MDAnalysis, in collaboration with the Thomas Young Centre, the JCMaxwell Node of CECAM, and CCPBioSim, will deliver a hybrid workshop on an Introduction to Molecular Dynamics Trajectory Analysis using MDAnalysis. The workshop will take place at University College London (United Kingdom) and online May 10, 2024 from 09:00 - 17:00 GMT.
Places are limited, so registration is required before the deadline, April 9, 2024. There is a £10 fee for in-person registration, which includes lunch (but not travel or accommodation). Due to high demand, the online spaces are already full. If you are unable to join us in person, we encourage you to check out the recording after the event on the MDAnalysis YouTube channel.
Further details and a link to register are available on the main event page.
There are exciting updates to announce regarding the 2024 MDAnalysis UGM (User Group Meeting), taking place August 21-23, 2024 in London, UK. Keep reading to learn more about the exciting talks you can expect from experts in the molecular dynamics simulations space, and a deadline extension to make sure you have time to submit your own abstract for giving a talk or presenting a poster during the UGM.
Keynote Speakers
We are proud to introduce two fantastic keynote speakers for the UGM: Dr. Antonia Mey and Dr. Francesca Stanzione! Read more about them and their work below.
Dr. Antonia Mey
Dr. Francesca Stanzione
Abstract Deadline Extended to April 15, 2024
The deadline for submitting abstracts to give a 15-minute talk, 5-minute talk, and/or poster presentation is extended to April 15, 2024. This extension also applies to travel bursary applications. If you would like to present your work in any area relevant to MDAnalysis (e.g., scientific applications, open source software, tools for molecular simulations data analysis, etc.), make sure to fill out the short abstract submission form. Applicants will be informed whether their abstract has been accepted shortly after the April 15th deadline.
We look forward to reviewing your abstracts and learning more about the work you have done with MDAnalysis!
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).
The application window deadline is April 2, 2024 - 18:00 UTC.
As part of the application process you must familiarize
yourself with Google Summer of Code 2024.
If you are interested in working with us please read on and contact us
on our GSoC with MDAnalysis discussion forum. Potential GSoC
Contributors are expected to familiarize themselves with application
requirements and mentoring organizations as soon as possible. It’s
also never too early to discuss application ideas with us!
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 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.
Our experience shows that having the listed skills increases the
chances that a project will be completed successfully, so we use them
as part of our decision criteria in choosing 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 eligibility criteria. Our GSoC
FAQ collects common questions from applicants.
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 member (and every
GSoC Contributor) agrees to follow the Code of Conduct.
Familiarize yourself with MDAnalysis
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.
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 attempt a pull request (see below). If you are invited to attempt 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 15, 2024. 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 (if you are invited to based on your pre-proposal)
GSoC contributors with MDAnalysis will need to demonstrate that they have been seriously engaged with the MDAnalysis project by merging a pull request prior to submitting their full application on the GSoC website.
You must have at least one commit in the development branch of MDAnalysis in
order 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.
Submit your pre-proposal before March 15, 2024, 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 18, 2024.
