Jekyll2026-05-22T23:04:34+00:00https://www.mdanalysis.org/atom.xmlMDAnalysisworking with data in the molecular sciencesThe MDAnalysis Teammdanalysis@numfocus.orgGoogle Summer of Code Students 20262026-05-21T00:00:00+00:002026-05-21T00:00:00+00:00https://www.mdanalysis.org/2026/05/21/gsoc-studentsWe’re excited to welcome three contributors to MDAnalysis through Google Summer of Code this year:
@jauy123, @kunjsinha, and @PardhavMaradani.
This marks our seventh consecutive year participating as an independent GSoC organization.
A big thank you goes out to Google for supporting these three exciting projects.
We’re looking forward to getting started!
This project will implement WESTPAParser and WESTPAReader inside westpa/westpa, exposing WESTPA’s HDF5 Framework simulation data as a standard MDAnalysis Universe. Post-simulation analysis currently requires custom boilerplate code via w_crawl which this project will replace with a single command, making the entire MDAnalysis toolkit accessible on WESTPA data.
Kunj is an undergraduate student at PES University, pursuing a Bachelor of Technology in Computer Science and Engineering. He has always had an interest in various fields of science and technology since his early school days. In his free time, he listens to music, plays different musical instruments and enjoys cooking as well.
This project will develop a browser-based, real-time dashboard for molecular dynamics simulations using the new IMDv3 streaming protocol, enabling live monitoring, analysis, and visualization of running simulations. The dashboard will leverage imdclient and MDAnalysis to receive and analyze data streams from running simulations.
Pardhav is an undergraduate student from India pursuing a Bachelors in Computer Science and Engineering from Vellore Institute of Technology (Vellore) and a BS in Data Science and Applications from Indian Institute of Technology (IIT) Madras.
This project intends to add web retrieval functionality to MDAnalysis by augmenting the existing fetcher module. By introducing new fetchers,
it is intended to allow MDAnalysis to download structures and trajectories from external databases such as AlphaFold and the Molecular Dynamics Data Bank by passing downloaded data to the in-built Universe class. Additionally, this project intends to introduce a new suite of functions that is capable of retrieving any molecular data from any database supporting REST API.
Joshua Raphael Uy is a Physics Ph.D student at Arizona State University. He earned a Bachelor of Science in Physics, a Bachelor of Arts in
Mathematics at Miami University in Oxford, Ohio, and a Master in Science in Physics at Arizona State University. He has a bio page and a Linkedin.
To follow this project, you can check out Josh’s blog.
]]>The MDAnalysis Teammdanalysis@numfocus.orgGoogle Summer of Code 20262026-02-19T00:00:00+00:002026-02-19T00:00:00+00:00https://www.mdanalysis.org/2026/02/19/gsoc2026
MDAnalysis has been accepted as an organization for Google Summer of
Code (GSoC) 2026! If you are interested in working with us and you
are new to open source, please read the advice and links below to learn how you can apply to participate in GSoC 2026 with MDAnalysis.
The application window deadline is March 31, 2026 - 18:00 UTC.
As part of the application process you must familiarize
yourself with Google Summer of Code 2026, including eligibility requirements, timelines, and generally how the program works.
We are looking forward to all applications from any new and beginner
open source contributors or students over 18 years old; see a full list of the eligibility requirements in the GSoC FAQ. Projects
are scoped as either 90-hour (small), 175-hour (medium) or 350-hour (large) size. The
duration can be extended from the standard 8 weeks to up to 12 weeks (for small projects), or from the standard 12 weeks up to 22 weeks (for medium or large projects).
For GSoC, MDAnalysis collaborates with other projects that have direct links with MDAnalysis and where it is especially useful to draw on the combined mentoring expertise.
This year, MDAnalysis is joining forces with WESTPA and Molecular Nodes. Applicants who want to work with one of the collaborating projects should familiarize themselves with MDAnalysis and the project that they are interested in. GSoC projects with either WESTPA or Molecular Nodes will be mentored by experts from the collaborating project and MDAnalysis.
Project Ideas
If you have your own idea about a potential project we’d love to work with you
to develop this idea; please write to us on the GSoC with MDAnalysis discussion forum to discuss it there.
We also have listed several possible projects for you to work on. Our
initial list of ideas (see summaries in the table below) contains various
projects of different scope and with different skill requirements. However,
check the ideas page — we might add more ideas after the posting date of
this post.
You must meet our own requirements if you want to be a GSoC
Contributor with MDAnalysis this year (read all the docs behind these
links!) and read the points below for the application process. You must also meet the GSoC eligibility criteria. Our GSoC FAQ collects common questions from applicants.
