GSoC 2026 Application Benchmarking and Performance Optimization Project 3

[yassinalamelden]

Hi MDAnalysis community!
My name is Yassin, and I am a computational biology research intern at Manipal University, Mahe, India. I have just submitted my GSoC 2026 proposal for Project 3: Benchmarking and Performance Optimization and wanted to introduce myself to the community.
My Background:
My current research involves building a unified Python framework for HP model protein folding simulations, implementing Genetic Algorithms and Simulated Annealing across 2D square, 2D triangular, and 3D cubic lattices. The work involves heavy NumPy-based numerical computation, performance profiling and optimization of iterative simulation loops, energy benchmarking against known optimal values, and TensorFlow-based GPU acceleration. Through this, I have developed hands-on experience with exactly the kind of performance challenges that Project 3 addresses.
Why Project 3:
After reading through the project ideas page and exploring the benchmarks repository and issues #1023, #1721, and #4577, I believe this project is the most natural extension of my current work. The lack of comprehensive ASV coverage is a clear gap that I feel well equipped to address, and I am genuinely excited about contributing to the MDAnalysis 3.0 performance roadmap.
My proposal covers:

Expanding ASV benchmark coverage for core library functionality including Universe creation, AtomGroup operations, and coordinate I/O
Benchmarking frequently used analysis modules including RMSD, RMSF, hydrogen bond analysis, and RDF
Systematic performance history analysis to produce a prioritized bottleneck report
Developer documentation and benchmarking tutorial
Stretch goal: implementing at least one concrete optimization

I am currently exploring the codebase and would love any early feedback or guidance from the mentors @orbeckst , @yuxuanzhuang, and @talagayev . I am also happy to make small contributions while waiting for the review period — please point me to any Good First Issues that would be relevant.
Looking forward to engaging with the community!
— Yassin

[BradyAJohnston]

Hi Yassin. For GSoC we require a pre-proposal among other things, outlined in out GSoC 2026 blogpost: https://www.mdanalysis.org/2026/02/19/gsoc2026/

This does mean that you won't be eligible for GSoC in 2026 as the pre-proposal deadlines have passed, but we welcome contributions outside of the GSoC program if you would still like to contribute!

[yassinalamelden]

Hi @BradyAJohnston ,
Thank you for the clarification! I completely understand and I appreciate you taking the time to explain.
I would love to contribute to MDAnalysis outside of GSoC. I am genuinely interested in the project and eager to start.
Looking forward to being part of the community!