Google Season of Docs 2019 Technical Writer

Google Season of Docs 2019

This year MDAnalysis is hosting Lily Wang (@lilyminium on GitHub) for the first iteration of Google Season of Docs. She will work with us over the coming months on a user guide for MDAnalysis, structured by topic.

Lily Wang: A User Guide for MDAnalysis

MDAnalysis is a library for the analysis of computational (primarily molecular dynamics, i.e. MD) simulations. Frequently these analyses are rare, novel, or individual enough that they are not immediately available as a predefined function within MDAnalysis. MDAnalysis provides a toolkit for interacting with simulations and constructing new analyses. Lily will create a high-level user guide structured by topic. This user guide will describe the building blocks of the data structures, analysis, topologies, and more. It will be targeted at a general audience; molecular dynamics users will be able to see the machine abstraction and technical considerations (e.g. MemoryReader) under the hood, while developers will be able to gain an understanding of the scientific background.


Lily Wang is a Ph.D. student at the Australian National University, Canberra. She aims to improve various aspects of molecular dynamics simulation over the course of her degree. During GSoD, she hopes to refine her technical writing skills while contributing to a package that she very much appreciates. In the tattered remnants of her free time, she enjoys reading and wandering around mountains. You can follow her progress on GSoD (and reading) on her blog.

@richardjgowers @orbeckst (mentors)

Google Summer of Code Student 2019

We are happy to anounce that MDAnalysis is hosting one GSoC students for NumFOCUS this year, Ninad Bhat (@NinadBhat) on GitHub).

Ninad Bhat: Better Periodic Boundary Handling

Ninad Bhat

Molecular simulations are predominantly ran under periodic boundary conditions, i.e., upon leaving one face of the simulation volume, you re-enter in the opposite face. This can lead to molecules being split over the periodic boundary, which requires rectification before performing calculations. In this project, Ninad will implement wrapping and unwrapping functionality in the various AtomGroup methods that use the position of particles, e.g., the calculation of the center of mass. In order to improve performance, the wrapping and unwrapping methods will be implemented in Cython.

Ninad is a senior undergraduate at IIT Bombay. He is working with Phase Field Modelling for his master thesis and has also used molecular dynamics for some of his projects. He has been contributing to different open source projects since 2016 and credits most of his programming knowledge to it. During GSoC, he aims to improve his software development skills while also getting a deeper understanding of molecular dynamics.

Ninad will describe his progress on his blog.

@jbarnoud @richardjgowers @micaela-matta @orbeckst (mentors)

Google Season of Docs 2019 with MDAnalysis

Google Season of Docs 2019

MDAnalysis was accepted for Google Season of Docs 2019. We are proud to be one of 50 participating open source organizations, which span all reaches of open source and includes the Wikimedia Foundation, NumPy and SciPy, the CERN High Energy Software Foundation, Drupal, Arduino, LLVM Compiler Infrastructure, and many more outstanding projects that really have been moving the open source community forward.

We would love to have a technical writer work with us to improve our documentation. If you want to work with scientists that write code to do science at the molecular scale then please contact us on the developer list.

Apply now. The deadline for applications is June 28, 2019 at 18:00 UTC.

More about Projects and MDAnalysis

Our recent post on our GSoD application explains more of the background and summarizes our project ideas.

You can find detailed project ideas on our wiki.

We also have a Frequently Asked Questions for GSoD with MDAnalysis, which is being continuously updated.

Written by scientists for scientists

MDAnalysis is a project written by scientists for scientists and is currently used for cutting edge research around the world. A writer with MDAnalysis will learn about the technical aspects of creating docs for open source code (such as documentation generation with Sphinx, continuous integration-based workflows and distributed development with git via our GitHub source code repository) and also about the science that MDAnalysis enables. Our developers have published many scientific publications that used our library or described innovative new methods that were implemented in MDAnalysis. A writer will interact with these accomplished scientists and learn about the science: How molecules are simulated (e.g., biomolecules such as proteins and DNA or novel materials) and how scientists analyze such simulations in order to better understand the world at the microscopic scale.

The video shows the result of a molecular dynamics simulation in which a sodium ion (magenta sphere) together with water molecules (red/white “L” shapes) bind to a protein (shown in cartoon representation as blue and green ribbons), a process that is important in maintaining the health of cells in the body. The MDAnalysis package enables us to write code which can perform calculations on these results, here allowing us to quantify the interaction between the ion and the protein and generate fundamental understanding of important processes in living beings.


If you have any questions or if you want to work with us please write to us on the developer list.

@orbeckst, @richardjgowers