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Simulating light propagation through matter.

By Sam Cunliffe, on 31 October 2023

Observing how light interacts with materials allows us to develop non-invasive medical imaging techniques, that rely on these interactions to assemble an image or infer an appropriate diagnosis.

Light interacts with materials in many different ways. One of the most commonly observed interactions is dispersion; which causes white light to split into individual colours, creating phenomena like rainbows (light from the sun dispersing through raindrops). Another commonly observed interaction is refraction; which causes light to change direction as it passes between two materials, responsible for straight objects like straws appearing to be disjointed when placed into water. To completely describe what is going on in these interactions, we have to use a system of equations known as Maxwell’s equations. We also have to consider some additional parameters that describe the particular material(s) that the light is interacting with. In their most general form, Maxwell’s equations are very complex but have the advantage that almost all materials and interactions can be modelled by them. Solving these equations is, in general, impossible to do with pen and paper, so we need software to do this for us.

Software like this has a wide variety of applications in biomedical optics; notably optical coherence tomography (non-invasive medical imaging of the eye), multiphoton microscopy, and wavefront shaping. For example; we can use this software to model light propagating in the retina: simulating a retina scan. Then we can perform a retina scan for a patient in real life, and use our simulation to better understand the scan. Retinal scans often hint at a particular change to the retina, without being definitive, in the early stages of disease. We can use our simulation to test what types of changes to a retina can lead to observed signatures in an image and therefore help in achieving a diagnosis.

The Problem

In collaboration with the UCL Medical Physics and Biomedical Engineering department, developers from ARC have worked to open up a legacy C and MATLAB library which simulates light propagating through matter. This software was initially developed as part of a PhD thesis approximately 20 years ago and has been continuously developed since then. However, the need to rapidly answer research questions led to the code becoming less sustainable and harder for others to use. Whilst the core functionality was already there; the library needed updating to a more modern language and aligning with the FAIR4SW principles.

What we did

The aim of the project was to be able to provide users with a program that they can give custom input which describes the material they want to simulate, pass this to the software and receive an output they can use in further analysis. We wanted users not to have to worry about the internal workings of the software; only having to download the library code, build and install it once, and be ready for future analyses. We used modern build tools to standardise the build and install of the software, we aimed to make our instructions as straightforward and operating-system-independent as possible. We also set up automated testing of the software and wrote example scripts that users can modify to easily create input files in the correct format.

The outcomes

Version 1.0.1 of the Time Domain Maxwell Solver (TDMS), is now available under a GPL-3.0 license. You can download from GitHub, and install and run on all operating systems. The project has a public-facing website and a growing collection of examples. We also have developer documentation so anyone can contribute in the future.

TDMS 1.0.1 now has a number of new features, including the option to switch between different solver methods (how the simulation is performed), select custom regions over which to compute (to save wasting computation time), and the ability select different techniques for extracting output information through interpolation.

The ARC software engineers were a joy to work with. They brought knowledge of modern software engineering practice and quickly understood the code, and the underlying physics, as required to very effectively re-engineer the code. This collaboration with ARC will hopefully allow for a new range of users to access TDMS and significantly increase its impact.

Will Graham and Sam Cunliffe

RSE and Education for Sustainable Development: A Call to Action

By Samantha Ahern, on 12 September 2023

RSECon23 opened with a keynote from Gael Varoquaux, introducing themes synergistic to my conference workshop “How do we design and deliver sustainable digital research education”.

The actual theme of the workshop, what role(s) does RSE have to play in Education for Sustainable Development probably wasn’t what most participants were expecting. However, there were some very good conversations and ideas for action.

The workshop opened with two questions:
1. What does Sustainable mean to you?
2. What does Education for Sustainable Development mean to you?

These set the scene for the discussion in the session.

Key definitions and the SDGs

Sustainability
“meeting the needs of the present without compromising the ability of future generations to meet their own needs.”

