Welcome to our April newsletter. Towards the start of the month, an impressive solar eclipse crossed over a large swathe of Canada, the US and Central America, and later in the month we saw the world’s largest 3D printer unveiled by the University of Maine! As ever, there’s been lots happening in the world of Science and Technology - and research software is no different! This month we have a wide range of event details, information and reading material to keep you busy as (we hope) some warmer, more spring-like weather arrives in London! We’re also excited to announce that the Research Software London community workshop will be running again this year in July at Imperial, check out the details below and save the date!
The next Turing Way Online Collaboration Cafe takes place on Wednesday 1st May, 15:00-17:00.
The abstract submission deadline for RSECon24 - the 8th annual conference for Research Software Engineering has been extended to Wednesday 8th May. The conference takes place 3rd-5th September 2024 and registration is open until 30th June.
Imperial’s Womens Health Network are hosting the “RE-DESIGN: Women’s Health Hackathon” over the weekend of 11th/12th May 2024 in the Dyson School of Design Engineering. See the Eventbrite page for full details and registration.
Karlsruhe Institute of Technology are hosting the first Summer School on Research Software Engineering from 23rd-27th September. Applications are open, the deadline is 17th May 2024.
King’s College London is hosting The King’s Festival of Artificial Intelligence, 21st-25th May 2024.
The Nordic-RSE Conference 2024 will take place, in person, at Aalto University, Espoo, Finland on the 30th/31st May 2024. See the conference webpage for more details and registration.
The next Byte-sized RSE session being run by the UNIVERSE-HPC project will be on FAIR Research Software for Reproducible Research, taking place on Tuesday 4th June 2024, 13:00-14:30. Registration is now open.
The RSLondonSouthEast2024 workshop will take place at Imperial on Tuesday 16th July 2024 - save the date! Abstract submissions will open shortly with a deadline of Wednesday 22nd May. Workshop registration will be available from mid-May.
Last month we highlighted that a new cohort of Research Software Champions have just got started, supported through the Beyond Open Research project being led by members of the team in Imperial’s Abdus Salam Library. This month, in our Research Computing at Imperial feature, we hear from three of our fifteen Champions about their research and their reasons for wanting to get involved in the Champions scheme.
I am a 1st Year PhD Student in the Materials department working with Stefano Angioletti-Uberti on in silico RNA structure prediction. I am also a Co-Founder of Nucleate’s AI in Biotech Initiative. For my prior studies, I graduated with MEng in Materials also from Imperial. Throughout that degree, I visited EPFL in Switzerland working on ML models for structure-property prediction for crystals, and attended MIT, where we developed a novel method for sampling molecular simulations using deep learning methods. In 2023, I joined Sam Rodrigues’ lab at the Francis Crick Institute and was the Founding Member of Technical Staff at FutureHouse, a San Francisco moonshot building an AI scientist to automate scientific discovery. My ambition is to start a company within computational molecular biology through a mix of physics- and ML-based means. As a Research Software Champion, my goal is to promote robust engineering practices within my department, as well as facilitate interdepartmental cross-talk, sharing insights and tips among other Imperial colleagues.
I am currently pursuing my PhD at the National Heart and Lung Institute, where my research focuses on understanding airway remodelling in chronic respiratory diseases. Specifically, I am mapping the airway walls of IPF, COPD, and severe asthma patients using spatial transcriptomics, and defining interactions between stromal, epithelial, and immune cells using imaging mass cytometry and second harmonic generation. I am also integrating these datasets with clinical parameters to identify shared pathways and cell-cell interactions driving tissue remodeling in the airway across chronic lung diseases. As part of my PhD program, I obtained a MRes in Data Science from Imperial College London. My background is predominantly wet lab and biology-based, having completed my MSc in Immunology at Trinity College Dublin and worked for several years in early drug discovery at a large pharmaceutical company in Cambridge, MA, USA. As a Research Software Champion, my strengths lie in understanding the barriers to entry and challenges faced by traditional wet lab scientists and clinicians in utilizing research software. I am committed to supporting wet lab scientists in integrating research software into their workflows by facilitating information about best practices surrounding coding and promoting the importance of reproducibility and open access to software and data in scientific research.