Participate in a video interview with developers of MDAnalysis and/or one of the partner organizations. You will be invited for interview based on your pre-proposal.
Submit your full GSoC application. You will be invited to submit your application based on your video interview.
Code of Conduct
The MDAnalysis community values diversity and is committed to providing a
productive, harassment-free environment to every member. Our Code of Conduct
explains the values that we as a community uphold. Every community member (and every
GSoC Contributor) agrees to follow the Code of Conduct.
Familiarize yourself with MDAnalysis and relevant partner projects
As a start to get familiar with MDAnalysis and open source development you
should follow these steps:
The MDAnalysis Trailer on YouTube
is a one minute introduction to MDAnalysis.
There are also additional introductory videos available to give you an idea of what problems MDAnalysis is solving.
Complete the Quick Start Guide
Start by installing the MDAnalysis package. We have a Quick Start Guide explaining the basics of MDAnalysis. You should go through it at least once to understand how MDAnalysis is
used. Continue reading the User Guide to learn more.
Learn More About WESTPA and Molecular Nodes
As some of the project ideas represent collaboration between MDAnalysis and other partner software projects, you should follow the recommended steps linked here to familiarize yourself (as relevant) with WESTPA and/or Molecular Nodes.
Interactions and engagement with MDAnalysis
GSoC contributors with MDAnalysis should demonstrate that they have been seriously engaged with the MDAnalysis project (and/or with a relevant partner software project). Submitting a pull request is a great way to know you as a good candidate. As is relevant to the GSoC project idea you are interested in, you should submit your PR in one of the following repositories:
We have a list of easy bugs and suggested GSOC Starter issues to work on in our issue tracker on GitHub. If you want to dive deeper, we encourage you to tackle some of the other issues in our issue tracker or create a new one. We also appreciate contributions which add more tests or update/improve our documentation. Note that some of the GSoC 2026 Project Ideas include related issues that you might want to explore.
We ask you to submit a short pre-proposal so that we can evaluate your understanding of the proposed project. In this pre-proposal you tell us what project you’d like to work on, what you consider the major challenges, and how you plan to solve the problem. MDAnalysis developers will review your proposal and then either invite you to continue with your application and participate in a video interview or tell you that we will not consider your application. Please note that this decision is final, and applicants should only submit one pre-proposal. A rejection is not a judgment on you or your abilities but an assessment of how well you fit the specific requirements of MDAnalysis as a scientific software package — we much rather you spend your energies on contributing to another exciting GSoC project than being rejected later by MDAnalysis.
We require GSoC applicants to submit a pre-proposal that will determine who is then invited to participate in a video interview. If you are invited to participate in an interview and ultimately submit a full application, the pre-proposal will help you gather some of the information you will need to include.
Submit your pre-proposal via our pre-proposal submission formby March 9, 2026. The submission form will go live a few days after this post is available from Feb 28, 2026.
❗Do not use generative AI to develop or write your pre-proposal. We need to hear your ideas and voice.
You are allowed to use AI tools for grammar and spell checking and for translation into English although we are more than happy to read your proposal in your own English words.
You should prepare the following information for your pre-proposal:
Email address
GitHub handle
Real name (optional)
Certify that you did not use AI tools to develop or produce the pre-proposal.
Basic information on your background (e.g., education, relevant experience with MDAnalysis and molecular dynamics or computational physics/chemistry/materials)
Project title
Project size (90h, 175h, 350h)
Problem: Describe the problem to be solved. What is the background? What is the overarching question? You can also comment on why this is an interesting or difficult problem. Clearly define the overall goal of what you want to find out.
Approach: Describe how you are going to reach your goal (i.e., answer the overarching question). Which algorithms are you going to use? Are there any libraries or other packages you want to use? Do you need to research different solutions? Be as concrete as possible; you want to convince your audience that it is feasible to solve this problem and you have an idea how to tackle it.
Objectives: Use a numbered list to state 3–5 measurable non-trivial outcomes that you need to achieve in order to reach the overall goal. These are the milestones that you have to reach; they are possibly dependent on each other. For each objective it must be clear how to decide if you fulfilled it or not. Objectives are formulated in terms of actions and deliverables.
