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 rse-committee@imperial.ac.uk - we look forward to hearing from you.
Now on with this month’s newsletter…
RSECon23, the 7th Annual Conference for Research Software Engineering, takes place this year in Swansea on 5th-7th September 2023. The abstract submission deadline has been extended to Wednesday 3rd May so there’s still time to submit something. The conference is an excellent opportunity to find out what’s happening in the world of RSE, with over 300 RSEs, researchers and research technology professionals expected to attend.
The next Byte-sized RSE session, looking at intermediate/advanced use of Git version control will take place on Wednesday 10th May, 13:00-14:30, online. Register here.
To link with this year’s Mental Health Awareness Week, we’ll be hosting a talk by Dave Horsfall as part of the DiveRSE series on “The importance of talking about mental health in the Research Software Engineering community”. Dave is a member of the Newcastle University RSE team and an SSI Fellow. This is a hybrid event, the talk will take place 10:00-11:00 on Tuesday 16th May at South Kensington Campus and on Zoom. See the event page for registration information.
On Wednesday 24th May, 12:00 BST, the Nordic RSE community are running a seminar on “Ethical and legal aspects of AI”. Further details including connection information will be made available via Nordic RSE’s Research Software Seminar Series page.
As part of the Pint of Science Festival, 7-9pm on Wednesday 24th May, researchers from the Alan Turing Institute will be leading an event on “AI for the planet, love online and the Big Fat Quiz of AI” - registration is only £5 and there are still a few tickets available.
IEEE eScience is another excellent conference for publishing RSE-related work. This year’s conference, eScience 2023 takes place in Limassol, Cyprus from 9th-13th October 2023. There’s still just under a month to submit something - the deadline for paper submissions is 26th May 2023. As part of this conference there will also be an RSEs in e-Science Workshop with the theme of “Sustainable RSE ecosystems within eScience”. The deadline for workshop abstract submissions is Friday 30th June 2023.
On Friday 9th June 2023, 12:30-16:30, the RSLondon Community and Alan Turing Institute will host a hybrid event looking at research software training. The event will offer a combination of talks and discussion around the challenges and opportunities of developing and delivering research software training to both RSEs and members of the research community. Registration is not yet open but save the date and further information will be shared with the community soon.
With 2023 being declared the Year of Open Science, CERN is hosting the one week CERN-NASA Open Science Summit 2023 - Accelerating the Adoption of Open Science. The event runs 10th-14th July 2023 - see the web page for details on how to apply to participate in this event.
Finally, a reminder of a couple of events that we highlighted last month - there’s still the chance to register for both: JupyterCon 2023 will take place in Paris, France on 10th-12th May 2023 and PyData London 2023 will take place on 2nd-4th June 2023.
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.
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-committee@imperial.ac.uk.
Our Research Software Champions are continuing their work to better understand how research software is used and built across Imperial’s departments. Over the coming weeks, look out for departmental surveys, events and related activities being run by our Champions. If you’d like to get in touch with a Champion working in your field you can contact Jeremy Cohen for more information.
After a break of several months, the DiveRSE talk series is restarting for 2023. We have a group of 5 talks planned for our 2023 series at present - see the “Dates for your diary” section for details of the first talk on 16th May - further talks will be added to the website soon. You can also go back and watch videos from the previous talks which are hosted on the Society of Research Software Engineering’s YouTube channel.
Led by the Research Software Alliance, the Amsterdam Declaration on Funding Research Software Sustainability is aiming to define the principles and approaches for funding the sustainability of research software. An updated draft of the declaration was released in mid-March and is available via Zenodo.
Have you just received a brand new, state-of-the-art Mac laptop? Great - now you just need to make your development setup work with the Apple Silicon chip! In this post on Python Development on M1 Macs, our colleague from the RSE Team, Adrian D’Alessandro, walks us through his solution to making this shift in a painless and user friendly manner.
Take a look at this GitHub template for FAIR and open data. The template repository comes pre-structured and configured with a set of key files and configuration that support FAIR and open data and which you can edit as necessary to ensure your project meets these aims.
Cristin Merritt’s article “Celebrate Two Women Highlighting Their Roles as Research Software Engineers” is part of a series of articles profiling women in HPC for Women’s History Month.
News on some work from Imperial’s Data Science Institute: “New computer model helps assess privacy risks of networked data collection”
A paper just published in PLOS Computational Biology looks at “Ten simple rules for working with other people’s code”.
An article on NVIDIA’s technical blog looks at “Fast Large-Scale Agent-based Simulations on NVIDIA GPUs with FLAME GPU”. Authors include members of University of Sheffield’s RSE team.
In our regular update on the Code for Thought podcast, we have three new episodes to highlight to you. The first is part of the Byte-sized RSE set of podcasts and covers the 6th Byte-sized RSE session on Integrated Development Environments. There is also an episode on funding for Research Software Engineering - “Funding it All” - and one on investigating Research Software Engineering itself - “Who are we?”.
Recently released as an early access publication in Computing in Science & Engineering, an article by Ian Cosden, Kenton McHenry and Dan Katz - Research Software Engineers: Career Entry Points and Training Gaps.
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 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.
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.