Data Analysis Methods & Platforms

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Data Analysis and Discovery Subgroup

NIH Liaisons:  Michele Ferrante (NIMH), Elizabeth Powell (NIAAA)

Subgroup Leads: TBD

Email addresses: See table of Subgroup members below

CURRENT AS OF DEC 22, 2020:

Email List: send email to: u19datasci-dadp at lists.columbia.edu

Email both bs2679@columbia.edu and ys3328@columbia.edu to request to subscribe or unsubscribe people from the list.

Only list subscribers--which include the people in the table below with Michele Ferrante, Grace Peng and Susan Wright and Elizabeth Powell from the NIH--can send email to the list, and there is no moderation.

 

November 23, 2020: Data Analysis and Discovery subgroup Zoom mtg: Datajoint discussion

Members of the MoC3, DOPE, Osmonauts, and SCC projects, along with Datajoint staff, held a meeting to informally discuss how Datajoint is being used as part of our data science strategies for workflow and dataflow capture and sharing, and other topics.

We discussed details like the options to use a relational database or the S3 protocol for data storage locally as an alternative to using AWS services that also use the S3 protocol. We also talked generally about the MoC3 project's relatively comprehensive efforts to put ownership and management of whole lab pipelines tracked by Datajoint into the hands of lab members, versus a more targeted approach of using Datajoint to primarily share final U19 data products with others.

 

August 18, 2020: Data Analysis and Discovery subgroup Zoom mtg

We welcomed and heard from the data science point people for the three newest U19 awards.

After a round of introductions, Raj Bose presented on the MoC3 U19 project as an example of a short summary of a U19 project approach:

Summary: Yaki Stern, the MoC3 Data Engineer who joined the team in July 2019, performed a review of existing data management tools centered around the U19 science community and our U19 project moved forward at the end of 2019 to use the Datajoint software provided by Vathes LLC in conjunction with an on-premises relational database on the backend for now and GitHub as a software repository. Yaki and Zuckerman Institute Research Computing team members are working with Datajoint staff on training and close coordination on a weekly basis with MoC3 lab members carrying out the U19 science to design basic workflows or pipelines to be captured and described using MATLAB and python tie-ins to Datajoint. The idea is for each lab to reach a level of comfort and independence to define and manage their own pipelines going forward with the Research Computing team managing the Datajoint system infrastructure. Once experimental and data analysis pipelines are captured in the MoC3 database, the data products and software details can be queried, translated into different formats and shared according to FAIR principles.

Next the following presented briefly on their data science/data management challenges, ideas and plans:

Osmonauts: Rick Gerkin (ASU)

SCC: Tanya Sharpee and Graziana Gatto (Salk)

DOPE: Akshay Jaggi (Harvard Med)

After a discussion with people expressing providing input about the logistics of the Sun May 31 U19 PI meeting and virtual booth materials as part of the 2020 BRAIN Initiative Investigators Meeting Virtual Booth Materials (May 31-Jun 2, 2020), Shan Shen from Vathes presented on Datajoint and the brainCOGs project.

 

2020 BRAIN Initiative Investigators Meeting: Virtual Booth Materials (May 31-Jun 2, 2020):

https://www.imagwiki.nibib.nih.gov/sites/default/files/U19%20NIH%20Data…

 

February 25, 2020 Data Analysis and Discovery subgroup "showcase" Zoom mtg

Agenda:

  1. Showcase presentations where each group gave a short 4-5 slides presentation reviewing the tools that supports their research (data storage, data sharing, software sharing, software version control, computation, workflow/analysis managing and monitoring etc.)  
  2. Round up of the the tools that were presented (moderated by Yaki Stern)
  3. BRAIN Investigators Meeting  - planning

Showcase presentations:

1. Ripple (Soltesz)

4. MSCZ (Engert)

5. Flyloops (Dickenson)

8. MouseV1 (Miller): Raj gave this verbal summary, mentioning that Globus, with an endpoint on the Zuckerman Institute local storage system, continues to be investigated as the appropriate approach for sharing data internally between distributed academic participants

Round up287.09 KB

(no member of the ABC (Kleinfeld) U19 team is currently part of our subgroup)

Thank you all for the active participation,

Raj and Yaki

MoC3 (Costa) and MouseV1 (Miller) U19s

 

January 21, 2020 Data Analysis and Discovery subgroup Zoom mtg

 

 

April 13, 2019 BRAIN PI meeting

 

 

 

 

February 1, 2019 Data Catalog Meeting

 

 

Member List (as of 8/17/20)

U19 Name (Contact PI)

Name

Email

brainCOGS (Brody)

Adam Charles

adamsc@princeton.edu

brainCOGS (Brody)

Jonathan Pillow

pillow@princeton.edu

brainCOGS (Brody)

Dimitri Yatsenko

dimitri@vathes.com

brainCOGS (Brody) Shan Shen shanshen@vathes.com
DOPE (Sabatini) Akshay Jaggi Akshay_Jaggi@hms.harvard.edu

FlyLoops (Dickinson)

Michael Dickinson

flyman@caltech.edu

FlyLoops (Dickinson)

Richard Murray

murray@cds.caltech.edu

Learning2Learn (Buffalo)

Ariel Rokem

arokem@gmail.com

MoC3 (Costa), MouseV1 (Miller)

Liam Paninski

liam@stat.columbia.edu

MoC3 (Costa)

Elizabeth M. C. Hillman

eh2245@columbia.edu

MoC3 (Costa) Darcy Peterka dp2403@columbia.edu

MoC3 (Costa)

Yaakov Stern

ys3228@columbia.edu

MSCZ (Engert)

Joshua Vogelstein

jovo@jhu.edu

Osmonauts (Rinberg) Rick Gerkin Richard.Gerkin@asu.edu

OXT (Tsien)

Christian Ebbesen

Christian.Ebbesen@nyulangone.org

OXT (Tsien)

Sam McKenzie

sam.a.mckenzie@gmail.com

OXT (Tsien)

Alisa Surkis

Alisa.Surkis@nyulangone.org

OXT (Tsien)

Peter Peterson

petersen.peter@gmail.com

Ripple (Soltesz)

Ben Dichter

ben.dichter@stanford.edu

Ripple (Soltesz)

Ivan Raikov

iraikov@stanford.edu

SCC (Goulding) Tatyana Sharpee sharpee@salk.edu
SCC (Goulding) Graziana Gatto ggatto@salk.edu
SCC (Goulding) Eiman Azim eazim@salk.edu

Sensation (Maunsell)

Wolfgang Losert

wlosert@umd.edu

Sensation (Maunsell) Madeline Diep mdiep@fc-md.umd.edu
Sensation (Maunsell) Adam Porter aporter@fc-md.umd.edu

NIH Liaison

Michele Ferrante (NIMH)

michele.ferrante@nih.gov

NIH

Grace Peng

penggr@mail.nih.gov

NIH

Elizabeth Powell

elizabeth.powell3@nih.gov

NIH

Susan Wright

susan.wright@nih.gov

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