Hello to everyone in our research software community. It’s hard to believe that we’re almost at the end of April already! I hope you enjoyed the extended long-weekend break during the College Easter closure and that, if you’re comfortable doing so, you’ve had some opportunities to start engaging with the various in-person workshops, events and activities that are now taking place. Indeed, we have a number of in-person events to highlight this month. These include September’s in-person RSE conference that we first highlighted last month, and the recently announced RSLondonSouthEast workshop that is back after a break of more than two years. Taking place in person at Imperial in early July, there is a call for RSLondonSouthEast abstract submissions currently open and I hope you’ll consider submitting something and joining us for this event. See below for further details.
Read on for our usual selection of dates for your diary, events, articles, Research Software of the Month and an introduction from Research Computing Service Director, Prof. Spencer Sherwin…
This month we have two in-person RSE conferences/workshops to highlight:
After a break of more than two years, the RSLondonSouthEast workshop is back! RSLondonSouthEast 2022 will take place On Monday 4th July 2022, at Imperial College London.
The call for abstract submissions is open. Please consider submitting a short abstract to give a talk or present a poster on your work, or ideas that you have for improving research software provision, training or community activities. There are submission options for a full talk (approx 15 minutes), a lightning talk (approx 5 minutes) or a poster. The abstract submission deadline is Thursday 12th May 2022.
Following last year’s online, month-long 5th RSE conference - SeptembRSE - the in-person RSE conference is returning for 2022. RSECon2022 will be held from 6th to 8th September 2022 in the Frederick Douglass Centre at Newcastle University.
The deadline for the call for submissions has been extended to Monday 9th May 2022. Submission options include talks, posters, panels, walkthroughs and workshops. We will keep you posted with further developments in relation to the conference in our upcoming newsletters. There is also a call currently open for volunteers and mentors which closes on Wednesday 18th May.
The next talk in the DiveRSE series on Equity, Diversity and Inclusion in Research Software Engineering will take place on Wednesday 4th May 2022 at 16:00 BST. Heather Turner from the University of Warwick will be talking about “Equity, Diversity and Inclusion (EDI) in the R Community”. You can find full details and registration information on the event page.
The 13th International Women in HPC workshop “Creating a diverse and inclusive community” will be held at ISC High Performance 2022 in Hamburg, Germany on Thursday 2nd June 2022. A call for posters is currently open - the submission deadline is Thursday 5th May.
As we highlighted last month, the Software Sustainability Institute’s next Research Software Camp - Next steps in coding - will be held from 16th to 27th May 2022. It will include a variety of sessions, a mentorship programme and software surgery. If you’re looking to develop your research software skills, have technical questions or you’d like to build on basic training gained through Software Carpentry or a similar introductory workshop, this is great opportunity. It’s a fully online event and all sessions are free to attend. You can get more information and sign up for updates on the event page.
Science and Engineering South (SES), in collaboration with RSLondon and the UCL eResearch Domain are running a Research Technology Professionals careers event on Thursday 26th May 2022 - Making the Magic Happen! Careers in research data, software and infrastructure. The morning session will include talks from leading researchers whose work benefits from the input of RTPs and from the practitioners who support this research. There will be a keynote talk from Professor Neil Ferguson, Imperial College London. More information and registration are available via the Eventbrite page.
Nordic-RSE’s next online event, the Nordic-RSE online unconference 2022 will take place on the 16th-17th August 2022. There are various opportunities to contribute ideas for the event - see the event page for details.
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 Spencer Sherwin, Director of Research Computing Service (RCS):
I originally did my undergraduate studies in Aeronautics at Imperial before going to the US to do my PhD and then returning in 1995 as a Lecturer in Aeronautics. I have since spent my whole career in the Department of Aeronautics but working with many other Departments including Mathematics, Bioengineering, Computing, Mechanical Engineering and Medicine. Underpinning my research has been the development of high fidelity numerical methods known as Spectral/hp Element discretisation for solving partial differential equations and in particular those related to aerodynamics/fluid mechanics. My early work focussed around more of the applied mathematics and computational development of these methods working on cardiovascular and bluff body flows. I then focussed on collaboratively developing open source parallel software, Nektar++, to make these methods more widely accessible. Over the past ten years I have been working on demonstrating the methods in application and industrial practice working with engineering industries such as McLaren Racing and Rolls Royce.
