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.
Applications are now open for the 16-week Open Life Science mentoring and training programme. A Q&A webinar will take place on the 4th January 2021 and the deadline for applications is January 11th 2021. The programme is being run by two of the Software Sustainability Institute’s Fellows and further details are available on the Applications section of the OLS web page.
SORSE (the Series of Online Research Software Events) is continuing into 2021 and they already have several events lined up. On Monday 11th January, 15:00-16:30 there will be a panel discussion “Research Software and the Modelling of COVID-19 in the UK”. On Tuesday 26th January, 14:00-15:00 there will be a pair of talks - My project expired and my team left, so let’s rewrite all the software from scratch and Applying Scrum to Research Software Projects. Registration is now open for both these events.
The Call for Papers for the 2021 International Workshop on Software Engineering for Computational Science (SE4Science21) is now open. The submission deadline is in late January (final date TBC). This year the workshop is being held in conjunction with the International Conference on Computational Science (ICCS21), 16th-18th June 2021.
Collaborations Workshop 2021 (CW21) will take place online from Tuesday 30th March to Thursday 1st April 2021. Registration is now open, as is the call for submissions for mini-workshops and demos - the deadline for submissions is 31st January 2021.
The Software Sustainability Institute’s (SSI) 2021 Fellowship Programme is now open for applications. The deadline for application submissions is the 5th February 2021. Our own community committee member Diego Alonso-Alvarez is a current SSI Fellow so if you’re interested to apply you are welcome to contact Diego for advice or information.
SAVE THE DATE: On Tuesday 9th March 2021, we’ll be hosting a ReproHack. Further details to follow in future newsletters but if you’re interested to help out with organising/running this event, please get in touch with Jeremy Cohen via email or our Research Software Community Slack.
Advent of Code (AoC) 2020 continues until 25th December. It’s not too late to get started and the series of fun and often challenging puzzles are a great way to enhance your coding skills and perhaps try out a new language. We have a local “private leaderboard”. If you’d like to join the Imperial leaderboard, send a message in the #general channel on the Imperial RS Community Slack to obtain the token required to join the leaderboard.
The FAIR (Findable, Accessible, Interoperable, Reusable) principles have been applied in the context of data for some time now. However, FAIR is now increasingly being considered in the context of research software. If this is an area that’s of interest to you, please consider completing the Towards FAIR principles for research software questionnaire which is currently gathering views on the use of FAIR for software. You may also be interested in this recent article: “Decoding the FAIR principles: Are they relevant to software?”
The hidden REF aims to recognise and celebrate research outputs beyond the traditional outputs that contribute to the regular REF exercise. This is particularly relevant to RSEs, with submission categories such as “Hidden Role”, “Training materials and courses” and “Research Citizenship”. The deadline for submissions to the hidden REF is 26th February 2021.
The Nordic-RSE online get-together took place on the 30th November-2nd December, replacing the in-person Nordic-RSE workshop that has now been postponed until late May 2021. Following an afternoon session of keynote talks and an introduction to the Nordic-RSE community on Monday 30th November, the following two days included a range of talks, discussions and a panel session. You can find slides and details from the discussions by following the links on the workshop programme.
The notes-jekyll project brings together the ability to take notes in Markdown with rendering of BibTeX references and easy insertion of citations. Take a look at this blog post describing the notes-jekyll project.
Are you planning to work on a hobby project over the upcoming break? Maybe there’s something you started months (or even years!) ago that you’ve just never got round to making any more progress on, but it still seems like a fun idea or a great opportunity to learn something new. If so, the “Tips to stay focused and finish your hobby project” post on the Stack Overflow blog may be of interest.
If you organise events (or are hoping to do so in 2021), take a look at the Software Sustainability Institute’s Event Organisation Guide that was recently announced. The guide contains an array of helpful information highlighting the various things you might need to think about when organising and running events.
The recently launched Belgium Research Software Engineers Community (BE-RSE) held its first Research Software Developers Day on the 3rd December. Recordings of the presentations are now available via the schedule on the Research Software Developers Day web page.
Do you use GitHub Actions to manage your software development and CI/CD workflows within GitHub? Were you aware that you can host your own GitHub Actions runners? Take a look at this post about self-hosted runners on the Research Software Engineers blog.
The Research Software Engineer Stories podcast has recently published two new episodes. The Founding Fathers episode speaks to Rob Haines, Head of Research IT at the University of Manchester while in Equal Footing, the podcast talks to Nooriyah Lohani of NESI in New Zealand.
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.
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.
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! rse-committee@imperial.ac.uk.
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.