UN, 1987

Sustainable Development
“An aspirational ongoing process of addressing social, environmental and economic concerns to create a better world.”

Advance HE / QAA 2021

Education for Sustainable Development
“The process of creating curriculum structures and subject-relevant content to support sustainable development.”

Advance HE / QAA 2021

The workshop participants were introduced to the 17 UN Sustainable Development Goals and asked to consider which are areas for development in RSE and which of these areas can we affect through education?

There was a general consensus that almost all are related in some way to RSE activity and impact that activity. The most notable being SDG 4: Quality Education.

Through RSE led education activity it was felt that the SDGs that could be affected were:

  • Goal 3: Good Health and Wellbeing
  • Goal 4: Quality Education
  • Goal 5: Gender Equality
  • Goal 8: Decent Work and Economic Growth
  • Goal 9: Industry, Innovation and Infrastructure
  • Goal 10: Reduced Inequalities
  • Goal 11: Sustainable Cities and Communities
  • Goal 12:Responsible Consumption and Production
  • Goal 13: Climate Action

For Goals 16 (Peace, Justice and Strong Institutions) and 17 (Partnerships For The Goals) it was unclear as to how these would apply.

Barriers and Opportunities

The discussion then focused on barriers to having an impact on the SDGs but also what opporunities we had for making a positive difference.

Barriers

Key themes from the discussion on barriers were:

  • Resources: time, people, data sets
  • Funding
  • Lack of training, confidence in education skills
  • Lack of recognition
  • Lack of support / mentorship

Opportunities

Key themes from the discussion on opportunities were:

  • Ability to design our own materials and select data sets
  • Work collaboratively, as a community
  • Ability to raise awareness of issues
  • Access to experts from across our institutions
  • Access to education related CPD (if in a university setting)
  • Our learners want to learn
  • Our educators are passionate about their work

Although there are some well recognised barriers, there is also a lot of opportunities and connections we can leverage to make change.

The Call to Action

The workshop concluded with a design task to identify concrete steps we could take to address the barriers and leverage the opportunities.

The calls to action were:

  • Never teach alone
    • Enables different ways to explain
    • Could lead to a variety of role models
    • Less pressure
    • More perspectives
    • Broader variety of disciplines
    • Different background knowledge
  • Encourage those who found it difficult to return as helpers and instructors
  • Humanise the educators
    • Introductions
    • Live coding
    • Coding confessiona
  • Co-development of lesson materials
    • Share ideas and examples
    • Examples from different domains
  • Talk to learners
    • What is needed?

Most importantly, we are community and should leverage that community to learn from and support each other.

So, let’s work together to make a positive change!

You can view the original results on Mentimeter.

View the Twitter / X thread from the workshop.

Two Senior RSE posts available at UCL ARC

By Jonathan Cooper, on 27 October 2022

The UCL Centre for Advanced Research Computing (ARC) is recruiting for two permanent Senior RSE members, with a closing date of 6th November 2022. One post has a focus on supporting UCL East, while the other is intended to be more teaching-focused, but any individual matching the job description is encouraged to apply. The most important attribute is an enthusiasm for reproducible, reliable and sustainable computational research!

ARC is UCL’s centre for digital research infrastructure and innovation: the software, supercomputers, data, and skills that underpin computational science and digital scholarship across the college. We are an innovative hybrid: a professional services department that delivers reliable and secure infrastructure and services to UCL research groups, and a laboratory for research and innovation in the application of advanced computational and data-intensive research methods, working in partnership with academics from all fields.

You will design, extend, refactor, and maintain scientific software in all subject areas, providing expert software engineering consulting services to world-leading research teams, training researchers in programming best practices, and working with scientists and scholars to build software to meet new research challenges. Whether this means using Python to build up a database of ancient Sumerian writings, parallelising Fortran codes for surface catalysis simulations, analysing live healthcare data within hospitals, or creating an MPI-distributed particle filter for data assimilation in Julia, we do it all. With such a varied job we don’t expect our candidates to know it all from the start. It is an excellent opportunity to develop new skills, spending time to study both the research areas we support and the specialist technologies applied.

