Imperial College Research Software Community Newsletter - December 2020

Welcome to our December 2020 Research Software Community newsletter. This month’s newsletter marks two full years of newsletters since our first edition in January 2019. The holidays are almost upon us, as is the end of what’s been a challenging year for everyone. I recall attending my last in-person research software-related event back at the end of February. Even then, it was almost impossible to imagine how different life would become in just a few weeks’ time.

In spite of the many difficulties, many of us have been kept very busy with research, writing software, teaching and attending online events. I know I, for one, will be very grateful for the opportunity to have a break from my computer screen once the holidays arrive!

With many traditionally in-person events, workshops and teaching activities moving online, it’s been amazing to see how much we can achieve working remotely using the tools that, in many cases, were already available, but which have rapidly advanced over recent months. While this will never be quite the same as having the opportunity to meet and work with colleagues and collaborators in person at meetings and conferences both locally and internationally, many of us have probably also observed benefits from things moving online. Indeed, workshops and training activities that would otherwise have been run in-person, attracting a mostly local group of attendees, now have the potential to reach out to a much larger international audience. RSEs and researchers who may not otherwise have been in a position to attend an in-person event as a result of the time commitment required, a lack of travel funding, etc., have seen new opportunities to develop their skills and grow their research network. Hopefully we can ensure that these opportunities are not lost as we eventually look to return to the types of event participation that have been more familiar to us in previous years.

On behalf of the Research Software Community committee, wishing you all a relaxing and refreshing break and all the best for 2021 where things will hopefully begin to return to a more familiar way of life as the year progresses.

Dates for your diary

RSE Bytes


Blog posts, tools & more

Research Software of the Month

Our Research Software of the Month for December is, in fact, a collection of software! We’re highlighting a series of tools developed by members of the MRC Centre for Global Infectious Disease Analysis (GIDA) at Imperial and their RSE team Reside-IC.

Together, the tools odin, dust and mcstate, along with some additional related tools, are used in the simulation of stochastic state space models, as described in a recent paper highlighted in this tweet. They are being used to support the Centre’s COVID-19 modelling efforts.

odin provides a domain specific language for describing sets of ordinary differential equations. Its power lies in the fact that it looks like R code and should appear familiar and accessible to R developers while being compiled to C to provide the speed and efficiency required when solving large quantities of complex mathematical equations.

dust offers an R interface for the parallel execution of stochastic models, written in C++ or in odin. It provides a parallel random number generator and distribution functions, and operates between layers of other tools to enable them to take advantage of parallel execution with repeatable randomness.

mcstate builds on dust to provide statistical support through particle filtering and Markov chain Monte Carlo (MCMC) functions.

Together, this stack of packages, along with odin.dust provides a flexible base for parallel statistical calculations which is being leveraged by a series of tools developed at MRC GIDA to support their COVID-19 modelling work. These tools include sircovid and squire.

If you have questions about these tools, you can get in touch with John Lees or Rich FitzJohn.

Some reminders…

RS Community coffee continues weekly via Zoom - normally on Friday afternoons at 3pm but check our Slack workspace for exact times and connection details. Please note that there will be no RS Community coffee this Friday (18th December) and we’ll restart on Friday 8th January.

The Slack workspace also features an #OpenFOAM channel where regular code review sessions are announced (amongst other CFD-related discussions…)

See the Research Computing Service’s Research Computing Tips series for a variety of helpful tips for using RCS resources and related tools and services.

Get in Touch, Get Involved!

Drop us a line with anything you’d like included in the newsletter, ideas about how it could be improved… or even offer to guest-edit a future edition!

If you’re reading this on the web and would like to receive the next newsletter directly to your inbox then please subscribe to our RSE Community Mailing List here.

That’s all for this month and for 2020. Thanks to everyone who provided content for this edition. Happy holidays and all the best for 2021.

This issue of the Research Software Community Newsletter was edited by Jeremy Cohen. All previous newsletters are available in our online archive.