Interactions: Describe the interactions you had with maintainers from MDAnalysis (or WESTPA/Molecular Nodes if you plan on working on a collaborative project). Be specific and link to specific instances of interactions (e.g. Pull Requests) if possible. (500 words)
Participate in a video interview (by invitation)
Applicants who are invited for a video interview will be contacted no earlier than 72 hours after they submit their pre-proposal. During the interview (15 minutes), you will discuss your pre-proposal with 1-2 developers. The video may be recorded for evaluation by other developers/mentors. During the interview, you will be required to share your (full) screen and respond live to questions. The interview may involve live programing and discussions of code sections of MDAnalysis that are relevant for your project. The interview will be conducted using Google Chats or an equivalent video conferencing software.
Submit full application (by invitation)
If you pass the interview stage, you will be invited to submit your full GSoC application through the GSoC site (starting March 16, 2026). We will only review invited applications.
❗Do not use generative AI to develop or write your application. We need to hear your ideas and voice.
You are allowed to use AI tools for grammar and spell checking and for translation into English although we are more than happy to read your application in your own English words.
Final remarks
Submit your pre-proposal before March 9, 2026, but the earlier the better! We will then let you know via the email you provide in the pre-proposal submission form if you have been selected to participate in a video interview and ultimately submit a full application. The GSoC contributor application period opens on March 16, 2026.
Feel free to ask any questions on the discussion forum. We are also happy to chat on our MDAnalysis Discord server in the #gsoc channel (join with the public invitation link). Please note that MDAnalysis as an organization highly values transparency and therefore we strive to conduct all discussions in public forums so please ask questions publicly and not via direct messages or emails.
]]>The MDAnalysis Teammdanalysis@numfocus.orgMDAnalysis Adopts the NumFOCUS Code of Conduct2025-11-07T00:00:00+00:002025-11-07T00:00:00+00:00https://www.mdanalysis.org/2025/11/07/NF-CoCAs part of our ongoing commitment to fostering an open, welcoming, and respectful community, the MDAnalysis project has updated its Code of Conduct and formally adopted the NumFOCUS Code of Conduct. This replaces our previous Code of Conduct, which had been in place since 2017, and brings our community standards into alignment with those of our fiscal sponsor, NumFOCUS.
Our decision to adopt the NumFOCUS Code of Conduct was motivated by a desire to better serve our growing and diverse community through a process that is impartial, transparent, and sustainable. By aligning with NumFOCUS’s framework, all Code of Conduct reports are reviewed by the NumFOCUS Code of Conduct Working Group, a team of trained responders who operate independently of the MDAnalysis team to ensure reports are reviewed, investigated, and advised upon with neutrality.
expected behavior, such as respectful communications and inclusion of diverse perspectives;
unacceptable behavior, including harassment and discrimination;
reporting procedures and contact points for individuals who experience or witness potential conduct violations;
enforcement procedures, namely, that the MDAnalysis Code of Conduct Committee is responsible for enforcement based on recommendations from the NumFOCUS Code of Conduct Working Group.
The Code of Conduct applies to all MDAnalysis project spaces — including GitHub and GitHub Discussions; Discord; LinkedIn; Bluesky; workshops and events; and all other forums associated with MDAnalysis.
Our Commitment
All MDAnalysis core developers have unanimously agreed to adopt the new Code of Conduct and are fully committed to upholding its principles. Our goal is to ensure that the MDAnalysis community continues to be a place where all contributors, users, maintainers, and other community members feel welcomed, valued, and safe. As it takes all of us, and not just core developers, to foster an inclusive environment, all MDAnalysis community members agree to share a common set of core values and act according to these principles in all interactions within our community.
If you have any questions or concerns regarding the Code of Conduct, we encourage you to reach out to the MDAnalysis Code of Conduct Committee. We thank you for joining us on our mission to foster a welcoming and inclusive community!
]]>The MDAnalysis Teammdanalysis@numfocus.orgRelease 2.10.0 of MDAnalysis2025-10-26T00:00:00+00:002025-10-26T00:00:00+00:00https://www.mdanalysis.org/2025/10/26/release-2.10.0We are happy to release version 2.10.0 of MDAnalysis!
This is a minor release of the MDAnalysis library, which means that it
contains enhancements, bug fixes, deprecations, and other
backwards-compatible changes.
Supported environments
This release supports NumPy 2.0+ and offers backwards compatibility
through to NumPy 1.26.0.
Supported Python versions: 3.11, 3.12, 3.13, 3.14.
Note: not all optional dependencies currently work with Python 3.14.
For more help with installation see the installation instructions in the User Guide.
Make sure you are using a Python version compatible with MDAnalysis
before upgrading (Python >= 3.11).
Notable changes
For a full list of changes, bug fixes and deprecations see the CHANGELOG.
