Imperial College Research Software Community Newsletter - October 2021

Hello Imperial RSEs and researchers, and welcome to our October 2021 newsletter. October marks the start of another academic year at Imperial and hopefully one where there is more opportunity to get back to in person teaching/learning and also the opportunity for the research software community to start thinking again about running in-person events and training as the academic year progresses. This October also marks the 6th anniversary of our Research Software Community, with the mailing list being set up and initial members signing up back in October 2015. Awareness of and support for research software engineering at Imperial has grown significantly during this time with the set up our central Research Software Engineering team, a range of new software-related training opportunities, local, departmentally-based RSE teams emerging/growing and individual departmental RSE roles beginning to appear around the College. We look forward to the continuation of these advances in the coming months and years to ensure that we can continue to enhance our skills and develop research software that can support the best possible research outputs.

This month we announce our first research software community event for some time that is taking place on Thursday 18th November, we hope that many of you will be able to join us for that. We also continue our “Research Computing at Imperial” series highlighting key members of the College community who are helping to develop research software or support and manage the processes and teams associated with it.

In this month’s newsletter:

Dates for your diary

Research Computing at Imperial

Continuing our series highlighting key members of the College community helping to provide, manage and support research computing and research software services, this month we have an introduction from Diego Alonso Álvarez, Acting Team Lead for the College’s RSE team based within the Research Computing Service:

I joined the RSE team in 2018 after 13 years working in research - in semiconductor materials and solar cells - as a PhD student, first, and then as a postdoc and research fellow. I was mostly an experimentalist and spent a fair amount of time working in the lab and making sense of the wealth of data I was collecting.

As a self-taught programmer, my skills in software development were sketchy at best at that time. However, they were more than enough to write small tools to simulate my experimental results and to control the equipment in the lab. I discovered that it was quite fulfilling, especially creating neat graphical user interfaces to facilitate other people using those tools. It came as a surprise to me that precisely doing that was the role of research software engineers.

As part of Imperial’s RSE Team, I have been involved in tens of projects on exciting areas of science that had little or no relationship with my background. I have been continuously learning during this time, shifting fields, trying new tools and advising others on how to write better software for their research. We are here to help researchers create impact with their work and to support a thriving community of RS specialists at Imperial.

Research Software of the Month

Our Research Software of the Month for October is EpiEstim.

EpiEstim is software which has become the gold-standard to estimate in real-time the epidemic reproduction number Rt, i.e. the average number of secondary infections generated by each case in an epidemic. EpiEstim is useful to evaluate at any time whether an epidemic is under control (Rt < 1) and if not, to quantify the extent of additional efforts necessary to bring the epidemic under control. In particular, it can be used to assess the effectiveness of interventions aimed at reducing transmission.

EpiEstim has been applied to quantify the transmissibility of various pathogens, including Ebola, influenza, Zika or cholera. It has become particularly prominent during the COVID-19 pandemic and is being widely used by academics, public health agencies and governments worldwide to monitor SARS-CoV-2 transmission.

EpiEstim is freely available in three versions: an Excel spreadsheet, an R package, and an interactive online application. The software and the underlying estimation method have been described in Cori et al. AJE 2013 and Thompson et al. Epidemics 2019.

RSE Bytes


Blog posts, tools & more

Some reminders…

RS Community coffee…

…continues weekly via Teams - normally on Friday afternoons at 3pm but check our Slack workspace for exact times and connection details.

RS Community Slack

The Imperial Research Software Community Slack workspace is a place for general community discussion as well as featuring channels for individuals interested in particular tools or topics. If you’re an OpenFOAM user, why not join the #OpenFOAM channel where regular code review sessions are announced (amongst other CFD-related discussions…). Users of the Nextflow workflow tool can find other Imperial Nextflow users in #nextflow. You can find other R developers in #r-users and there is the #DeepLearners channel for our new AI/ML group. Take a look at the other available channels by clicking the “+” next to “Channels” in the Slack app and selecting “Browse channels”. If you want to start your own group around a tool, programming language or topic not currently represented, feel free to create a new channel and advertise it in #general.

Research Computing Tips

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.

Research Software Directory

Imperial’s Research Software Directory provides details of a range of research software and tools developed by groups and individuals at the College. If you’d like to see your software included in the directory, you can open a pull request in the GitHub Repository or get in touch with the Research Software Community Committee.

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 Research Software Community Mailing List.

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