https://wiki.wormbase.org/api.php?action=feedcontributions&user=Ajauhal&feedformat=atomWormBaseWiki - User contributions [en]2024-03-29T14:01:50ZUser contributionsMediaWiki 1.33.0https://wiki.wormbase.org/index.php?title=2018_Advisory_Board_Meeting&diff=330902018 Advisory Board Meeting2018-07-05T15:32:31Z<p>Ajauhal: /* Attending */</p>
<hr />
<div>The 2018 edition of the WormBase project meeting / Scientific Advisory Board meeting will take place at OICR on 12/13 July 2018.<br />
<br />
= Logistics =<br />
<br />
== Attending ==<br />
<br />
* Hinxton<br />
** Matt Berriman, Kevin Howe, Michael Paulini, Paul Davis, Gary Williams, Matt Russell, Faye Rodgers<br />
<br />
* Caltech<br />
** Chris Grove, Kimberly Van Auken, Raymond Lee, Karen Yook, Paul Sternberg, Wen Chen, Ranjana Kishore, Juancarlos Chan<br />
<br />
* OICR<br />
** Lincoln Stein, Todd Harris, Adam Wright, Paulo Nuin, Sibyl Gao<br />
<br />
= Presentation slides, drafts, etc =<br />
** https://drive.google.com/drive/folders/161gEkCTxIAy22iVm1gRWmhYu_yhavMf6<br />
** Login with WormBase account to edit.<br />
<br />
= Project meeting = <br />
== Agenda (tentative) ==<br />
<br />
* 0900: ''Coffee''<br />
* 0930: Lightning talks 1<br />
* 1045: ''Break''<br />
* 1100: Lightning talks 2<br />
* 1215: ''Lunch''<br />
* 1330: Lightning talks 3<br />
* 1445: ''Break''<br />
* 1500: Discussion session<br />
* 1700 (or whenever): ''Close''<br />
<br />
=== Lightning talks ===<br />
<br />
--5 minutes per person with 5 minutes discussion<br />
10 x 20 = ~3.5 hours<br />
<br />
* Paul Davis -- ''CGC, Variants and Strains''<br />
* Kevin Howe -- ''WormBase -> AGR dataflow''<br />
* Michael Paulini -- ''WormBase Data @ Other Resources [ENA UCSC NCBI UniProt EnsEMBL]''<br />
* Faye Rodgers -- ''The IRIS whipworm annotation project - status and lessons learned''<br />
* Gary Williams -- ''Curation and analysis of nematode RNASeq data''<br />
* Chris Grove -- ''Phenotype curation & community phenotype curation, interactions (genetic & physical)''<br />
* Kimberly Van Auken -- ''gene function annotation using GO and GO-CAM modeling''; ''new AFP (Author First Pass) pipeline''<br />
* Raymond Lee -- ontology tools etc.<br />
* Karen Yook -- ''making more use of microPublication''<br />
* Daniela Raciti (Wen Chen) -- ''expression pattern''<br />
* Wen Chen -- ''microarray, expression cluster, SPELL, SimpleMine''<br />
* Ranjana Kishore -- ''Automated gene descriptions and disease models''<br />
* Juancarlos Chan -- curation forms<br />
* Paul Sternberg -- ''Transcriptional Regulation, what we need to do''<br />
* Todd Harris -- ''website status; use and users; associated costs and management; third party projects we support''<br />
* Adam Wright -- ''New REST API and modernizing production deployment with Docker and AWS services''<br />
* Paulo Nuin<br />
* Sibyl Gao -- ''Technology stack modernization for UI and search, Name server UI''<br />
* Matt Russell -- ''Using Datomic for curation data capture (Name server project)''<br />
<br />
=== Discussion session ===<br />
<br />
* Database migration project<br />
** Datomic migration status<br />
** How can we dovetail with the Alliance infrastructure work?<br />
** Plans for using Datomic in curation(?)<br />
<br />
* What processes/tools should we centralise in the Alliance?<br />
** Curation tools?<br />
** WormMine?<br />
<br />
<br />
= Thursday dinner for staff and SAB member =<br />
Evening, Thursday July 12<br />
<br />
= SAB = <br />
== Advisors ==<br />
=== attending ===<br />
* [https://www.sysbiol.cam.ac.uk/Investigators/val-wood Valerie Wood] - PomBase<br />
* [http://mcw.marquette.edu/biomedical-engineering/mary-shimoyama.php Mary Shimoyama] - RGD<br />