Enhancements:
Support for setting custom dt when reading/writing XTC and TRR trajectories (PR #4908)
New parallelization support for the following analyses:
The output precision for LAMMPS DATA files is now set to 10 decimals (PR #5053)
Support for Python 3.10 was removed in line with SPEC 0 (PR #5121)
Bond order and charges inferring code from the RDKit converter has been moved to
a new RDKitInferring module (PR #4305)
Author statistics
This release was the work of 25 contributors, 16 of which are new contributors.
Our new contributors are:
@namiroues
@lexi-x
@BHM-Bob
@yuyuan871111
@jpkrowe
@TRY-ER
@Abdulrahman-PROG
@pbuslaev
@tulga-rdn
@Gareth-elliott
@schuhmc
@gitsirsha
@Pradyumn-cloud
@amruthesht
@gitzhangch
@raulloiscuns
Acknowledgements
MDAnalysis thanks NumFOCUS for its continued support as our fiscal sponsor and
the Chan Zuckerberg Initiative for supporting MDAnalysis under EOSS4 and EOSS5 awards.
]]>The MDAnalysis Teammdanalysis@numfocus.orgUGM 2025 Announcements – Keynote Speakers, Workshop Hosts, and Registration Deadline Extension2025-07-15T00:00:00+00:002025-07-15T00:00:00+00:00https://www.mdanalysis.org/2025/07/15/ugm2025-updatesWe’re excited to share updates for the upcoming 2025 MDAnalysis User Group Meeting (UGM), taking place November 9–11, 2025 at Arizona State University in Tempe, Arizona (USA). This in-person event unites a global community of users, developers, and researchers to discuss advancements in molecular dynamics analysis and to foster collaborations across disciplines. This year’s UGM will feature not only contributed talks from the community, but also insightful talks from our two keynote speakers, Drs. Lillian Chong and Matthias Heyden and hands-on workshops/tutorials. To accommodate continued demand from the community, we are now accepting registrations on a rolling basis.
Meet the Keynote Speakers
Dr. Lillian Chong
Dr. Lillian Chong, Professor of Chemistry at the University of Pittsburgh, leads the Chong Lab, where her team develops cutting-edge tools at the interface of chemistry, physics, and biology to investicate biomolecular dynamics and function. Her research group pioneered using weighted ensemble (WE) simulation techniques to study rare events, such as large-scale conformational changes and protein-protein binding, and for creating implicitly polarized AMBER force fields. Her work garned the 2020 Gordon Bell Special Prize for high-performance computing in COVID-19 research leveraging analyses that would otherwise take years but were achieved in weeks using WE and WESTPA, an open-source software for weighted ensemble path sampling.
Dr. Matthias Heyden
The second keynote, Dr. Matthias Heyden from Arizona State University’s School of Molecular Sciences, brings expertise in modeling solvation dynamics and vibrational energy transport in crowded biomolecular environments. His research integrates realistic atomistic simulations to illuminate solute-solvent interactions and energy transfer. His group has contributed to the development of interactive molecular dynamics (IMD) workflows through tools like IMDClient, enabling real-time streaming and manipulation of molecular trajectories. These capabilities, also showcased in the MDAnalysis IMD workshop materials, open new avenues for exploring simulations dynamically and interactively. This work enhances our understanding of biochemical processes in realistic settings, informing both simulation methodology and experimental interpretation.
Contributed Workshops
Alongside invited presentations, the 2025 UGM will feature community-led workshops that cover a range of tools and methods relevant to the MDAnalysis user base. Confirmed contributed workshops will include sessions from:
These workshops are a great opportunity to learn new skills and connect with fellow developers and researchers in the field.
Registration and Bursary Applications Now Rolling
We encourage all users, from first-time analysts to veteran contributors, to join us this November in-person in Arizona or to follow along with the online recordings. There are limited travel bursaries available. Registration is now accepted on a rolling basis, until participation limits are met. If you’re interested in attending or applying for support, we encourage you to submit as early as possible to maximize your chances of receiving a bursary and securing a spot. Visit the UGM 2025 page for full details and links to the application forms.
We look forward to seeing you there!
— The 2025 MDAnalysis UGM Organizing Committee
]]>The MDAnalysis Teammdanalysis@numfocus.orgGoogle Summer of Code Students 20252025-05-23T00:00:00+00:002025-05-23T00:00:00+00:00https://www.mdanalysis.org/2025/05/23/gsoc-studentsWe are proud to announce that MDAnalysis — in collaboration with Molecular Nodes, ProLIF, and WESTPA —
is hosting fourGoogle Summer of Code (GSoC) contributors: @jpkrowe, @nilay-v3rma, @PardhavMaradani, and @yuyuan871111. MDAnalysis has been accepted as its own organization with GSoC
for the sixth year in a row. We are grateful to Google for granting us the opportunity to get started on these four very exciting projects!
