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, Ranjana Kishore, Juancarlos Chan, Marie-Claire Harrison
  
 
* OICR
 
* 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 =  
 
= Project meeting =  
−
== Agenda ==
+
== 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  =  
 
= SAB  =  
 
== Advisors ==
 
== Advisors ==
 +
=== attending ===
 +
* [https://www.sysbiol.cam.ac.uk/Investigators/val-wood Valerie Wood] - PomBase
 +
* [http://mcw.marquette.edu/biomedical-engineering/mary-shimoyama.php Mary Shimoyama] - RGD
 +
* [https://wormbase.org/resources/person/WBPerson540 Ann Rougvie]
 +
* [https://www.wormbase.org/resources/person/WBPerson13749 Brian Oliver]
 +
* [https://www.wormbase.org/resources/person/WBPerson9159 Gary Bader]
 +
* [https://wormbase.org/resources/person/WBPerson137 Brent Derry]
 +
* [https://www.wormbase.org/resources/person/WBPerson720 Mei Zhen]
 +
* [https://wormbase.org/resources/person/WBPerson6500 John Calarco]
 +
 +
=== regrets ===
 +
* Oliver Hobert
 +
* Julie Ahringer
 +
* Andrew Chisholm
 +
* Mike Cherry
 +
 
== Agenda ==
 
== 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

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

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