* [https://wormbase.org/resources/person/WBPerson540 Ann Rougvie]<br />
* [https://www.wormbase.org/resources/person/WBPerson13749 Brian Oliver]<br />
* [https://www.wormbase.org/resources/person/WBPerson9159 Gary Bader]<br />
* [https://wormbase.org/resources/person/WBPerson137 Brent Derry]<br />
* [https://www.wormbase.org/resources/person/WBPerson720 Mei Zhen]<br />
<br />
=== regrets ===<br />
* Oliver Hobert<br />
* Julie Ahringer<br />
* Andrew Chisholm<br />
* Mike Cherry<br />
* [https://wormbase.org/resources/person/WBPerson6500 John Calarco]<br />
<br />
== Agenda ==<br />
<br />
0800 coffee???<br />
<br />
0830 introduction and overview -Paul Sternberg<br />
Overview of Project, Funding, The Alliance, Big Picture, Issues, Outreach, <br />
<br />
0900 Dataflow and backend -Kevin Howe<br />
Overview of dataflow<br />
Progress/plans for back-end migration<br />
Plans for integrating with Alliance<br />
<br />
0945 Curation -Chris Grove<br />
Prioritization of datatypes<br />
How this is impacted by Alliance<br />
<br />
1030 ''break''<br />
<br />
1100 Website and service - Todd Harris<br />
Usage status<br />
DevOps<br />
Running on datomic<br />
<br />
1130 Tools and displays<br />
WormMine -<br />
Ontology Browsing - Raymond Lee<br />
ParaSite - Kevin Howe<br />
<br />
1200 lunch<br />
<br />
1300 SAB discussion<br />
<br />
1430 Feedback, and Discussion<br />
<br />
1630 conclude<br />
<br />
= Dinner for those who are not departing immediately =<br />
Evening, Friday, July 13</div>Ajauhalhttps://wiki.wormbase.org/index.php?title=2018_Advisory_Board_Meeting&diff=330892018 Advisory Board Meeting2018-07-05T15:31:53Z<p>Ajauhal: /* Lightning talks */</p>
<hr />
<div>The 2018 edition of the WormBase project meeting / Scientific Advisory Board meeting will take place at OICR on 12/13 July 2018.<br />
<br />
= Logistics =<br />
<br />
== Attending ==<br />
<br />
* Hinxton<br />
** Matt Berriman, Kevin Howe, Michael Paulini, Paul Davis, Gary Williams, Matt Russell, Faye Rodgers<br />
<br />
* Caltech<br />
** Chris Grove, Kimberly Van Auken, Raymond Lee, Karen Yook, Paul Sternberg, Wen Chen, April Jauhal, Ranjana Kishore, Juancarlos Chan<br />
<br />
* OICR<br />
** Lincoln Stein, Todd Harris, Adam Wright, Paulo Nuin, Sibyl Gao<br />
<br />
= Presentation slides, drafts, etc =<br />
** https://drive.google.com/drive/folders/161gEkCTxIAy22iVm1gRWmhYu_yhavMf6<br />
** Login with WormBase account to edit.<br />
<br />
= Project meeting = <br />
== Agenda (tentative) ==<br />
<br />
* 0900: ''Coffee''<br />
* 0930: Lightning talks 1<br />
* 1045: ''Break''<br />
* 1100: Lightning talks 2<br />
* 1215: ''Lunch''<br />
* 1330: Lightning talks 3<br />
* 1445: ''Break''<br />
* 1500: Discussion session<br />
* 1700 (or whenever): ''Close''<br />
<br />
=== Lightning talks ===<br />
<br />
--5 minutes per person with 5 minutes discussion<br />
10 x 20 = ~3.5 hours<br />
<br />
* Paul Davis -- ''CGC, Variants and Strains''<br />
* Kevin Howe -- ''WormBase -> AGR dataflow''<br />
* Michael Paulini -- ''WormBase Data @ Other Resources [ENA UCSC NCBI UniProt EnsEMBL]''<br />
* Faye Rodgers -- ''The IRIS whipworm annotation project - status and lessons learned''<br />
* Gary Williams -- ''Curation and analysis of nematode RNASeq data''<br />
* Chris Grove -- ''Phenotype curation & community phenotype curation, interactions (genetic & physical)''<br />
* Kimberly Van Auken -- ''gene function annotation using GO and GO-CAM modeling''; ''new AFP (Author First Pass) pipeline''<br />
* Raymond Lee -- ontology tools etc.<br />
* Karen Yook -- ''making more use of microPublication''<br />
* Daniela Raciti (Wen Chen) -- ''expression pattern''<br />
