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MDAnalysis Workshop @ PRACE / SURF

MDAnalysis will be delivering a 3 half-day remote (online) workshop hosted by PRACE / SURF on the 26-28th of May 2021.

The workshop will include both lecture and practical portions. We will cover topics including:

  • The fundamentals and basics of MDAnalysis
  • How to use existing analyses
  • How to write your own analyses
  • Parallel analysis in an HPC setting (using SURFsara supercomputing facilities)
  • Advanced functionality such as universe construction and transformations

The workshop is aimed at users in academia and industry who are already familiar with Python and molecular dynamics. We will have separate sessions at different levels, ranging from introductory to advanced use. MDAnalysis developers will be present to help you during practical portions of the sessions and to answer your questions about how to work productively with MDAnalysis. We will also be holding office hours for extended tutoring – ask us for help with the design of your own workflows!

Register soon (places limited)

The workshop is open to everyone, but places are limited. Apply early!

For more information and the registration form, please see the workshop overview website.

MDAnalysis Discord Server

We created the MDAnalysis Discord server for users and developers of MDAnalysis to talk and hang out, as an additional avenue to participate in our community.

Join us!

In order to join, use the sign-up link https://discord.gg/fXTSfDJyxE.

By joining the MDAnalysis Discord Server you agree to our Code of Conduct.

MDAnalysis Discord

First steps

We encourage you to introduce yourself in the #introductions channel. Please include anything you’d like us to know – for example, if you have a preferred pronoun or a GitHub account!

For discussions around using MDAnalysis, go to #using-mdanalysis and for development — you guessed it — #developing-mdanalysis.

Google Summer of Code 2021

Google Summer of Code with
MDAnalysis 2021

MDAnalysis has been accepted as an organization into Google Summer of Code 2021! If you are a student who is interested in working with us this summer, please read the advice and links below and write to us on the mailing list.

We are looking forward to all applications from interested students (undergraduate and postgraduate).

The application window deadline is April 13, 2021 11:00 (Mountain Standard Time). As part of the application process you must familiarize yourself with Google Summer of Code 2021.

If you are interested in working with us please read on and contact us on our mailing list. Apply as soon as possible; the application window opens on March 29, 2021.

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 developer list to discuss it there.

We also have listed several possible projects for you to work on, on our wiki. Our initial list of ideas (see summaries in the table below) contains 6 projects at different levels of difficulties and with different skill requirements. However, check the ideas page — we might add more ideas after the posting date of this post.

You don’t need to have all the skills that we are listing, although that helps, of course. But you need to demonstrate to us that you’re able and keen to learn anything that you don’t know yet, and we will be happy to help you learn during your project with us.

project name difficulty description skills mentors
1 Molecular volume and surface analysis easy use an existing package for molecular surface area calculations to build a new analysis module Python, MDAnalysis.analysis @orbeckst, @IAlibay, @hmacdope
2 Generalise Groups medium Generalise concept of groups Python @lilyminium, @fiona-naughton, @richardjgowers, @IAlibay
3 Cythonisation of AtomGroup easy Cythonise AtomGroup for use with C/++ Python, Cython, C/++ @richardjgowers, @hmacdope
4 Extend MDAnalysis Interoperability medium Extend converters module to other relevant packages Python @lilyminium, @IAlibay, @fiona-naughton, @hmacdope
5 General unit cell representation easy change unit cell representation to keep track of box rotations and so improve analysis of simulations under periodic boundary conditions Python @orbeckst, @fiona-naughton

Information for Students

You must meet our own requirements if you want to be a student with MDAnalysis this year (read all the docs behind these links!). You must also meet the eligibility criteria. Our GSoC FAQ collects common questions from students.

The MDAnalysis community values diversity and is committed to providing a productive, harassment-free to every member. Our Code of Conduct explains the values that we as a community uphold. Every member (and every GSoC student) agrees to follow the Code of Conduct.

As a start to get familiar with MDAnalysis and open source development you should follow these steps:

Complete the Quick Start Guide

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.

Introduce yourself to us

Introduce yourself on the mailing list. Tell us what you plan to work on during the summer or what you have already done with MDAnalysis.

Close an issue of MDAnalysis

You must have at least one commit in the development branch of MDAnalysis in order to be eligible, i.e. you must demonstrate that you have been seriously engaged with the MDAnalysis project. We have a list of easy bugs and suggested GSOC Starter issues to work on in our issue tracker on GitHub. We also appreciate if you write more tests or update/improve our documentation.

We recommend you start your application by working on an issue. It will give you a better understanding of MDAnalysis as a project and improve the quality of your application.

To start developing for MDAnalysis have a look at our guide on contributing to MDAnalysis and write to us on the mailing list if you have more questions about setting up a development environment or how to contribute.

@IAlibay, @orbeckst, @richardjgowers, @fiona-naughton, @hmacdope, @lilyminium