Welcome to our March Research Software Community newsletter. Along with our regular mix of dates for your diary, our research software of the month feature and some suggestions for interesting blog posts to take a look at, we have exciting news for you this month. Imperial is leading a new project to help improve recognition, career opportunities and support for digital Research Technical Professionals (RTPs), including research software, data and infrastructure professionals. Announced last week, this project, STEP-UP, in collaboration with UCL, King’s College London and University of Westminster will provide a fantastic opportunity for us to grow the support that we can offer members of our research software community, both at Imperial and in the wider London region, via the RSLondon community. Take a look at the News section of this newsletter for more details on STEP-UP. This month, we’re also launching our 2024 cohort of Research Software Champions. Look out for more from our new group of Champions in our newsletters over the coming months.
Enjoy reading this month’s newsletter and with the College Easter closure approaching, we wish you an enjoyable extended long weekend.
The next Byte-sized RSE session being run by the UNIVERSE-HPC project will be on property-based testing for Python, taking place on Friday 19th April 2024, 13:00-14:30. Registration is now open. This is a great opportunity to learn about a more advanced approach to testing your Python code!
On Friday 26th April, 10:30-17:30, Imperial is hosting R Dev Day @ Imperial 2024. This is an open, collaborative event for people interested in contributing to base R. Both new and experienced contributors are welcome! Register now!
SatRDays are coming to London! Hosted by CUSP London at King’s College London, and co-organised by Jumping Rivers this one-day event on Saturday 27th April will feature talks on all things R! SatRdays events are for everyone with an interest in R, whether you’re a seasoned pro or just getting started.
Continuing our theme of R-related events, the Cloud-SPAN project are running a free two-hour “Core R” workshop covering basic use of R and RStudio on Thursday 25th April, 14:00-16:00. Places are limited and you can register your interest in joining this workshop via the workshop info page. Applications close at midday on Monday 15th April.
From the 6th-10th May 2024, Durham University will host the Durham HPC/AI Days 2024 event. Registration is open.
ISC High Performance 2024 takes place 12th-16th May 2024 in Hamburg, Germany. Registration for the conference is now open and the discounted early-bird registration rate ends on 27th March.
As part of ISC24, the RSEHPC@ISC24 workshop will take place on Thursday 16th May, bringing together the RSE and HPC communities. [Note that separate registration is required for the workshops day of the conference]
And a few reminders of upcoming events that we highlighted last month…
The “FAIR Implementation Workshop - Assessing national current FAIR-enabling capabilities” will take place on Tuesday 14th May 2024. Secure your spot by confirming your registration. Quick reminder: Workshop registration is both free and mandatory.
Registration for the Software Sustainability Institute’s Collaborations Workshop 2024 (CW24) is still open! The event will take place from the 30th April to the 2nd of May as a hybrid event, with the in-person venue in Warwick. The themes for CW24 are Environmental Sustainability, AI/ML tools for science and Citizen Science.
For this month’s Research Software of the Month, we highlight HL2-DINO from the Mechatronics in Medicine lab within Imperial’s Hamlyn Centre:
As part of our research at the Mechatronics in Medicine lab at Imperial College London, we have worked on integrating augmented reality (AR) headsets with commercial surgical robotic systems for orthopaedic surgery. Specifically, we have written software which enabled the Microsoft HoloLens 2 to detect and track infrared reflective markers. These types of markers are commonly used in computer/robot-assisted surgery.
Imagine a scenario where surgical tools or patient anatomy equipped with IR markers are tracked in real time, allowing the surgeon to interact with virtual ‘holograms’ that appear directly on the patient or their tools. Our aim was to provide a hands-on experience of tool-tracking, and better integrate the real surgical world with the virtual world of AR. We recently open-sourced a set of repositories which allow you to try this out yourself if you have access to a HoloLens 2. The projects are all contained within the GitHub organisation HL2-DINO.
There are two main software repositories in HL2-DINO:
For more details check out the landing page of the HL2-DINO organisation on GitHub!
As highlighted in the introduction, we are delighted to have had a new project funded under EPSRC’s Strategic Technical Platforms call. Announced by EPSRC last week, with further details provided in Imperial’s announcement, STEP-UP is a £2m consortium led by Imperial and in collaboration with UCL, King’s and Westminster. It’s one of a group of 11 new projects supporting Research Technical Professionals. STEP-UP provides a fantastic opportunity to change the way we recognise, support and develop digital Research Technical Professionals – technical professionals (and researchers) whose work focuses on building software, analysing and managing data or building and maintaining research computing infrastructure.
The project will build on a range of regional research software community activities developed through our Research Software London (RSLondon) community, which we’ll be growing to provide wider community support for data and computing infrastructure professionals. Look out for more about STEP-UP in the coming months. There will be a variety of ways for you to get involved as we look to develop opportunities to support technical secondments of staff between our partner institutions, set up a technical mentoring scheme and create a Research Technical Champions programme.
Talking of Champions, we’re really pleased to announce the launch of our 2024 Research Software Champions programme this week. This programme is a second pilot of the Champions scheme, building on our experiences from last year. The programme is funded via Imperial, supported by Research England research culture funding, and this year it’s part of a project “Beyond Open Research”. The wider project will be running a set of workshops over the coming months looking at a variety of aspects of open research, research integrity and ethics, including in areas such as AI and medical data. If you’d like to get involved with the project and participate in one or more of the upcoming workshops, contact Jose Sousa, Engagement Officer: Research Culture for more details.
Our 15 Champions from 13 different Imperial departments will be working to raise awareness of good practices for research software. They will also be providing advice and guidance on opportunities around the College for getting support and training for building and working with research software. If you’re keen to speak to a Champion in your department, let us know at rse-committee@imperial.ac.uk.
You’ll be hearing more from our Champions in these newsletters over the coming months.
Our most recent byte-sized RSE session covered CITATION.cff files and the cffinit tool, providing details on opportunities to make your code citable. You can also listen to the companion podcast from this session released as part of the Code for Thought series - “ByteSized RSE: the Citation File Format”
The Software Sustainability Institute report on Software and skills for research computing in the UK looks at the required software and skills, in the context of three areas - people, infrastructure and policy - that are required for the UK to respond effectively to research computing challenges over the next five years.
CodeRefinery have undertaken a complete rewrite of their “Introduction to version control” lesson covering Git and GitHub. You can find the updated lesson in CodeRefinery’s core lessons.
Do you work with Jupyter notebooks? Have you ever thought about reproducibility of materials you publish based on these notebooks? An interesting article in GigaScience looks at “Computational reproducibility of Jupyter notebooks from biomedical publications”.
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.