Imperial College Research Software Community Newsletter - April 2022

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…

Dates for your diary

Research Computing at Imperial

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):

Spencer writes:

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!

Research Software of the Month

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.

RSE Bytes


Blog posts, tools & more

Some reminders…

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.

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.