* Wen Chen -- ''microarray, expression cluster, SPELL, SimpleMine''<br />
* Ranjana Kishore -- ''Automated gene descriptions and disease models''<br />
* Juancarlos Chan -- curation forms<br />
* Paul Sternberg -- ''Transcriptional Regulation, what we need to do''<br />
* Todd Harris -- ''website status; use and users; associated costs and management; third party projects we support''<br />
* Adam Wright -- ''New REST API and modernizing production deployment with Docker and AWS services''<br />
* Paulo Nuin<br />
* Sibyl Gao -- ''Technology stack modernization for UI and search, Name server UI''<br />
* Matt Russell -- ''Using Datomic for curation data capture (Name server project)''<br />
<br />
=== Discussion session ===<br />
<br />
* Database migration project<br />
** Datomic migration status<br />
** How can we dovetail with the Alliance infrastructure work?<br />
** Plans for using Datomic in curation(?)<br />
<br />
* What processes/tools should we centralise in the Alliance?<br />
** Curation tools?<br />
** WormMine?<br />
<br />
<br />
= Thursday dinner for staff and SAB member =<br />
Evening, Thursday July 12<br />
<br />
= SAB = <br />
== Advisors ==<br />
=== attending ===<br />
* [https://www.sysbiol.cam.ac.uk/Investigators/val-wood Valerie Wood] - PomBase<br />
* [http://mcw.marquette.edu/biomedical-engineering/mary-shimoyama.php Mary Shimoyama] - RGD<br />
* [https://wormbase.org/resources/person/WBPerson540 Ann Rougvie]<br />
* [https://www.wormbase.org/resources/person/WBPerson13749 Brian Oliver]<br />
* [https://www.wormbase.org/resources/person/WBPerson9159 Gary Bader]<br />
* [https://wormbase.org/resources/person/WBPerson137 Brent Derry]<br />
* [https://www.wormbase.org/resources/person/WBPerson720 Mei Zhen]<br />
<br />
=== regrets ===<br />
* Oliver Hobert<br />
* Julie Ahringer<br />
* Andrew Chisholm<br />
* Mike Cherry<br />
* [https://wormbase.org/resources/person/WBPerson6500 John Calarco]<br />
<br />
== Agenda ==<br />
<br />
0800 coffee???<br />
<br />
0830 introduction and overview -Paul Sternberg<br />
Overview of Project, Funding, The Alliance, Big Picture, Issues, Outreach, <br />
<br />
0900 Dataflow and backend -Kevin Howe<br />
Overview of dataflow<br />
Progress/plans for back-end migration<br />
Plans for integrating with Alliance<br />
<br />
0945 Curation -Chris Grove<br />
Prioritization of datatypes<br />
How this is impacted by Alliance<br />
<br />
1030 ''break''<br />
<br />
1100 Website and service - Todd Harris<br />
Usage status<br />
DevOps<br />
Running on datomic<br />
<br />
1130 Tools and displays<br />
WormMine -<br />
Ontology Browsing - Raymond Lee<br />
ParaSite - Kevin Howe<br />
<br />
1200 lunch<br />
<br />
1300 SAB discussion<br />
<br />
1430 Feedback, and Discussion<br />
<br />
1630 conclude<br />
<br />
= Dinner for those who are not departing immediately =<br />
Evening, Friday, July 13</div>Ajauhalhttps://wiki.wormbase.org/index.php?title=2018_Advisory_Board_Meeting&diff=329982018 Advisory Board Meeting2018-06-21T16:05:14Z<p>Ajauhal: /* Agenda */</p>
<hr />
<div>The 2018 edition of the WormBase project meeting / Scientific Advisory Board meeting will take place at OICR on 12/13 July 2018.<br />
<br />
= Logistics =<br />
<br />
== Attending ==<br />
<br />
* Hinxton<br />
** Matt Berriman, Kevin Howe, Michael Paulini, Paul Davis, Gary Williams, Matt Russell, Faye Rodgers<br />
<br />
* Caltech<br />
** Chris Grove, Kimberly Van Auken, Raymond Lee, Karen Yook, Paul Sternberg, Wen Chen, April Jauhal, Ranjana Kishore, Juancarlos Chan<br />
<br />
* OICR<br />
** Lincoln Stein, Todd Harris, Adam Wright, Paulo Nuin, Sibyl Gao<br />
<br />
= Project meeting = <br />
