I’m here to recruit some help from the open-source, scientific python community!
Nextstrain (from Trevor Bedford’s lab) is an open-source project that does real-time tracking of pathogen evolution around the world. You may have seen this project on Twitter—they have quickly become one of the world’s best resources for tracking the evolution of SARS-CoV-2 (virus that causes COVID-19).
They need help! I spoke with Colin Megill, a research scientist from the Bedford lab, and he said an immediate need they have is optimizing Nextstrain’s backend library, augur. It’s in pure Python and includes the phylogenetic models and bioinformatics calculations that power Nextstrain.
Augur could use a significant speed-up. Colin said the expertise of OSS/Scipy ecosystem to optimize their calculations would be huge. If you scan the codebase and have ideas for improving Augur’s efficiency, open an issue there and start a discussion that might lead to PR. Further, they would love some contributors from this group to help them address issues open on the repo. PRs, of course, are welcome. This is a really tangible way in which we, OSS developers, can get involved in tools that directly translate to impact on the current COVID-19 crisis.
You shouldn’t need prior knowledge about bioinformatics or phylogenetics to help—just some Python chops. They have some tests and documentation that can help us get started.
To summarize their two immediate needs:
- Help address any open issues in Augur
- Scan Augur’s codebase and see if we can improve its speed.
I know this isn’t a specific question for the help desk, but I think directing some OSS contributors their way would greatly impact the world.
Reach out if you have any questions. Thanks, all!
Project Jupyter | Cal Poly