On July 10, 2022, the Broad Institute's Data Sciences Platform presented a one day workshop as part of the ISMB 2022 conference.
In this workshop, we guided participants through a research journey that highlighted the capabilities of cloud components like Terra, Dockstore, Galaxy, and Single-Cell Portal that allow you to find data that meets your research interests, process and interrogate that data with community-developed tools, and share your reproducible analysis results. Via hands-on exercises, participants integrated tools from these interoperable platforms to complete an example end-to-end analysis with single-cell RNA sequencing data.
Materials
The slides and Terra registration materials are at http://broad.io/ismb_0722. Additionally, you can try the accompanying tutorial workspace.
Agenda
Times are Central Time
|
11:00 |
Welcome/opening remarks/review agenda and learning goals (slides) |
|
11:05 |
Introduction to Terra: A scalable platform for biomedical research (slides) |
|
11:10 |
Terra Platform Tour and Think Pair Share Data Tables (slides) |
|
11:40 |
Demo: Cloning workspaces and importing data from NeMO |
|
11:45 |
Creating workspaces and importing data from NeMO (hands-on Steps 0-1) |
|
12:00 |
Demo: Modifying data tables and adding workspace variables |
|
12:30 |
Modifying data tables and adding workspace variables (hands-on Step 2) |
|
13:00 |
Lunch |
|
14:00 |
Overview of WDLs (slide), Optimus (slide), and Demo: WDL Fundamentals, Finding Optimus Dockstore WDL and Running in Terra |
|
14:30 |
Finding Dockstore WDLs and processing data in Terra with WDL workflows - (hands-on Steps 3-5) |
|
15:15 |
Coffee Break |
|
15:30 |
Analyze data with Scanpy in a Jupyter Notebook (hands-on Step 6 continued) |
|
16:00 |
Overview: Harnessing Terra and Single Cell Portal for cloud collaborations and publications (slides) |
|
16:10 |
Demo: Single-cell Portal study |
|
16:45 |
Coffee Break |
|
17:00 |
Demo: Additional applications in Terra (Galaxy, RStudio) |
|
17:30 |
Wrap up (slides), Survey, Q&A (TAs will stay) |
|
18:00 |
End of tutorial |