Imperial College Research Software Community Newsletter - April 2023

Hello everyone! Welcome to your April edition of the Research Software Community newsletter! I hope you all had a good break over the College’s recent Easter closure days.

Unlike the experiment mentioned in last month’s newsletter intro, I decided not to invite ChatGPT to provide me with advice on how to create the perfect newsletter this month! Not that I claim to be an expert newsletter editor - instead, I hope the wide range of events we have to tell you about and the interesting articles and blog posts we are highlighting in this month’s edition speak for themselves. I hope you find some events to attend and that the other materials help to provide you with new skills and ideas to take you further on your research software journey.

There’s lots going on over the coming months so look out for a number of upcoming conference deadlines. The annual RSE conference deadline has been extended slightly so if you’d like to submit something, there’s still a chance over the next few days. Also look out for information about the RSLondonSouthEast workshop, our 1-day regional community workshop that will be taking place at Imperial in mid-July - a call for short abstracts will be opening soon.

As ever, if you have RSE-related questions, are keen to get more involved with the community, or you have an event, article or some software you’d like to tell the community about, get in touch at - we look forward to hearing from you.

Now on with this month’s newsletter…

Dates for your diary

Research Computing at Imperial

For our Research Computing at Imperial feature this month, we’ll be introducing another three of our new Research Software Champions. As highlighted last month, the Champions are working as part of a project on enhancing research software culture. The project is also developing an updated Research Software Directory to promote the software that is developed at Imperial.

We’d also like to welcome a new member of the Research Software Engineering team - Lokesh Ragta. Lokesh joined Imperial’s RSE team as a Senior Research Software Engineer in March 2023. Look out for an introduction from Lokesh in an upcoming newsletter.

The three Research Software Champions we’re introducing this month are Sara Llorente-Armijo, Nier Bian and Christoforos Galazis:

Sara Llorente-Armijo:

I’m a computational biologist PhD student at the MRC London Institute of Medical Sciences (LMS) in the Hammersmith campus. My PhD focuses on understanding how the whole genome folds inside the tiny cell nucleus while still allowing regulatory sequences to access the correct set of genes at the right time. To study this, I am analysing and integrating different genomic datasets (Hi-C, ChIP-seq, RNA-seq) using bioinformatic command line tools and my own R and Python scripts. I am constantly trying to improve my coding practices by implementing strategies and tools to ensure my analyses are well-documented and reproducible. I signed up as a Research Software Champion to better understand the challenges science community is facing when publishing code and data analyses, and to help by raising awareness of the importance of good coding practices and teaching some tools that are helpful for code reproducibility.

Xueni (Nier) Bian:

Hello. I’m a PhD student at the Life Sciences department. My thesis is in the field of molecular phylogenetics, where we build evolutionary trees based on genetic information we have collected about the organisms of interest. In particular, my PhD is focussed on detecting heterogeneity in evolutionary processes in large datasets, and how best to build large phylogenetic trees with these large datasets while acknowledging that the underlying heterogeneity exists. I started to code in 2019 and, although it’s been four years, I am still a beginner in many ways. I joined the Research Software Champions scheme because (1) I know what it’s like to be overwhelmed by being told “you can code, now do it better” and (2) I strongly believe in the idea that “if we choose forward-momentum over quality again and again we’ll end up with neither.” Having to make use of (or wrestle with) a mushrooming ecology of software tools has become a daily reality for experimentalists and somewhat-seasoned programmers alike in life science research. Sustainability in development of said software is an ideal that I am thrilled to be able to “champion”.

Christoforos Galazis:

I am a 3rd year Ph.D. student in the Computer Science Department, working within the AI4Health CDT. My research project focuses on the structural and functional analysis of cardiac MRI using deep neural networks to improve diagnostic and prognostic capabilities. Structural analysis of the heart involves examining its physical characteristics and components, while functional analysis assesses its motion across the cardiac cycle to perform vital functions. My research interests lie at the intersection of computer science and healthcare, with a specific focus on computer vision and medical imaging. Additionally, I am passionate about software engineering and believe that it plays a crucial role in developing effective and efficient solutions in medical imaging. The use of software engineering principles to ensure the reliability, scalability, and maintainability of critical healthcare tools is of utmost importance. That is why I decided to become a Research Software Champion to convey the significance of software engineering principles in research that extend beyond healthcare, share my experiences and knowledge, and learn from my peers.

Research Software of the Month

With such a wide range of other content to highlight this month, our Research Software of the Month feature is taking a break for April!

Instead, we’d like to make a call for you to suggest software for the RSotM feature in future newsletters. Do you have a piece of research software that you work on and you’d like to see highlighted in this column? Have you used other research software, that has an Imperial link, that you’d like to tell the community about? Maybe you are using some open source software as part of your research workflow that doesn’t have a link to Imperial but you think is something we should all know about!

Get in touch with your suggestions for RSotM at

RSE Bytes


Blog posts, tools & more

Some reminders…

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 AI/ML-related questions and discussion. 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 Software Engineering support

If you need support with your code, seek no more! The Central RSE Team, within the Research Computing Service is here to help. Have a look at the variety of ways the team can work with you:

HPC documentation and tips

All the documentation, tutorials and howtos for using Imperial’s HPC are available in the HPC Wiki pages. See also 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.