[2019 May] Terra Workshop for BroadE

Robert Majovski
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On May 22, 2019, members of the Broad Institute community participated in a Terra workshop as part of the BroadE workshop series. The goal of the workshop was to empower members of the Broad community, including those who may be entirely new to cloud computing, to use Terra to access data, run analysis tools, and collaborate -- all in a secure and scalable environment.

Workshop synopsis

Focus on your science: How to work and collaborate easily and securely on the cloud with Terra

This workshop will get you up and running with Terra, the new scalable platform for biomedical research developed at the Broad Institute in collaboration with Verily Life Sciences. (If you’ve seen or used FireCloud, think of Terra as the new and improved user interface that makes doing research easier than before!). We will first cover the basics of doing research on the cloud and introduce you to Terra and the Data Biosphere.

You’ll then get hands-on with Terra, learning how to access research data, run analysis tools, and seamlessly collaborate, all in a secure and scalable environment. We will guide you through running example workflows, interacting with Jupyter Notebooks, and working with the BigQuery data warehouse to help accelerate your own project in Terra.

We will also show you how to manage data, security, and billing in Terra so that you can relax and focus on your science.

 

Workshop sessions and materials

0. Introduction to the workshop, Terra, and the Data Biosphere 

What is the Data Biosphere, and how does Terra fit into this ecosystem? We set the stage with the story behind Terra before you get hands-on in the application.
Instructor: Robert Majovski, Lead Educator, Data Sciences Platform, Broad Institute
Materials: Slides; Video

1. Interactive analysis with Jupyter Notebooks in Terra

We give you a crash-course on interactive analysis in Terra with Jupyter Notebooks.
Instructor: Anton Kovalsky, Science Writer, Data Sciences Platform, Broad Institute
Materials: Slides; Video 

2. Hands-on with Jupyter Notebooks in Terra

Now is your chance to try out notebooks in Terra as we guide you through how to install the R environment and software packages you need for the next lesson in this workshop.
Instructor: Anton Kovalsky, Science Writer, Data Sciences Platform, Broad Institute
Materials: VideoJupyter Notebook 

3. BigQuery: Interacting with structured data sets

We teach you how to analyze data in real time in Terra using Google BigQuery and Jupyter notebooks.
Instructor: Allie Hajian, Science Writer, Data Sciences Platform, Broad Institute
Materials: Slides; Video; Terra workspace

4. Billing, cost management, and security in Terra 

Definitely not as exciting as your research, but important to know, are how to set up billing accounts, manage costs, and collaborate securely.
Instructor: Alex Baumann, Senior Principle Software Engineer, Data Sciences Platform, Broad Institute
Materials: Slides; Video

5. Running a real workflow in Terra (CRAM to BAM)

This exercise on how to run genomic data workflows in Terra gives you a chance to try out a quick and easy step in genomic data processing, converting the format of sequencing data files.
Instructor: Kate Noblett, Senior Project Coordinator, Data Sciences Platform, Broad Institute
Materials: Video (we're working on it, there was a technical issue with the recording that needs to be resolved); Terra workspace

6. Understanding and using Docker

Knowing how to use Docker containers in Terra can help you scale your compute and enable more reproducible research. Here we introduce you to Docker and tell you a bit about how to containers are used in running both workflows and notebooks in Terra.
Instructor: Adelaide Rhodes, Senior Computational Associate, Data Sciences Platform, Broad Institute
Materials: Slides; Video

7. Terra case study: Tetralogy of Fallot

We take you in-depth with a real study that was reproduced on Terra, showing you how the data, workflows and analysis were organized to reproduce the scientific findings, illustrating how you can perform an end-to-end analysis in Terra.
Instructor: Anton Kovalsky, Science Writer, Data Sciences Platform, Broad Institute
Materials: Slides; Video; Terra workspace

 

Additional resources

The Data Biosphere

Terra Resources

Running workflows on Terra

Terra's Jupyter Notebooks Environment

Jupyter Notebooks Resources

R Resources

Data wrangling, visualization, and analysis

Developing and (finding the best) R packages

BigQuery Resources

Google Cloud Platform

Chrome

 

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