Team:Virginia/Contribution
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Contributions
Index:
Giving to iGEM's Future
Introduction
Through our work on modeling and human practices this year, we have created resources to help future iGEMers succeed in their research.
Developing ProtKit
Our modeling team developed ProtKit, an open-source command-line bioinformatics tool for working with protein structure-encoding files. ProtKit can be downloaded as an executable file from GitHub and run on any Windows machine to combine, manipulate, and analyze Protein Data Bank (.pdb) files. The source code can be viewed on GitHub.
Installing AlphaFold on Rivanna
Upon the public release of AlphaFold on July 15th, we worked with Ruoshi Sun, PhD at UVA Research Computing to get AlphaFold up-and-running on Rivanna, UVA's primary supercomputer. Through more than a week of downloading from overtaxed servers and troubleshooting path issues, we got AlphaFold up-and-running on Rivanna's GPU partition. Because of our work, future researchers at the University of Virginia, including future members of Virginia iGEM, will be able to enjoy AlphaFold's unrivaled accuracy as a structural biology research tool. UVA Research Computing published the article "Breaking News: AlphaFold is now available on Rivanna!" showcasing some of our early results protein structure prediction results.
Recording Tutorial Videos
In collaboration with our human practices team, our wet lab and modeling teams made introductory tutorial videos teaching future iGEM researchers about important synthetic biology lab techniques, protein databases, and ProtKit. The videos are publicly available on YouTube, as well as on the Public Engagement page of this wiki.
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