PyRosetta JupyterNotebooks Teach Biomolecular Structure Prediction and Design · 2020-05-02 ·...
Transcript of PyRosetta JupyterNotebooks Teach Biomolecular Structure Prediction and Design · 2020-05-02 ·...
PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design
Students can access the PyRosetta workshops in Google Colaboratory
Kathy H. Le1, Jared Adolf-Bryfogle2, Jason C. Klima3,4, Sergey Lyskov1, Jason Labonte1,5, Steven Bertolani6, Shourya S. Roy Burman1, Andrew Leaver-Fay7, Brian Weitzner3,4, Jack Maguire7, Ramya Rangan8, Matt A. Adrianowycz8, Rebecca F. Alford1, Aleexsan Adal1, Morgan L. Nance1, Yuanhan Wu8, Jordan Willis2, Daniel Kulp8, Rhiju Das9, Roland L. Dunbrack, Jr.10, William Schief2, Brian Kuhlman7, Justin B. Siegel6, Jeffrey J. Gray1*
Student version Notebooks are automatically generated with nbgrader tool
Instructor version
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Student version
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Keyword Index and ToC are automatically generated with nbpages tool
Jupyter Notebook Workshopsnbpages
Keyword Index Table of Contents
Topics in The New Notebooks
Multimedia examples in PyRosetta Notebooks
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Download PyRosetta package and workshops from GitHub Repository.
Follow instructions in Chapter 1 to configure PyRosetta with Google Colaboratory (~12 min).
Access PyRosetta Notebooks in Google Colaboratory:
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Solution: Hands-on learning with PyRosetta
Goal: to add compelling and relevant multimedia to the set of Jupyter Notebook workshops (Clark & Mayer, 2016)
Jupyter Notebooks:
Shareable web application that supports live code, equations, visualization, and text
Google Colaboratory:
Free Jupyter Notebook environment that requires no setup and runs entirely on the cloud
Acknowledgements
1Johns Hopkins University, 2The Scripps Research Institute, 3University of Washington, 4Lyell Immunopharma, 5Franklin & Marshall College, 6University of California, Davis, 7University of North Carolina at Chapel Hill, 8Wistar Institute, 9Stanford University, 10Fox Chase Cancer Center, *Corresponding author: [email protected]
SummaryHands-on learning with PyRosetta:1. Google Drive-based• Familiar to most students• No local machine setup necessary
2. Adaptable for class or independent learning3. Interactive exercises and multimedia4. Easily expandable by adding more notebooksMoving GIF from Chapter 5.01:
High-Resolution MoversSchematic from Chapter 12:
Working with Antibodies
Schematic from Chapter 2.08: Visualization
and pyrosetta.distributed.viewer
Goal: to add compelling and relevant multimedia to the set of Jupyter Notebook workshops
Jupyter Notebooks:Shareable web application that supports live code, equations,
visualization, and text
Google Colaboratory:Free Jupyter Notebook
environment that requires no setup and runs entirely on the cloud
Part II: Advanced10. Working with Symmetry
11. Working with Density12. Working with Antibodies
13. Carbohydrates14. RNA Basics
15. Membrane Modeling16. Running PyRosetta in Parallel
Part I: Introduction1. How to Get Started2. Intro to PyRosetta
3. Rosetta Energy Score Function4. Intro to Folding
5. Structure Refinement6. Intro to Packing & Design
7. Protein Docking8. Ligand Docking9. Loop Modeling
Need for Interactive Teaching MaterialFinding ways to train people in molecular modeling is a longstanding problem, but certain challenges remain.
100,000+ downloads of print material12,000+ lecture video views in ~4 years
Beginner Intermediate Advanced
Rosetta REU C++ BootcampPython Bootcamp XML docs
Cyrus GUI
Technical Challenges
• Need for constantly-updated material
• Personal computer incompatibility
• Difficult for students to independently set up software
Pedagogical Challenges
• Need for multimodal engagement (Sankey, et al., 2010)
• Need material for active learning (Berge, 2002)
• Self-paced learning vs. classroom setting
Links:GitHub Repository
Preprint
Links:GitHub Repository
Preprint
We would like to thank the JHU Center for Educational Resources, NIH, NSF, and Rosetta Commons for funding and support. We would also like to thank Jeffrey Kantor for his advice and insight.
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