Projects per cycle
MDAnalysis, 2016 to 2026
View as table
| Projects | |
|---|---|
| 2016 | 0 |
| 2017 | 0 |
| 2018 | 0 |
| 2019 | 0 |
| 2020 | 3 |
| 2021 | 2 |
| 2022 | 2 |
| 2023 | 2 |
| 2024 | 3 |
| 2025 | 4 |
| 2026 | 3 |
PROJECTS
MDAnalysis GSoC projects
19 accepted projects across 7 cycles, 2020 to 2026. Each one links to its contributor, mentors and code.
Projects listed
19
Across 7 cycles
In GSoC 2026
3
4 in 2025
Busiest cycle
2025
4 projects
Mentors named
25
Across all listed projects
First cycle
2020
Latest 2026
Adding Additional Functionality and Enhancements to the Fetcher Module
jauy123
A major goal for MDAnalysis 3.0 is the “support for streaming and cloud stor- age.”1. A natural extension of this object simply adding the ability to...
Interface for post-simulation analysis (“crawling”) of WESTPA simulations
Kunj Sinha
This project aims to implement a WESTPAParser and a WESTPAReader in WESTPA which will expose WESTPA’s HDF5 Framework simulation data as a standard...
Dashboard for tracking MD simulation progress with the new streaming interface
Pardhav Maradani
This project will develop a browser-based, real-time dashboard for molecular dynamics simulations using the new IMDv3 streaming protocol, enabling...
Integrating MDAnalysis streaming analysis within WESTPA propagators
Jamie RoweMentored by Oliver Beckstein, Fiona Naughton, Lillian Chong +2
Weighted ensemble (WE) simulations enhance the exploration of a molecular system’s phase space by running numerous short, parallel simulations and...
Enhancing ProLIF Visualizations: A Hybrid Approach for Automated, Customizable 2D Interaction Layout
Nilay VermaMentored by Cédric Bouysset, Valerij Talagayev
ProLIF’s current 2D interaction diagrams often suffer from overlapping protein residues and tangled edges due to reliance on a default physics engine...
Better interfacing of Blender and MDAnalysis
Pardhav MaradaniMentored by Yuxuan Zhuang, Brady Johnston
Blender is an industry leading open-source 3D modelling and animation software. MDAnalysis is an open-source Python library for analyzing molecuar...
MDAnalysis x ProLIF Project 5: H-Bond interactions from implicit hydrogens
Yu-Yuan (Stuart) YangMentored by Cédric Bouysset, Valerij Talagayev
ProLIF, a tool for identifying protein-molecule interactions in molecular dynamics trajectories, lacks a straightforward method for evaluating...
2D visualization for small molecules
Valerij TalagayevMentored by Richard Gowers, yuxuanzhuang, Cédric Bouysset
The proposed project will revolve around the 2D visualization of chemical molecules. Currently MDAnalysis has a tool, which allows the conversion of...
Zarrtraj: Streaming H5MD trajectories from cloud services into MDAnalysis using Zarr
LawsonMentored by Hugo MacDermott-Opeskin, yuxuanzhuang
Adding support for streaming and cloud storage is one of the major themes of improvement for MDAnalysis 3.0. Achieving this goal will improve the...
Extend MDAnalysis Interoperability with OpenBabel
Luna MorrowMentored by Hugo MacDermott-Opeskin, Xu Hong Chen, Cédric Bouysset
Direct interoperability between molecular dynamics software is critical for enabling collaboration, data transfer and easy use by scientists....
Add Calculations for Self-Diffusivity and Viscosity
Xu Hong ChenMentored by Hugo MacDermott-Opeskin, orion cohen
MDAnalysis provides minimal support for calculating transport properties, measurable values which define the transfer of mass, heat, momentum, or...
Project 5: Implementation of parallel analysis in MDAnalysis
Egor MarinMentored by Oliver Beckstein, Richard Gowers, RMeli +2
The proposal introduces parallel backend based on `dask` for MDAnalysis package. Potentially, it will allow researchers to run analysis of the...
Adding Energy Readers to MDAnalysis
BFedderMentored by Oliver Beckstein, Irfan Alibay, Hugo MacDermott-Opeskin +1
In molecular dynamics simulations, users frequently have to inspect energy-like terms such as potential or kinetic energy, temperature, or pressure....
Context-aware guesser (implementing PDB and Martini guessers)
Aya M. AlaaMentored by Irfan Alibay, Richard Gowers, Jonathan Barnoud +2
MDAnalysis deals with various topologies with different structures, each of which has its specifications for presenting its data. The challenge is...
MDAnalysis module to calculate membrane curvature
Estefania Barreto-OjedaMentored by fiona, Oliver Beckstein, Lily
Elements of differential geometry enable us to quantify the curvature of a surface. The core elements of biological membranes, phospholipids, provide...
A Solvation Module for MDAnalysis
orion cohenMentored by Irfan Alibay, Richard Gowers, Hugo MacDermott-Opeskin
MDanalysis (MDA) is a powerful open-source package for exploring and performing calculations on molecular dynamics trajectories. Despite MDAs broad...
Serialize Universes for parallel
Yuxuan ZhuangMentored by IAlibay, orbeckst, fiona-naughton +1
MDAnalysis is a flexible and relatively fast framework for complex analysis tasks in molecular dynamics (MD) simulations. To achieve a flawless...
From RDKit to the Universe and back
Cédric BouyssetMentored by IAlibay, fiona-naughton, Richard Gowers
The aim of the RDKit interoperability project is to give MDAnalysis the ability to use RDKit’s Chem.Mol structure as an input to an MDAnalysis’...
Trajectory New Generation: the trajectory format for the future of simulation
Hugo MacDermott-OpeskinMentored by Paul Bauer, Richard Gowers, orbeckst
Trajectory storage has always proved problematic for the molecular simulation community, as large volumes of data can be generated quickly....
Data: Google Summer of Code public archive. Official GSoC archive