The team is friendly and diverse, currently with over 45 research technology professionals collaborating on research projects and teaching. All our positions are permanent, on open-ended contracts, and enjoy good opportunities for personal development and career progression within the group, in both technical and managerial tracks. We support a range of flexible working options, including part-time appointments at all levels.

For more details of the vacancies and to apply check out the full adverts linked above. The closing date will be 6th November 2022, with interviews taking place using Microsoft Teams or in person between 17-25 November. The salary range is from £47,414 – £55,805 per annum.

Further vacancies across all ARC’s professions will be coming soon!

Hack the (ARC) Teaching workshop

By David Pérez-Suárez, on 4 July 2022

Two weeks ago (20th – 23rd June) we ran an internal workshop in our group to reflect about our teaching activities. As any good workshop, it also included a fun hack day at the end to work on pet projects or ideas that we haven’t had the time to work on it before. This is a summary of these four days and a reflection for the future.

The workshop was set with two main purposes: review all the teaching activities we are involved, and learn some techniques to become better teachers. The workshop was attended by roughly 8 people every session, this contributed to allow everyone to participate. The event was fully hybrid, with roughly a 50-50% participation of people joining physically and remotely (the trains and tube strike shifted the participation towards a 30-70% towards the end of the week).  Thanks to the big screen and the semi-separated areas we have in our collaboration space, together with how the workshop was run with smaller physical and virtual small groups, contributed to a nice flow of the workshop.

Each day of the workshop was broken into two 2-hour blocks, one in the morning from 10:00 to 12:00 and one in the afternoon form 14:00 to 16:00. This helped to disconnect a bit, catch up with other commitments or have time to enjoy lunch in the park while recharging our solar batteries.

In terms of tooling, we used MS Teams as the conferencing tool (our calendars and the big screen are linked to it) – we also explored the breakout rooms feature it provides; HackMD and Etherpad for note-taking; Google’s Jamboard for collaboratively moving cards in a digital medium; IdeaBoardz to collect feedback; and tried (with only partial success) Visual Studio Code’s Live Share to pair-program during the hack day.

Now that the logistics and tooling has been explained, let’s dive into the content of the workshop.

The workshop started with a short review of the Carpentries instructor training lessons. That workshop lasts two full days, and this session lasted only two hours. Therefore, many things were not covered (like practising the teaching), however, we covered some basics about how learning works and how to create a positive learning environment. As any Carpentries workshop, they are full of activities and discussions, and we had good and interesting discussions. The afternoon of that day, we spend it discussing a set of uncomfortable scenarios that may happen during a teaching activity. These scenarios were created by Yanina Bellini Saibene for Metadocencia and translated by J.C Szamosi. They are a very useful resource to explore before they manifest in a real situation. The scenarios were distributed between the different small groups and then shared with the bigger group our suggested actions. Of course, sharing it in the bigger group was also a source of new point of views and ideas. We highly recommend doing this exercise to everyone who takes part in any teaching activity! The day finished with a review of the Science of Learning paper. As with the previous exercise, we distributed the sections across us and discuss it first in small groups and then as a whole. This is a nice quote about the paper from Sarah in our team:

I want to print this out and stick it all over my office so I can see it whenever I teach.

The second day was focused on our teaching activities and an overview of Submitty, the autograding tool we use in a couple of master courses we teach. We started with a set of lightning talks (aiming for 1 minute each, but all of us overran a bit) for each teaching activity we are involved in. Each talk has to describe the teaching activity with its topics, the audience to whom it is aimed to, the format, what is going well and what can be improved, and finish it with the challenges presented for next year – all that in one minute! We had 13 talks, some of these talks are from courses or workshops we run once a year, others are about courses that happen multiple times. Two of them were from the UKRI Data Science Training in Health and Bioscience (DaSH) projects we are involved with: IDEAS and Learn to Discover. The last one was a short summary of the teaching activities from our friends at Digital Education. The afternoon was focused on Submitty. First with an overview of how the system looks from the different point of views (student and instructor) and then how to set up the exercises. We completed the day with an exercise about thinking how to plan the autograding of two questions from past assignments. The main conclusion of this exercise was that for autograding to work, we need to be more specific on what we ask the students. This, however, may have its disadvantages as it limits the freedom of how the students may approach a problem.