James’ project is a collaboration between MDAnalysis and WESTPA, a toolkit for running Weighted Ensemble simulations. In Weighted Ensemble simulations, many short trajectories are run in parallel and evaluated after each iteration to identify those that have progressed along a predefined coordinate. This analysis step can become a bottleneck, as all trajectories must be loaded and processed before the next iteration can begin. The goal of this project is to use MDAnalysis’ trajectory streaming capabilities to analyze trajectories on-the-fly, reducing analysis overhead and decreasing the time between iterations.
Nilay’s project focuses on improving the 2D interaction visualizations in ProLIF, a tool for analyzing molecular interactions such as protein–ligand and protein–protein binding. He is enhancing LigNetwork plots by implementing graph-based algorithms to automate residue placement, reduce edge overlaps, and improve overall readability. Additionally, he is exploring the integration of visualization approaches from tools like InteractionDrawer and Flareplot to improve the visual representation of interactions. The goal is to create a more user-friendly and informative visualization tool for researchers.
Nilay is a sophomore at Indian Institute of Technology Gandhinagar (IITGN), pursuing a dual major in B.Tech Computer Science and Materials Science. He is passionate about computational materials science, machine learning, and generative AI and its applications.
MDAnalysis has a basic interface with Blender through a popular extension called Molecular Nodes, which allows importing MDAnalysis universes and provides advanced rendering capabilities through a GUI. The ability to script and support advanced visualizations of MDAnalysis results is currently limited. This project attempts to define, prototype and implement various APIs along with an integrated GUI within Blender as part of GGMolVis and Molecular Nodes that will together provide advanced visualization capabilities for MDAnalysis.
Pardhav is an undergraduate student from India pursuing a Bachelors in Computer Science and Engineering from Vellore Institute of Technology (Vellore) and a BS in Data Science and Applications from Indian Institute of Technology (IIT) Madras.
ProLIF, a MDAnalysis/RDKit-based tool for identifying protein-molecule interactions in molecular dynamics trajectories, lacks a straightforward method for evaluating hydrogen bonds when only heavy atoms are present. This project introduces an “implicit hydrogen bond (H-bond) interaction method” directly using heavy atom positions to detect H-bonds. This new feature for ProLIF will help many users (especially, beginner-level programming users) compare their experimental and computational structures without explicit hydrogens.
]]>The MDAnalysis Teammdanalysis@numfocus.orgAnnouncement and Call for Abstracts for MDAnalysis UGM 20252025-04-13T00:00:00+00:002025-04-13T00:00:00+00:00https://www.mdanalysis.org/2025/04/13/ugm2025We are pleased to announce the 2025 MDAnalysis UGM (User Group Meeting), taking place on the 9-11th November, 2025, in Arizona, USA at Arizona State University. Abstracts are welcomed from all areas relevant to MDAnalysis’s work, from scientific applications (e.g., biomolecular simulations, soft matter and materials science, drug discovery and more) to the use and development of open source software and tools for data analysis of molecular simulation output. Additionally this UGM will have sessions focusing on ongoing work towards enabling simulation streaming being undertaken at ASU (see our previous workshop on this topic). When submitting your abstract, you may indicate whether you prefer to give a 15 minute talk, 5 minute lighting talk, or poster presentation.
MDAnalysis strives to be a diverse and welcoming community for all. A limited number of travel bursaries are available to enable those facing financial barriers to attend and present their work. If you would like to apply, please follow the prompts on the abstract submission form.
The deadline for submitting your abstract and/or bursary application is July 15th, 2025. Submissions will be reviewed by the end of July 2025; we will contact applicants shortly after.
Follow the official event page on our website for the most up-to-date information about the UGM. If you have any questions or special requests, please contact ugm@mdanalysis.org.
]]>The MDAnalysis Teammdanalysis@numfocus.orgRelease 2.9.0 of MDAnalysis2025-03-11T00:00:00+00:002025-03-11T00:00:00+00:00https://www.mdanalysis.org/2025/03/11/release-2.9.0We are happy to release version 2.9.0 of MDAnalysis!
This is a minor release of the MDAnalysis library, which means that it
contains enhancements, bug fixes, deprecations, and other
backwards-compatible changes.
Supported environments
This release supports NumPy 2.0+ and offers backwards compatibility
through to NumPy 1.23.2.
For more help with installation see the installation instructions in the User Guide.