I am a 1st year PhD student in the department of Mechanical Engineering, working in the Nonlinear Dynamics and Controls group at Imperial. My research project focuses on the development of machine learning (ML) techniques to augment traditional unsteady flow simulations. The ability to perform these simulations quickly and without a loss in accuracy affords more room for optimisations in component designs in many industries. This not only allows for greater innovation in design and manufacture but also adds to the level of confidence in the predicted behaviours of these redesigned components.
I am passionate about software design and following best practices during the development and implementation of research tools developed by fellow researchers. The use of proper software engineering principles allows for maintainability, reliability and scalability of many of the tools we, as researchers, develop during our studies. I decided to become a research software champion to help make these principles more accessible and known to the engineers in the department, as well as, to share my experiences and knowledge with other like-minded people. I am also excited to learn from my peers about other best practices that I may not be aware of myself.
This month, our Research Software of the Month is “Gutenberg” a research and teaching platform developed by the Oxford Research Software Engineering Group (OxRSE) at the University of Oxford.
Gutenberg is being developed as part of activities on the UNIVERSE-HPC project in which Imperial is a partner. The platform provides a visual interface for browsing and engaging with training material. The interface, based on, Next.js, React and React Flow can be seen in action in OxRSE’s public deployment of the Gutenberg platform by viewing the teaching materials and selecting one of the topic areas.
Materials are grouped by the topic they cover with different pathways available for specialisations and, in a number of cases, for different programming languages. This provides a novel and engaging way to follow through a set of training content, understanding the topics involved and how they build on each other.
A range of existing open source training material has been ported to the Gutenberg platform. This involves converting the material to a set of Markdown files with a specific structure and associated YAML metadata block that details the ordering of the training material’s sections as well as other metadata. Further details can be found in the course material contributing guidelines. A range of existing course material is available in the UNIVERSE-HPC course-material repository. A Gutenberg deployment can be configured to read in training materials from multiple GitHub repositories.
In addition to displaying the material itself, Gutenberg also provides a powerful course management interface for trainers. Course organisers can group material that has been added to a Gutenberg platform deployment into a course syllabus. Students then register with the system and can enrol on courses. Course organisers/trainers then have access to an administrative interface that lets them view student progress in terms of modules undertaken and which exercises/challenges within the training material have been completed. Students can also add questions or comments as they move through the materials which can be answered by trainers or by other course attendees.
This powerful platform is under ongoing development and we welcome engagement from members of the research software community in terms of contributing to the platform’s codebase or making new or existing open source training material available in Gutenberg format.
We’re delighted to announce that the RSLondonSouthEast workshop series, run by the Research Software London regional research software community, will continue this year, supported by the STEP-UP project (see last month’s newsletter). RSLondonSouthEast2024 will take place on Tuesday 16th July 2024 in the Huxley Building on Imperial’s South Kensington campus. Save the date! A call for abstracts will open this week and registration will be available from mid-May. Look out for announcements.
If you’d be interested to help out on the day of the workshop, for example by assisting visitors with finding their way around or helping out with AV management during the talks/panels, please get in touch with us at rse-committee@imperial.ac.uk to volunteer.
Check out Dr. Heidi Seibold’s 3 simple rues for creating Open Science Policies.
Continuing the Open Science / Open Research theme, Infra Finder is a directory containing details of a wide range of infrastructure services, aiming to provide support with finding resources to support open research and scholarship.
Find out what the Software Sustainability Institute’s Fellows have been doing as part of their Fellowship activities in March 2024’s Fellows Newsletter.
How can we inspire inclusion within the HPC community? reports on a Women in HPC (WHPC) event hosted as part of the ARCHER2 Celebration of Science.
The Living with Machines project, a collaboration between the Alan Turing Institute, the British Library and a group of UK universities has a YouTube playlist with a number of videos looking at their work to analyse historical collections using Data Science and Machine Learning.
There are many such guides out there but the “The guide to Git I never had.” offers a great overview of both the key Git features as well as more advanced capabilities.
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. 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.
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.
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This issue of the Research Software Community Newsletter was edited by Jeremy Cohen. All previous newsletters are available in our online archive.