== Agenda ==<br />
<br />
Short talks from Everyone<br />
--5 minutes pe peson with 5 mintues discussion<br />
10 x 24 = 4 hours<br />
<br />
It would be a good idea if wrote down below the general theme of what we will each be talking about, so that we can group the talks into themes. This might fall-out as per-site groupings, but some things (e.g. back-end migration) are cross-site and would benefit from being grouped together. <br />
<br />
* Kevin Howe<br />
* Michael Paulini<br />
* Paul Davis<br />
* Gary Williams<br />
* Matt Russell<br />
* Faye Rodgers<br />
<br />
* Chris Grove - phenotype curation & community phenotype curation, interactions (genetic & physical)<br />
* Kimberly Van Auken - gene function annotation using GO<br />
* Raymond Lee<br />
* Karen Yook ''??making more use of microPublication??''<br />
* Wen Chen<br />
* April Jauhal -- gene regulation interactions<br />
* Ranjana Kishore - Automated gene descriptions and disease models<br />
* Juancarlos Chan<br />
• Paul Sternberg ''Transcriptional Regulation, what we need to do''<br />
* Todd Harris -- ''website status; use and users; associated costs and management; third party projects we support''<br />
* Adam Wright<br />
* Paulo Nuin<br />
* Sibyl Gao<br />
<br />
topics<br />
Backend: datomic migration, curation, Alliance plans<br />
<br />
WormMine etc.<br />
<br />
= Thursday dinner for staff and SAB member =<br />
Evening, Thursday July 12<br />
<br />
= SAB = <br />
== Advisors ==<br />
=== attending ===<br />
* [https://www.sysbiol.cam.ac.uk/Investigators/val-wood Valerie Wood] - PomBase<br />
* [http://mcw.marquette.edu/biomedical-engineering/mary-shimoyama.php Mary Shimoyama] - RGD<br />
* [https://wormbase.org/resources/person/WBPerson540 Ann Rougvie]<br />
* [https://www.wormbase.org/resources/person/WBPerson13749 Brian Oliver]<br />
* [https://www.wormbase.org/resources/person/WBPerson9159 Gary Bader]<br />
* [https://wormbase.org/resources/person/WBPerson137 Brent Derry]<br />
* [https://www.wormbase.org/resources/person/WBPerson720 Mei Zhen]<br />
<br />
=== regrets ===<br />
* Oliver Hobert<br />
* Julie Ahringer<br />
* Andrew Chisholm<br />
* Mike Cherry<br />
* [https://wormbase.org/resources/person/WBPerson6500 John Calarco]<br />
<br />
== Agenda ==<br />
<br />
0800 coffee???<br />
<br />
0830 introduction and overview -Paul Sternberg<br />
Overview of Project, Funding, The Alliance, Big Picture, Issues, Outreach, <br />
<br />
0900 dataflow and backend: status and plans -Kevin Howe<br />
Status<br />
<br />
0945 curation: status and plans -Chris Grove<br />
Prioritization of datatypes<br />
How this is impacted by Alliance<br />
<br />
1030 break<br />
<br />
1100 website: status and plans - Todd Harris<br />
DevOps<br />
Tools<br />
Running on datomic<br />
<br />
1130 tools and displays;status and plans<br />
WormMine -<br />
Ontology Browsing -Raymond <br />
ParaSite - Kevin Howe<br />
<br />
1200 lunch<br />
<br />
1300 SAB discussion<br />
<br />
1430 Feedback, and Discussion<br />
<br />
1630 conclude<br />
<br />
= Dinner for those who are not departing immediately =<br />
Evening, Friday, July 13</div>Ajauhalhttps://wiki.wormbase.org/index.php?title=2018_Advisory_Board_Meeting&diff=327332018 Advisory Board Meeting2018-04-23T21:20:57Z<p>Ajauhal: /* Attending */</p>
<hr />
<div>The 2018 edition of the WormBase project meeting / Scientific Advisory Board meeting will take place at OICR on 12/13 July 2018.<br />
<br />
= Logistics =<br />
<br />
== Attending ==<br />
<br />
* Hinxton<br />
** Matt Berriman, Kevin Howe, Michael Paulini, Paul Davis, Gary Williams, Matt Russell, Faye Rodgers<br />
<br />
* Caltech<br />