The third day was an ABC Learning Design workshop led by Nataša Perović from UCL’s Office of the Vice Provost Education & Student experience. The workshop starts with an overview of the different learning activities types as described in Diana Laurillard’s work “Teaching as a design science”. We spent the practical side of the workshop, focusing on three of our courses. It was a very useful exercise that we should do more frequently to keep improving and fine-tuning our courses. In the afternoon, we learnt how to migrate our notes from Jamboard into the Learning designer tool from UCL’s Knowledge Lab at IOE. One cool feature that Nataša demonstrated to us is how our Learning Design structure can be exported into Moodle.

The last day was the hack day. We have a collection of mini-projects that we would like to work on, but that normally get postponed till we have the time… Well, finally the time arrived! We tackled four of these projects, two were completed quite quickly, and the other two got started (and that’s sometimes the harder bit!) and hopefully the inertia keeps them moving to a complete state soon. One project that involved an analysis of students grades included a good discussion at the start about the ethics and privacy of the project. This helped to make some decisions of which dataset we were going to use (e.g., the anonymous dataset provided by Moodle before the marks get released), and future ideas about how to clarify to the students how the assignments get graded anonymously.

That was how we’ve spent four days last week learning how to improve our teaching, reflecting on what we’ve done so far and planning what we can do to have better courses in the future. After the positive feedback and seeing how useful a focus week without other distractions can be, we may make this a recurrent annual activity!

Further expansion of UCL’s RSE group, with permanent roles at assistant through senior levels

By Jonathan Cooper, on 31 May 2022

The UCL Research Software Development Group is again looking for new RSE members at 3 grades up to senior, with a new ‘assistant’ role suitable for applicants straight out of undergraduate degrees. We are planning to appoint at least 4 new staff, ideally more, depending on the strength of the field.

TL;DR: Apply via the UCL jobs system before the end of Monday 13th June 2022! Ensure you state in your application which grade you are applying for.

The group, founded in 2012, was the first of its kind, and is one of the leading university-based research programming groups in the UK. We work across college developing high-quality software, collaborating with world-leading scientists, engineers and scholars from all research domains, within UCL and beyond. Whether this means using Python to build up a database of ancient Sumerian writings, parallelising Fortran codes for surface catalysis simulations, analysing live healthcare data within hospitals, or creating an MPI-distributed particle filter for data assimilation in Julia, we do it all. Given the variety of areas in which we work, and the regular turnover of new projects, we welcome a wide range of backgrounds and technical skill sets and support staff to learn on the job. Experience in Django, high-performance computing or “ML Ops” would be a bonus, but if the general job description matches your profile do not hesitate to apply – all skill sets are welcome. The most important attribute is an enthusiasm for reproducible, reliable and sustainable computational research!

The team is friendly and diverse, currently with over 35 members. All our positions are permanent, on open-ended contracts, and enjoy good opportunities for personal development and career progression within the group, in both technical and managerial tracks. We support a range of flexible working options, including part-time appointments at all levels.

For more details of the vacancy and to apply check out the full advert. Note that job descriptions for all 3 grades are given, and you should state in your application which you consider best fits you; the depth of interview will be selected accordingly. The closing date is 13th June 2022, with interviews taking place using Microsoft Teams around 2 weeks later. The salary range is from £29,802 to £53,757 per annum depending on grade.