I have held the position of Director of Research Computing Service (RCS) for the past four and a half years, originally working with Matt Harvey to develop and broaden RCS from purely HPC focussed to include the RSE team, which was originally under the guidance of Mark Woodbridge, the introduction of the Research Data Store, and also the development of the Research Computing Training team under the guidance of Katerina Michalickova. More recently I have worked closely with Andy Richards and the expanded academic leadership team involving the Directors of User Engagement, Research Data Strategy and Research Software Engineering Strategy. This has been an exciting development which has positioned Research Computing as part of the ICT Leadership team which continues to develop the original strands of HPC, RSE and a wider and more complete engagement with Research Data. As you may be aware Research Computing Training also continues to grow but is now coordinated from within the Graduate School.
Although there have been many challenges during this time it has been very rewarding to see the Research Computing Service continue to grow with the increasing demands and requirements of computational research, not only in the traditional computing focussed research but also as a complementary tool for experimental methods. I will soon be stepping down as Director of the service as I take up another role in the Department of Aeronautics. I therefore encourage you all to consider how you might help jointly engage with the Research Computing Service and hope some of you might consider applying for the new Director position!
For our Research Software of the Month feature, we’re highlighting 4Dsurvival, an open source cardiac motion analysis code that uses deep learning for survival prediction.
Motion analysis is used in computer vision to understand the behaviour of moving objects in sequences of images. Optimising the interpretation of dynamic biological systems requires accurate and precise motion tracking as well as efficient representations of high-dimensional motion trajectories so that these can be used for prediction tasks. Here we use image sequences of the heart, acquired using cardiac magnetic resonance imaging, to create time-resolved three-dimensional segmentations using a fully convolutional network trained on anatomical shape priors. This dense motion model formed the input to a supervised denoising autoencoder (4Dsurvival), which is a hybrid network consisting of an autoencoder that learns a task-specific latent code representation trained on observed outcome data, yielding a latent representation optimised for survival prediction. To handle right-censored survival outcomes, our network used a Cox partial likelihood loss function. This work demonstrates how a complex computer vision task using high-dimensional medical image data can efficiently predict human survival.
You can inspect, edit and run the code interactively via Code Ocean and you can find the project repository on GitHub.
Call for additional helpers for the next RSLondon Software Carpentry workshop taking place 9th-12th May 2022. This training workshop is now fully booked up with a number of people on the waiting list. We would like to find a few additional volunteers to help out for 2 days at the workshop supporting learners with either bash shell and git (9th/10th May) or Python (11th/12th May).
This is a great opportunity to get involved with Software Carpentry workshops and lead a breakout group of learners as part of the sessions. Contact Jeremy Cohen via email or Imperial RS Community Slack if you’d like to volunteer or would like more information.
DiveRSE is a new international talk series focusing on Equity, Diversity and Inclusion in Research Software Engineering. The series aims to bring the talks, themes and discussions from the Vive la différence - Research Software Engineers workshop, which took place earlier this month, to a wider audience. The series was launched on 22nd March 2022 with a keynote talk “Normalizing inclusion by embracing difference” from Mary Ann Leung, Ph.D., Founder and Director of the Sustainable Horizons Institute. You can watch the video of the keynote talk via the link on the event page. Our next talk, on Wednesday 4th May, is advertised above and further talks will be taking place later in May and in June.
The Society of Research Software Engineering’s jobs page provides a space to advertise opportunities to the RSE community internationally. It currently lists a wide range of RSE and RSE-related vacancies from employers both within the UK and abroad.
GitHub has recently announced the availability in public beta of new colourblind themes for red/green colour blindness.
The latest episodes in the Code for Thought podcast series are now available. There’s a look at Digital Humanities - Putting the Digital into Humanities - and also, in A Museum for All, a discussion with Kati Price, Head of Digital Media at the Victoria and Albert Museum. Also, meet Connah Kendrick, one of the Software Sustainability Institute’s Fellows in this episode.
Have you heard other developers talking about “linting” and wondered what this is all about?! In his excellent blog post Linting: What is all the fluff about?, Neil Shephard from University of Sheffield’s RSE team provides some background and examples on this important aspect of software engineering best practice.
What Unix/Linux command line tools do you use most frequently? Are any of them in this list of new(ish) command line tools?! A great resource for refreshing/updating your knowledge of command line tools.
On a similar theme to the above list, take a look at moreutils, “a collection of the unix tools that nobody thought to write long ago when unix was young”.
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.
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! firstname.lastname@example.org.
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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.