Make sure you are using a Python version compatible with MDAnalysis
before upgrading (Python >= 3.10).
Notable changes
For a full list of changes, bug fixes and deprecations see the CHANGELOG.
Enhancements:
Support for Gromacs v2024.4 and v2025 TPR files.
A new “water” keyword for selecting water residues.
Support for distopia 0.4.0 as an optional distance library
backend that now supports many more distance
functions
for all box types (including general triclinic unit cells).
On supported x86-64 platforms, install distopia with
protein=u.select_atoms("protein and not name H*")lipids=u.select_atoms("resname POPC CHOL and not name H*")d=MDAnalysis.lib.distances.distance_array(protein,lipids,box=u.dimensions,backend="distopia")
If you want to see if distopia is available as a backend in a running
program, check that the variable MDAnalysis.lib.distances.HAS_DISTOPIA is
True.
Parallel analysis support for MDAnalysis.analysis.nucleicacids, MDAnalysis.analysis.contacts, and MDAnalysis.analysis.density.
XYZ writer can now write positions up to a user-supplied precision via the precision keyword argument.
Changes:
MDAnalysis.analysis.hole2, MDAnalysis.analysis.psa, and
MDAnalysis.analysis.waterdynamics, are now only available via
optional dependencies (the mdahole2, pathsimanalysis, and
waterdynamics MDAKits). By default these will not be installed, you
will need to install them separately if you wish to use them from
within MDAnalysis.analysis. Please
note that in v3.0 theses modules will be removed completely from the
MDAnalysis core library and you will need to use the MDAKits
directly.
fasteners dependency has been switched to filelock.
Codebase is now formatted with black (version 24)
Author statistics
This release was the work of 10 contributors, 3 of which are new contributors.
Our new contributors are:
@ChiahsinChu
@tanishy7777
@jauy123
Acknowledgements
MDAnalysis thanks NumFOCUS for its continued support as our fiscal sponsor and
the Chan Zuckerberg Initiative for supporting MDAnalysis under EOSS4 and EOSS5 awards.
]]>The MDAnalysis Teammdanalysis@numfocus.orgGoogle Summer of Code 20252025-02-28T00:00:00+00:002025-02-28T00:00:00+00:00https://www.mdanalysis.org/2025/02/28/gsoc2025
MDAnalysis has been accepted as an organization for Google Summer of
Code (GSoC) 2025! If you are interested in working with us and you
are new to open source, please read the advice and links below to learn how you can apply to participate in GSoC 2025 with MDAnalysis.
The application window deadline is April 8, 2025 - 18:00 UTC.
As part of the application process you must familiarize
yourself with Google Summer of Code 2025, including eligibility requirements, timelines, and generally how the program works.
We are looking forward to all applications from any new and beginner
open source contributors or students over 18 years old; see a full list of the eligibility requirements in the GSoC FAQ. Projects
are scoped as either 90-hour (small), 175-hour (medium) or 350-hour (large) size. The
duration can be extended from the standard 8 weeks to up to 12 weeks (for small projects), or from the standard 12 weeks up to 22 weeks (for medium or large projects).
If you have your own idea about a potential project we’d love to work with you
to develop this idea; please write to us on the GSoC with MDAnalysis discussion forum to discuss it there.
We also have listed several possible projects for you to work on. Our
initial list of ideas (see summaries in the table below) contains various
projects of different scope and with different skill requirements. However,
check the ideas page — we might add more ideas after the posting date of
this post.
This year, MDAnalysis is joining forces with three other open source projects to offer even more far-reaching collaborative projects: WESTPA, Molecular Nodes, and ProLIF (an MDAKit).
Expose the predicted local distance difference test metric (pLDDT) via the MDAnalysis topology system
OpenFold or structural prediction tools more generally, Python, Solving parsing problems
@ljwoods2, @orbeckst
Information for prospective GSoC Contributors
You must meet our own requirements if you want to be a GSoC
Contributor with MDAnalysis this year (read all the docs behind these
links!) and read the points below for the application process. You must also meet the GSoC eligibility criteria. Our GSoC FAQ collects common questions from applicants.
If you have been invited to proceed with your application (based on your pre-proposal)have a pull request merged in MDAnalysis or a partner organization.
Code of Conduct
The MDAnalysis community values diversity and is committed to providing a
productive, harassment-free environment to every member. Our Code of Conduct
explains the values that we as a community uphold. Every community member (and every
GSoC Contributor) agrees to follow the Code of Conduct.