Recruiting a dedicated RSE for open-source image-guided surgery tools

By Jonathan Cooper, on 27 May 2022

UCL’s Research Software Development Group is strengthening its expertise in medical imaging through a new joint post with the Wellcome / EPSRC Centre for Interventional and Surgical Sciences (WEISS). WEISS is located at Charles Bell House in London, and is well supported by state-of-the-art computational facilities and surgical laboratories. Members of WEISS collaborate with world-leading centres such as the UCL Centre for Medical Image Computing (CMIC), the Institute of Healthcare Engineering (IHE) and the Division of Surgical and Interventional Science.

This Research Software Engineer role is available at standard or senior level depending on your knowledge and experience. You will support the development, maintenance, and dissemination of open-source software tools to accelerate research and create clinical impact in image guided surgery. Until May 2024 the work will focus on further development of the SciKit-Surgery libraries. SciKit-Surgery aims to support researchers globally working on applications in image guided surgery. The successful candidate will have the opportunity to create novel open-source software libraries. The exact nature of the libraries may change based on research priorities but includes areas such as hardware accelerated deep learning, novel visualisation and user interface design, computer vision, and scientific education and outreach. You will also contribute to publications in international journals and conferences.

If the following describes you, then you should consider working with us:
  • You have created and maintained software addressing complex problems in one or more fields. Imaging or healthcare experience is beneficial but by no means essential!
  • You can build an understanding of new scientific questions, and connect research needs to IT requirements.
  • You are committed to software development best practices, and know how to apply these in research contexts.
  • You share our enthusiasm for reproducible, reliable computational research, and are able to help to spread that to our research community.
  • You are keen to expand your knowledge.

There are good opportunities for personal development and career progression within the group, in both technical and managerial tracks. The role includes time to study the research areas with which we work, and the specialist technologies applied in digital research. Funding for training and conference travel is also readily available.

For more details check out the formal advert and job specification. The closing date is 19th June 2022, with interviews later in June/July (exact dates TBC). This position is permanent (on an open-ended contract), with salary negotiable up to £53,757. Part-time applicants are welcome (unfortunately it’s only the small print of the formal ad that mentions this!) and various forms of flexible working are available.

UCL’s Medical Imaging Research Software Group is growing again

By Jonathan Cooper, on 7 February 2022

In 2019 the Research Software Development Group launched an exciting new collaboration with the Centre for Medical Imaging Computing (CMIC) to develop services for and support researchers across the institution who are working with medical research data sets, particularly imaging data. This sub-group, branded as the UCL Medical Imaging Research Software Group, has been so successful that we are again looking for new staff to expand our activities: collaborating on more research projects, and extending support to new areas such as pathology data and more general microscopy.

You will be able to take an active role in the deployment and support of cutting-edge image analysis techniques and infrastructure for large scale studies. If the following describes you, then you should consider working with us:
  • You have created and maintained software addressing complex problems in one or more fields.
  • You can build an understanding of new scientific questions, and connect research needs to IT requirements.
  • You are committed to software development best practices, and know how to apply these in research contexts.
  • You share our enthusiasm for reproducible, reliable computational research, and are able to help to spread that to our research community.
  • You are keen to expand your knowledge.

There are good opportunities for personal development and career progression within the group, in both technical and managerial tracks. The role includes time to study the research areas with which we work, and the specialist technologies applied in digital research. Funding for training and conference travel is also readily available.

For more details check out the formal advert and job specification. The closing date is 27th February 2022, with interviews in March (exact dates TBC). This position is permanent (on an open-ended contract), with salary negotiable up to £48,167.

More entry & senior level RSE posts created at UCL

By Jonathan Cooper, on 20 December 2021

The UCL Research Software Development Group is again looking for new RSE members at either entry or senior level. We are planning to appoint at least 2 new staff, ideally many more, depending on the strength of the field.

TL;DR: Apply via the UCL jobs system before the end of Sunday 9th January 2022!

