[2021 Jan] BICCNomics Workshop

Derek Caetano-Anolles
  • Updated

On January 27, 2021, instructors from the Broad Institute taught a 4-hour virtual webinar as a part of a 2-day workshop series for BICCN (BRAIN Initiative Cell Census Network). This webinar took users from gathering their data in the NeMO archive, analyzing it in Terra, and demonstrated how to publish their finished study in the Single Cell Portal (SCP).

 


 

Materials

You can find all the materials at broad.io/BICCN2101, though links below may specify a specific file folder. If you would like to follow along with this workshop, please follow these setup instructions before proceeding.

 


 

Agenda & Video

This webinar was recorded and published here. The video corresponds to the time stamps listed below.

 

00:00:00 - Welcome, setup & agenda (Slides 1-2)

Instructor: Elizabeth Kiernan, Science Writer, Data Sciences Platform, Broad Institute

 

00:01:37 - Intro to Terra (Slides 3 -15)

Instructor: Elizabeth Kiernan, Science Writer, Data Sciences Platform, Broad Institute

 

00:12:45 - Terra Guided Tour

Instructor: Elizabeth Kiernan, Science Writer, Data Sciences Platform, Broad Institute

 

00:35:39 - Data in NeMO (Slides)

Instructor: Anton Kovalsky, Science Writer, Data Sciences Platform, Broad Institute

 

00:44:17 - Select your data

Instructor: Elizabeth Kiernan, Science Writer, Data Sciences Platform, Broad Institute

 

00:54:07 - Running workflows (Optimus pipeline)

Instructor: Elizabeth Kiernan, Science Writer, Data Sciences Platform, Broad Institute

 

01:19:00 - Set up your notebook cloud environment

Instructor: Elizabeth Kiernan, Science Writer, Data Sciences Platform, Broad Institute

 

01:23:03 - Running workflows (Cumulus pipeline)

Instructor: Elizabeth Kiernan, Science Writer, Data Sciences Platform, Broad Institute

 

01:32:27 - Explore outputs using notebooks

Instructor: Elizabeth Kiernan, Science Writer, Data Sciences Platform, Broad Institute

 

02:00:00 - Running workflows (checking outputs)

Instructor: Elizabeth Kiernan, Science Writer, Data Sciences Platform, Broad Institute

 

02:04:43 - Single Cell Portal Intro (Slides)

Instructor: Tim Majarian, Computational Associate II, Data Sciences Platform, Broad Institute

 

02:16:52 - Demo an existing SCP study

Instructor: Allie Hajian, Senior Science Writer, Data Sciences Platform, Broad Institute

 

02:39:55 - Wrap-up (Slides)

Instructor: Elizabeth Kiernan, Science Writer, Data Sciences Platform, Broad Institute

 


 

Further Resources

For more information on Terra, visit https://terra.bio/

For more information on NeMO, visit https://nemoarchive.org/

For more information on Single Cell Portal, visit https://singlecell.broadinstitute.org...

For more information on BICCN, visit https://biccn.org/

For more information on the BICCN Omics Virtual Workshop, visit https://nemoarchive.org/biccn-omics-w...

 

 

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