ViralSim
Very cool and very fun to build!
ViralSim is a cool little project I’ve been working on for about a year now. Essentially, ViralSim simulates viruses moving through populations with a focus on accurate geographic data through an agent-based model. Also, ViralSim involves an older project that focused on identifying transmission clusters (genetically similar sequences from the same location) along with a couple of available analysis metrics for measuring fitness (which I defined as a virus’s ability to propagate through its family tree).
It is pretty cool! You can see a more detailed paper here, and you can find the codebase here. This project was very fun!
Couple points to improve would be connecting fitness with transmission clusters directly. I thought about that for a long time but could not find a logical connection. Something else would be benchmarking along with fitness in real-world viruses. I do quite like how this turned out though!