18 Aug 2026
We are excited to announce a two-day, in-person Molecular
Nodes workshop at
King’s College London on September 17–18, 2026. Registration is
free, with 30 spots available — apply by September 4, 2026.
What Is Molecular Nodes?
Molecular Nodes
(MN) is an add-on for Blender, the
industry-leading open-source 3D visualisation and animation program,
that brings structural biology data into Blender. MN is built on top of
MDAnalysis and can import structures from
.pdb and .mmCIF files, molecular dynamics trajectories and
topologies from a range of simulation packages, and density data from
cryo-EM and cryo-ET in formats such as .map and .star. Once loaded,
this data can be styled in highly customisable ways, animated from
static crystal structures, and played back as full trajectories — all
using Blender’s rendering engine.
Workshop Programme
Day 1 (September 17, 10:00–17:00): Learn the basics of working in
Blender, importing molecular data (.pdb, .cif, MD simulations), and
building animations from it. No prior Blender or Molecular Nodes
experience is required.
Day 2 (September 18, 10:00–15:30): Using the skills from Day 1, you
will work on your own simulation data to produce images and animations,
supported by our instructors.
Details
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Dates: September 17–18, 2026
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Location: King’s College London, Strand Campus
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Cost: Free! Light lunch and coffee breaks provided.
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Capacity: 30 spots (first-come first-serve, with a waitlist)
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Application deadline: September 4, 2026, 23:59 BST
What to bring:
- Laptop (the more powerful the GPU, the better)
- Laptop charger (you will run out of battery)
- External 3-button mouse (strongly encouraged, not required)
- Your own simulation data (optional)
Apply Now
Apply via the registration form on Luma.
Registration requires approval and closes on September 4, 2026.
Questions? Reach out to
[email protected].
We hope to see you there!
10 Aug 2026
Release 2.10.0 of MDAnalysis introduced support for interactive MD (IMDv3) stream reading using the IMDReader and the imdclient package. This allows analyzing MD simulation trajectories live while they are being generated and thus enabling analysis of sub-picosecond dynamics in trajectories.
As part of a Google Summer of Code (GSoC) 2026 project, we built a new tool called mdadash (short for ‘MDAnalysis Dashboard’) that provides a browser-based real-time dashboard for monitoring, tracking and analyzing running MD simulations using this new IMDv3 streaming interface.
The dashboard provides an interactive GUI for defining and running real-time analyses. There is support for per-frame observables and buffered, time-dependent analyses along with live visualization of analysis results as real-time plots. Custom user-defined analyses are also supported through built-in Notebook functionality.
Workshop Overview
The program will run from 9:30 am to 11:30 am Pacific time (UTC 16:30 – 18:30) on Thursday, August 20th. The workshop will introduce mdadash, demonstrate its various features, use cases and how it can be customized for your own analysis needs. The interactive activities will allow participants to try out the dashboard in an easy-to-use workshop environment.
Registration
Attendance at this workshop will be free, and we encourage anyone with an interest in attending to register below.
Register
Workshop materials
All materials are made available in the github.com/PardhavMaradani/mdadash-mini-workshop-2026 repository.
Prepare for the interactive workshop activities by following the setup instructions.
If you have any questions or special requests related to this workshop, you may contact the organizing committee.
21 May 2026
We’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.
You can find Kunj on Github and LinkedIn.
To keep up with his work, you can check out his blog.
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.
You can find Pardhav on GitHub @PardhavMaradani.
To see updates on this project, you can check out his blog.
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.
— @amruthesht @BradyAJohnston @HeydenLabASU @jeremyleung521 @ltchong @nilay-v3rma @orbeckst @talagayev @yuxuanzhuang @IAlibay @jennaswa (@MDAnalysis/gsoc-mentors and org admins)