Familiarize yourself with MDAnalysis and relevant partner projects
As a start to get familiar with MDAnalysis and open source development you
should follow these steps:
The MDAnalysis Trailer on YouTube
is a one minute introduction to MDAnalysis.
There are also additional introductory videos available to give you an idea of what problems MDAnalysis is solving.
Complete the Quick Start Guide
Start by installing the MDAnalysis package. We have a Quick Start Guide explaining the basics of MDAnalysis. You
should go through it at least once to understand how MDAnalysis is
used. Continue reading the User Guide to learn more.
Learn More About WESTPA, Molecular Nodes and ProLIF
As some of the project ideas represent collaboration between MDAnalysis and other partner software projects, you should follow the recommended steps linked here to familiarize yourself (as relevant) with WESTPA, Molecular Nodes and/or ProLIF.
Submit a pre-proposal
We ask you to submit a short pre-proposal so that we can evaluate your understanding of the proposed project. In this pre-proposal you tell us what project you’d like to work on, what you consider the major challenges, and how you plan to solve the problem. MDAnalysis developers will review your proposal and then either invite you to continue with your application and work on an issue to get involved in the code development or tell you that we will not consider your application. Please note that this decision is final, and applicants should only submit one pre-proposal. A rejection is not a judgment on you or your abilities but an assessment of how well you fit the specific requirements of MDAnalysis as a scientific software package — we much rather you spend your energies on contributing to another exciting GSoC project than being rejected later by MDAnalysis.
We require GSoC applicants to submit a pre-proposal that will determine who is then invited to contribute a pull request for evaluation (see below). If you are invited to contribute a pull request and ultimately submit a full application, the pre-proposal will help you gather some of the information you will need to include.
Submit your pre-proposal via this submission formas soon as possible, but no later than March 21, 2025. You should prepare the following information for your pre-proposal:
Email address
GitHub handle
Real name (optional)
Basic information on your background (e.g., education, relevant experience with MDAnalysis and molecular dynamics or computational physics/chemistry/materials)
Project title
Project size (90h, 175h, 350h)
Problem: Describe the problem to be solved. What is the background? What is the overarching question? You can also comment on why this is an interesting or difficult problem. Clearly define the overall goal of what you want to find out.
Approach: Describe how you are going to reach your goal (i.e., answer the overarching question). Which algorithms are you going to use? Are there any libraries or other packages you want to use? Do you need to research different solutions? Be as concrete as possible; you want to convince your audience that it is feasible to solve this problem and you have an idea how to tackle it.
Objectives: Use a numbered list to state 3–5 measurable non-trivial outcomes that you need to achieve in order to reach the overall goal. These are the milestones that you have to reach; they are possibly dependent on each other. For each objective it must be clear how to decide if you fulfilled it or not. Objectives are formulated in terms of actions and deliverables.
Have a pull request merged (by invitation)
Based on your pre-proposal we may invite you to contribute a pull request.
GSoC contributors with MDAnalysis will need to demonstrate that they have been seriously engaged with the MDAnalysis project and/or the partner software projects (WESTPA, Molecular Nodes, ProLIF) by having a pull request (PR) merged prior to submitting their full GSoC application on the GSoC website. Submit the PR in one of the repositories under the MDAnalysis org or, for projects related to Molecular Nodes (i.e., Project 4) or ProLIF (i.e., Project 5, Project 6, Project 7), in the relevant repositories (MolecularNodes: BradyAJohnston/MolecularNodes, ProLIF: chemosim-lab/ProLIF).
You must have at least one commit merged in one of the organizations to be eligible. Note that the earlier you submit your pre-proposal (which are reviewed on a rolling basis), the more time you may have to work on having code merged!
We have a list of easy bugs and
suggested GSOC Starter issues to work on in our issue tracker
on GitHub. We only accept one GSOC Starter issue per
applicant so that all contributors invited to attempt pull requests get a chance. If you want to dive deeper, we encourage you to tackle some of the other issues in our issue tracker. We also appreciate contributions which add more tests or update/improve our documentation. Note that some of the project ideas include related issues that you might want to explore.
Submit your pre-proposal before March 21, 2025, but the earlier the better! We will then let you know via the email you provide in the pre-proposal submission form if you have been selected to attempt an issue on GitHub and ultimately submit a full application; we strive to inform you of a decision within a week of your submission. The GSoC contributor application period opens on March 24, 2025.
Feel free to ask any questions on the discussion forum. We are also happy to chat on our MDAnalysis Discord server in the #gsoc channel (join with the public invitation link). Please note that MDAnalysis as an organization highly values transparency and therefore we strive to conduct all discussions in public forums so please ask questions publicly and not via direct messages or emails.
