at NIH with respct to data science and funding?
 +
                        How should we proceed with datomic migration, given the Alliance?
  
0830 introduction and overview -Paul Sternberg
+
'''0900''' Dataflow and backend: status and plans -- ''Kevin Howe''
                Overview of Project, Funding, The Alliance, Big Picture, Issues, Outreach,
+
 +
'''0945''' Curation: status and plans -- ''Chris Grove''
  
0900 Dataflow and backend -Kevin Howe
+
'''1030''' ''break''
                Overview of dataflow
 
                Progress/plans for back-end migration
 
                Plans for integrating with Alliance
 
  
0945 Curation -Chris Grove
+
'''1100''' Website: Overview; Community; Architecture -- ''Todd Harris''
                Prioritization of datatypes
 
                How this is impacted by Alliance
 
  
1030 ''break''
+
'''1115''' Evolving the website architecture -- ''Sibyl Gao''
  
1100 Website and service - Todd Harris
+
'''1125''' The Datomic architecture and devops at WormBase -- ''Adam Wright''
                Usage status
 
                DevOps
 
                Running on datomic
 
  
1130 Tools and displays
+
'''1135''' WormMine -- ''Paulo Nuin''
                WormMine -
 
                Ontology Browsing  - Raymond Lee
 
                ParaSite - Kevin Howe
 
  
1200 lunch
+
'''1140''' WormBase ParaSite - ''Faye Rodgers''
  
1300 SAB discussion
+
'''1150''' Ontology Browsing  -- ''Raymond Lee''
 +
* Graph summaries (SObA)
 +
         
 +
'''1200''' ''lunch'' (Catering, vegan option available)
  
1430 Feedback, and Discussion
+
'''1300''' SAB discussion
  
1630 conclude
+
'''1430''' Feedback, and Discussion
  
= Dinner for those who are not departing immediately =
+
'''1630''' conclude
Evening, Friday, July 13
 

Latest revision as of 13:32, 13 July 2018

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

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, Disease models
  • Juancarlos Chan -- curation forms
  • Paul Sternberg -- Transcriptional Regulation, what we need to do
  • Todd Harris -- The Four Ages of WormBase
  • Adam Wright -- New REST API and modernizing production deployment with Docker and AWS services
  • Paulo Nuin
  • Sibyl Gao -- Website updates and plans;, 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 6pm at Reds Midtown Tavern (Gerrard and Yonge).

382 Yonge Street, Unit 6 Toronto ON M5B 1S8

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

                       questions:      
                       What new data types (and data) are coming soon? (e.g. single cell sequencing, metabolomics, nerual ciruits)
                       How can we better serve our communities?
                       How can we do better outreach?
                       How can we better relate C. elegans knowledge to human genetics and health.
                       How can we improve our community input to curation?
                       How do best take advantage of current flux at NIH with respct to data science and funding?
                       How should we proceed with datomic migration, given the Alliance?

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 Evolving the website architecture -- 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

  • Graph summaries (SObA)

1200 lunch (Catering, vegan option available)

1300 SAB discussion

1430 Feedback, and Discussion

1630 conclude