20 Mar 2021
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.
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.
09 Mar 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
|
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
10 Sep 2020
Google Summer of Code 2020 wrapped up! It was a very
successful GSoC Summer for MDAnalysis with
three great projects. Even more importantly, we got
to engage with three outstanding students: Hugo MacDermott-Opeskin,
Yuxuan Zhuang, and Cédric Bouysset.
You can read more about their projects in their blog posts:
Finally, a big thank-you to our GSoC mentors: @IAlibay, @acpmnv,
@fiona-naughton. Their constant and enthusiastic engagement was
crucial to the success of our students.
— Org Admins (@richardjgowers, @kain88-de, @orbeckst)