April definitely feels as if we have left behind the worst of winter and the world has started to sprout all around us. Young leaves, beautifully green, cover the trees, gardens seemed hit by an explosion of flowers, and there is a general desire to have a drink in beer gardens - unless you have hay fever, of course. You can never be sure here since it might start raining any time, but even with that threat, it does not matter - it is marvellous to be outside!
The world of research software - and digital research software professionals, in general - is also as alive in the coming months as the gardens, with multiple events local and international for all tastes, blogs and podcasts. They offer a fantastic opportunity to expand your knowledge and skills, or your network of contacts, so do not be afraid of going out there and trying new things. If you are thinking about career progression, we even have a job offer in this edition, so keep reading - ideally outside, enjoying the whether!
As we highlighted last month, PyCon UK 2025 will take place in Manchester, UK on the 19th-22nd September 2025. The call for proposals for talks, interactive workshops and collaborative sessions is now open and the deadline for proposals is Sunday 11th May 2025.
When is it better for digital research technical professionals (dRTP) to be embedded in research groups vs in central teams? What factors affect embedding this expertise within discipline-specific teams, or within central teams? Join us on Monday 12th May, 13:00-16:00, for this STEP-UP project event, hosted by University of Westminer, to explore how different universities in London organise their software, data and computing infrastructure professionals. A light lunch will be available from 13:00 with the talks starting at 14:00. Free registration is now open.
A new ARCHER2 training course on Green software use on HPC will be taking place, in person, on Tuesday 13th May 2025 in Edinburgh. Registration is open.
Registration is still open for the Software Sustainability Institute’s Collaborations Workshop 2025. This is a hybrid event taking place 13th-15th May 2025. As in previous years, the final day of the event, 15th May, is a hackday where there will be the chance to work with a group of other attendees on a fun, technical project. The event is hybrid, taking place at the Stirling Court Hotel, University of Stirling, and online.
The Imperial College London Research Software Engineering community will be organising the Research Software Conversation Series: Tools and techniques for modern research in different domains from May to July 2025. This monthly series will run in hybrid mode, is free, and is open to anyone interested in research and research software. You can register already to the first session, Keeping track: version control for reproducible research, to be held on Thursday 22nd of May, 12:30 to 14:00.
On Friday 30th May, 14:00-17:00 at White City Campus, we will be having an Imperial RS Community / STEP-UP / RSLondon event with a few talks followed by snacks and refreshments and a chance for everyone to chat. Please register now to secure your spot, as places are limited. We’re also looking for lightning talk speakers - if you have anything you’d like to present to the community, send us a message at rse-committee@imperial.ac.uk
The 17th International Workshop on Science Gateways (IWSG2025) will take place at the University of Westminster on the 17th-19th June 2025. Registration will open soon.
The flagship research software and digital RTP event in London, the STEP-UP RSLondon 2025 Conference, will take place on Monday 7th of July. This year’s event will be our biggest yet, with separate parallel tracks focusing on research software, research data and research computing infrastructure. Abstract submissions will open in a couple of days and registration will be available soon. Save the date, submit an abstract and get ready for a day full of exciting talks and networking!
This month, in our series highlighting members of the Imperial community helping to support research computing, we hear from Stephanie Wills:
I am currently part of a 6-month Experience Programme with the Research Computing Service, designed to provide RSE and HPC exposure to early career researchers. My background prior to joining Imperial is somewhat varied: my undergraduate degree was in Biomedical Sciences with Management, which was followed by a couple of years in academic publishing. Returning to academia for my Master’s in Drug Design provided my first introduction to computational research, which involved becoming familiar with tools in bio/cheminformatics and computational chemistry.
Following this, I undertook my DPhil at Oxford, on the ‘Sustainable Approaches to Biomedical Science’ CDT. My research focused on developing computational methods to help optimize crystallographic fragment hits (low-molecular-weight compounds found to bind to a drug target) into more potent molecules with desirable properties. My later work involved using chemistry-based and deep learning models to develop novel scoring functions to evaluate a compound’s ‘elaboratability’, referring to its tractability to undergo further synthesis. The work was highly interdisciplinary, and I enjoyed working at the interface between computational and wet-lab scientists, particularly when collaborating on active campaigns to develop antivirals.
Following my DPhil, I was keen to diversify my technical skills, particularly in software development, as I found that the impact of research is highly dependent on the quality of the codebase and accessibility of our tools. Since starting the Experience Programme in March, I’ve predominantly worked with the HPC team, helping with user support, software installations and migrating users between clusters. I am now starting to work with the central RSE team, and I look forward to learning more about all the exciting work being done by the Imperial research software community!
This month, our Research Software of the Month is Virtual Ecosystem.
The Virtual Ecosystem is a collaboration between the Department of Life Sciences and the Research Software Engineering team at Imperial to develop a holistic ecosystem model.