The group, founded in 2012, was the first of its kind, and is one of the leading university-based research programming groups in the UK. We work across college developing high-quality software, collaborating with world-leading scientists, engineers and scholars from all research domains, within UCL and beyond. Whether this means using Python to build up a database of ancient Sumerian writings, parallelising Fortran codes for surface catalysis simulations, analysing live healthcare data within hospitals, or creating an MPI-distributed particle filter for data assimilation in Julia, we do it all. Given the variety of areas in which we work, and the regular turnover of new projects, we welcome a wide range of backgrounds and technical skill sets and support staff to learn on the job. Experience in health data science, high-performance computing or “ML Ops” would be a bonus, but if the general job description matches your profile do not hesitate to apply – all skill sets are welcome. The most important attribute is an enthusiasm for reproducible, reliable and sustainable computational research!

The team is friendly and diverse, currently with over 30 members. All our positions are permanent, on open-ended contracts, and enjoy good opportunities for personal development and career progression within the group, in both technical and managerial tracks. We support a range of flexible working options, including part-time appointments at either level.

For more details of the vacancy and to apply check out the full advert. Note that job descriptions for both grades are given, and you should state in your application which you consider best fits you; the depth of interview will be selected accordingly. The closing date is 9th January 2022, with interviews taking place using Microsoft Teams during the week commencing 24th January. The salary range is from £36,770 to £53,757 per annum depending on grade.

Entry and Senior level RSE posts available at UCL

By Jonathan Cooper, on 1 October 2021

The UCL Research Software Development Group is again looking for new RSE members at either entry or senior level. We are hoping to appoint at least 2 new staff, possibly more, depending on the strength of the field.

The group, founded in 2012, was the first of its kind, and is one of the leading university-based research programming groups in the UK. We work across college developing high-quality software, collaborating with world-leading scientists, engineers and scholars from all research domains, within UCL and beyond. Whether this means using Python to build up a database of ancient Sumerian writings, parallelising Fortran codes for surface catalysis simulations, analysing live healthcare data within hospitals, or designing and building a big data image processing library in C++11 and Python, we do it all. Given the variety of areas in which we work, and the regular turnover of new projects, we welcome a wide range of backgrounds and technical skill sets. The most important attribute is an enthusiasm for reproducible, reliable and sustainable computational research!

The team is friendly and diverse, currently with 30 members. All our positions are permanent, on open-ended contracts, and enjoy good opportunities for personal development and career progression within the group, in both technical and managerial tracks. We support a range of flexible working options, including part-time appointments at either level.

For more details of the vacancy and to apply check out the full advert. Note that job descriptions for both grades are given, and you should state in your application which you consider best fits you; the depth of interview will be selected accordingly. The closing date is 17th October 2021, with interviews taking place using Microsoft Teams (dates TBC). The salary range is from £36,770 to £53,757 per annum depending on grade.

How to get started with HPC and AI in your research

By Anastasis A Georgoulas, on 28 September 2021

The Tech Socials are back after our summer break, this time with a twist. For September’s social, we decided to follow up on a SeptembRSE event with our own discussion.

The topic was how to get started with technologies like high-performance computing and artificial intelligence. The panel members came from UCL’s Centre for Advanced Research Computing (ARC), research institutes in molecular biology and sociology, as well as industry. We wanted a range of perspectives, and we think we got it!

There’s lots to talk about on this topic and the discussion proved that, as we moved away from practical tips (such as keeping in mind the scale of your data and workloads) to consider the broader context. We covered policy issues, like the availability of seed funding, ideas for tackling the “skills gap” that researchers and students have to overcome, the importance of wrapping your head around what is possible to do with new technologies, all the way to the right attitude, and how technologists can more efficiently communicate with researchers in the social sciences and humanities (hint: some humility is advised).

If this sounds interesting, do watch the recording (unfortunately missing the first few minutes of introductions!). We are still exploring how ARC can best serve UCL, so get in touch if you think we can work together – you can find out more about what we do on the Research Programming Hub pages until the website reflects our change to ARC.

Thank you to all panel and audience members for their contributions!