** Chris Grove, Kimberly Van Auken, Raymond Lee, Karen Yook, Wen Chen, April Jauhal<br />
<br />
* OICR<br />
** Lincoln Stein, Todd Harris, Adam Wright, Sibyl Gao<br />
<br />
= Project meeting = <br />
== Agenda ==<br />
<br />
= SAB = <br />
== Advisors ==<br />
== Agenda ==</div>Ajauhalhttps://wiki.wormbase.org/index.php?title=WormBase-Caltech_Weekly_Calls&diff=32666WormBase-Caltech Weekly Calls2018-04-12T17:59:32Z<p>Ajauhal: /* April 12, 2018 */</p>
<hr />
<div>= Previous Years =<br />
<br />
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]<br />
<br />
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]<br />
<br />
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]<br />
<br />
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]<br />
<br />
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]<br />
<br />
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]<br />
<br />
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]<br />
<br />
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]<br />
<br />
<br />
GoToMeeting link: https://www.gotomeet.me/wormbase1<br />
<br />
<br />
= 2018 Meetings =<br />
<br />
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]<br />
<br />
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]<br />
<br />
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]<br />
<br />
<br />
== April 5, 2018 ==<br />
<br />
=== GoToMeeting ===<br />
* Todd would like access to run GoToMeetings<br />
* Chris can send access credentials and GoToMeeting calendar details<br />
<br />
=== Data Mining Tool comparison ===<br />
* https://docs.google.com/spreadsheets/d/1vBTDBOKfXn9GcdpF1bXI62VEJ7hwyz2hOyAZcoV1_ng/edit?usp=sharing<br />
* Chris and Ranjana will work on summarized blog post with link to table<br />
<br />
=== Neuro Topic Meeting ===<br />
* Submitting abstract for meeting, due April 13<br />
* Wen will submit an abstract<br />
<br />
=== Rutgers worm meeting ===<br />
* We spoke to Andrew Singson; mentioned Rutgers meeting<br />
* Kimberly will look into joining/speaking<br />
<br />
=== Andy Golden disease and phenotype submission ===<br />
* Andy had sent a sample file of alleles with disease and phenotype data<br />
* Chris discussed phenotype details with Andy<br />
* Andy will eventually send bulk data submission<br />
<br />
=== Chen Institute furniture meeting ===<br />
* Today at new building; reviewing office furniture<br />
* Ranjana and Valerio will go<br />
<br />
=== Alliance curation ===<br />
* Paul needs to present on 5-year Alliance plan<br />
* Maybe could discuss curation plan<br />
<br />
=== Seek/modSeek ===<br />
* Troyanskaya lab; have we been in touch?<br />
* They may have new version that can be used<br />
* Paul S. will see her soon; will ask about it<br />
<br />
=== Alliance Entity Summaries ===<br />
* Have been working on gene summaries<br />
* Do we want to start working on summaries for other entities, like variations?<br />
* Ranjana can put together some proposal<br />
<br />
=== Alliance Tutorial ===<br />
* For reverse-site SAB meeting (April 23), need a sample query/tutorial<br />
* April has worked on a script for a tutorial; maybe we can use<br />
<br />
<br />
== April 12, 2018 ==<br />
<br />
=== Topic 1 ===<br />
<br />
<br />
<br />
=== Preliminary AGR Tutorial ===<br />
https://docs.google.com/document/d/1iwKs7K87DgbDopIzg9uRlZ9eoxbza2Gd05eaEPjpxn8/edit?usp=sharing<br />
Document includes screenshots and text, which is subject to change. Voiceover/basic video should be ready by the end of this week. Additional video editing will be added later, including captions, an intro with footage of scientists, and visual aids (eg. arrows, boxes etc.)</div>Ajauhal