An ecosystem encompasses all of the organisms, resources and processes responsible for maintaining life and functionality within an area. The scale of an ecosystem might be large - the Earth is a big ecosystem - or a specific smaller region of interest, such as a conservation protected area or a farmland. Whatever the scale, ecosystems are astonishingly complex systems and have been described as “more complex than the space station, and more connected than the internet”. We might take issue with that last statement, but it is undeniable that countless organisms from bacteria to large mammals interacting in a complex three-dimensional environment with constant environmental change presents a thorny issue for simulation.
However, this is what the Virtual Ecosystem is attempting to do. The reasons for this attempt are pressing: real world ecosystems are facing unprecedented challenges from changing patterns of land use and climate change and we need to be able to explore how the complex interactions within an ecosystem may lead to tipping points or unexpected acceleration or decceleration rates of the vital processes and functions. We cannot rely on field experiments - we need to investigate how ecosystems react over decades leading to many potential pathways and we do not have the time or money to explore the ecosystems in the real world.
So instead, we turn to simulation. There are many existing models of ecosystem processes available on a wide range of scales, ranging from global circulation models all the way to down to models of soil bacteria. However, existing models only tackle specific parts of ecosystems, such as the soil or the hydrology or primary productivity, thus providing only a limited understanding of the critical connectedness within ecosystems.
With the Virtual Ecosystem, we aim to address this limitation for simulation of terrestrial ecosystems at the “landscape” scale (hundreds of hectares). We aim to represent microclimate and hydrological processes in their full complexity and explicitly model all three relevant terrestrial biotic domains (plants, animals and soil microbes) using metabolic principles. In order to ensure that our model accurately captures the behaviour of real ecosystems, we are able to draw on a huge resource of field data for model calibration and validation from the Stability of Altered Forest Ecosystems (SAFE) project in the rainforest of Sabah, Borneo.
Eventually we hope that the Virtual Ecosystem can be used to understand the likely outcomes of land management or conservation actions across a wide range of terrestrial ecosystems.
The Earth Science and Engineering (ESE) department at Imperial College London has a job opening for an open-ended Senior Research Software Engineer position. The successful candidate will join a 4-person computing team embedded in the ESE department and become part of the wider Imperial College RSE community. Applications close on Friday 2nd of May!
UKRI is developing a new research data policy, which will update and streamline the expectations for sharing and managing research data and other research-relevant digital objects, including algorithms, software code and workflows, arising from UKRI-funded research. Between April and July 2025, they are welcoming stakeholder feedback on a draft version of the UKRI research data policy. You can also find out more about the policy and how they are developing it by joining the UKRI research data policy information webinar on 7 May 2025.
In collaboration with the UKRI-EPSRC-funded STEP-UP Strategic Technical Platform project, we’ll be running a variety of training across different skill levels over the coming months. Rather than simply selecting and running a set of training courses, we’re keen to understand what training you’d like to have access to. You can tell us, anonymously, via our Training Requirements Form. If you’d like to discuss training with us, you can get in touch with the Research Software Community committee via our usual address - rse-committee@imperial.ac.uk.
The Software Sustainability Institute has announced a new £4.8m Research Software Maintenance Fund, supported by the UKRI Digital Research Infrastructure programme. The fund will offer awards that can be used to support and maintain an existing piece of software, or to support teams working on multiple software tools. You can find full details on the Research Software Maintenance Fund web page. The first funding round opened for Expressions of Interest on 7th April 2025 and submissions close on Friday 30th May 2025. An information webinar is taking place on 7th May.
Do you define yourself as being from an underrepresented group within the research software community? If you have also written software or scripts for research purposes, would you be interested in participating in a study exploring the barriers and enablers to developing research software for underrepresented groups? If so, you can find out more about the study and how to get involved on the inclusive RSE study web page.
Do you know you can acknowledge contributions from collaborators in your software development with git via commit messages? This is a great way to encourage and reward collaboration in your projects, and acknowledge efforts that may otherwise go unnoticed. So if you did not know about it, read this fantastic blog post from Daniel Cummins.
More on git in the next blog post. Many of us use git daily without thinking much on why it does things the way it does or on its global configuration. But git has an extensive set of options that can be configured to make it more performant, automate things or simply adapt it to our specific needs. In How Core Git Developers Configure Git we learn about many of these things, including a new set of defaults that you might very well want to adopt.
The Code for Thought podcast brings a lot of interesting episodes this month, from the ByteSized RSE: AI assisted coding episode featuring our Imperial colleague at the Early Career Research Institute, Liam (Jianliang) Gao, to moving From Research to Production? or a career switch story in From Volcanos to Open Source!
Do you work with workflows as part of your research? Have you heard about the FAIR principles? Do you know how to marry these two things? If not, Applying the FAIR Principles to computational workflows is the article you were looking for.
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.
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:
All the documentation, tutorials and howtos for using Imperial’s HPC are available in the Imperial RCS User Guide.
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.
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 Research Software Community Mailing List.
This issue of the Research Software Community Newsletter was edited by Diego Alonso Álvarez. All previous newsletters are available in our online archive.