]]>The MDAnalysis Teammdanalysis@numfocus.orgMeet our New Core Developers!2025-02-14T00:00:00+00:002025-02-14T00:00:00+00:00https://www.mdanalysis.org/2025/02/14/new_coredevsWe are thrilled to announce that MDAnalysis has elected three new Core Developers to the project: @BradyAJohnston, @marinegor, and @p-j-smith. We thank each of them for the many contributions they have already made to the MDAnalysis project, and look forward to having them help shape the future direction of the project. Keep reading to learn more about Brady, Egor, and Paul, as well as the process behind becoming a Core Developer of MDAnalysis.
Introductions
Brady Johnston (@BradyAJohnston)
I originally did my PhD in structural biology at the University of Western Australia. Starting out doing crystallography, I became interested instead with ways to better visualise molecular data instead of collecting it. I created Molecular Nodes (MN) for cinematic visualisation of molecular data inside of the 3D modelling and animation program Blender. Molecular Nodes relies heavily on MDAnalysis for import and handling of molecular dynamics (MD) datasets, with projects going forward also allowing Blender to become a tool for analysing MD trajectories. I have now left academia and do freelance scientific illustration and development full time. You can contact me on on BlueSky, GitHub, Discord and LinkedIn as @bradyajohnston, or see my website. I’m always excited to chat about anything related to Blender and data visualisation.
Egor Marin (@marinegor)
I started my career as a scientist from macromolecular crystallography, and during my PhD slowly moved towards structural bioinformatics and relevant machine learning methods.
I am currently employed at ENPICOM B.V. as Machine Learning Scientist, and continue contributing to open-source as much as I can.
You can find me as @marinegor almost everywhere, and check out marinegor.dev for some short-form tech posts about my research and open-source work.
Paul Smith (@p-j-smith)
I did my PhD in computational biophysics at King’s College London, using molecular dynamics simulations to study the biophysics of lipid membranes. During my PhD, I began contributing to open-source scientific software, including MDAnalysis. I created LiPyphilic - an open-source Python package for analysing simulations of lipid membranes, built on top of MDAnalysis.
I’m now a Research Software Engineer at University College London, working on projects broadly related to medical imaging. I’m excited to join the Core Developer team, and always happy to chat about biophysics and open-source software. You can get in touch with me on LinkedIn or GitHub.
Becoming a Core Developer
MDAnalysis is a dynamic, ever-changing community, with many new contributors joining continuously. It is important to us that the leadership of MDAnalysis reflects the community that builds it. Therefore, the MDAnalysis Core Developer team regularly holds elections for new core developers, as described in our governance section. While this voting process is conducted in private, we are publishing and formalizing what we consider when voting, in the interests of transparency.
Firstly, potential Core Developers are identified based on their past contributions to MDAnalysis and potential to move the MDAnalysis project forward. Contributions we account for include both those that are technical in nature, and also less quantifiable ones which add value to the MDAnalysis organization. Examples include:
Mentoring either in an official capacity (e.g., Google Summer of Code) or unofficially (e.g., through reviewing PRs)
Promoting a culture which reflects the core values of MDAnalysis, as detailed in our Code of Conduct (e.g., promoting diversity and inclusion within our community)
Involvement in ongoing community projects (e.g., applying for grants) and liaising with other organisations, such as our fiscal sponsor, NumFOCUS
If a candidate has shown a history of participating in these activities, they are put forward for election. The Core Developer team reviews the candidate and votes on whether or not they wish to elect an individual, following our standard voting procedures.
Finally, being an active Core Developer requires some amount of active participation in meetings, decisions, and other administrative business. As MDAnalysis does not have any guaranteed long-term funding, this work is usually unpaid. Therefore, the final decision to accept or decline the election is left to the developers themselves: do they have the time and willingness to keep contributing?
If you are interested in becoming a Core Developer, we highly encourage you to participate in some of the activities listed above, especially reviewing pull requests and mentoring other developers. Learn more about the many roles MDAnalysis community members take on to move the project forward on our MDAnalysis team page, and reach out to us on our GitHub discussions forum or Discord server (join the server using the invitation link, https://discord.gg/fXTSfDJyxE. On our end, the MDAnalysis Core Developer team will, to the best of its abilities, aim to offer mentorship and other opportunities to people who express an interest in becoming a Core Developer.
Being a Core Developer is work, but it’s also a fantastic opportunity to work with and for a wonderful and welcoming community. As part of our mission, we welcome anyone who cares for this community and wants to help it grow.
