Summer is upon us, both astronomically speaking and also weather-wise (at least for now), which is not always the case. During the last month I have been setting up my back garden so I can work there the days I am staying at home. I had to do some stone work, painting, buying a set of chairs and table, and adding some shade. Then, I realised - which now seems obvious - that working in front of a computer outdoors is not that great as even with the highest brightness setting in the screen, it is often uncomfortable to read anything for long periods of time.
So, do not try to do everything at once like myself. Enjoy the time outdoors by doing outdoor things, like talking to friends around a BBQ or walking in the park, taking breaks from your indoor work often. And also enjoy your software-related work and the multiple opportunities and resources that this edition of the newsletter brings you.
Happy summer!!
The RSECon24 conference registration deadline is Sunday 30th June 2024. The event is hybrid and the organisers are offering a limited number of bursaries for those who would otherwise be unable to attend the conference in person.
The next RCDS hackathon 2024: The fast and the curious! - will take place on July 12, 2024. Register via Inkpath, the same way as for other RCDS courses (instructions at the top of this page).
The RSLondonSouthEast2024 workshop will take place at Imperial on Tuesday 16th July 2024! Join us for talks, posters, discussion and an opportunity to meet other researchers and technical professionals from across the London and South East of England region. Register now, workshop registration closes soon.
The HPCRSE@RSECon24 Birds of a Feather (BoF) session at RSECon24 on Thu 5th Sep 2024 is accepting submissions for short presentations until July 16th. This RSECon24 BoF session aims to bring together the community of RSEs working in High Performance Computing (HPC), to share their knowledge and experiences.
The next talk in the DiveRSE series of seminars on diversity, equity and inclusion in the research software community will take place on Tuesday 31st July. Ella Kaye, University of Warwick and Malvika Sharan, The Alan Turing Institute will have “A conversation about Equity, Diversity, Inclusion and Accessibility (EDIA) in the RSE community: reflections on successes and challenges”. Registration is now open.
The International Conference for High Performance Computing, Networking, Storage, and Analysis (SC24), will take place from 17th-22nd November 2024 in Atlanta, GA, USA. There is a detailed submission site accounting for all announcements and deadlines, some of which close in June and July.
In this month’s newsletter, we feature another two of our 2024 cohort of Research Software Champions. Our Champions are continuing to work within their departments, funded through the Beyond Open Research project, to help better understand how software is used as part of research processes, the challenges that researchers and students face, and what opportunities exist to provide better support for the development of research software in departments across the University.
I am a PhD student in the Department of Electrical and Electronic Engineering. My research is in the area of model order reduction of complex dynamical systems. Several systems of significance in engineering and science exhibit complex behaviour governed by high-dimensional nonlinear partial differential equations. The nonlinear terms in these equations inhibit the successful application of projection-based methods for model order reduction. Yet, the ability to solve such problems would unlock new directions in simplifying the control design, real-time simulation and optimization, and uncertainty quantification of several large-scale dynamical systems.
My research aims to address some of these challenges by exploring numerical methods for model order reduction of nonlinear systems that can be reliably applied to a diverse set of applications such as energy systems, fluid dynamics, and neuroscience. A key goal of my research is to design easy-to-use model reduction algorithms for linear and nonlinear systems both from a model-based and a data-driven perspective. As a part of this work, I would like to develop software tools that can help the user undertake the model reduction exercise in a systematic fashion.
Before joining the PhD program at Imperial, I was a software developer for a scientific computing company in the United States. This experience helped me understand the nuances involved in the development of computational machinery used by researchers in the area of control theory. The Research Software Champion scheme helps strengthen this experience by exposing me to issues faced by researchers from other disciplines. This is immensely beneficial for me since I aim to develop easy-to-use model reduction software that can be used by users from a plethora of application domains.
My research at the Dyson School of Design Engineering focuses on interdisciplinary collaborations within healthcare design project teams. I am particularly investigating how discipline-specific training, methods, and mental frameworks create boundaries that hinder knowledge transformation. This research involves stakeholders from various backgrounds, including medicine, engineering, design, and business. The early stage of the design process, especially when establishing a shared understanding of the problem, is chosen as the initial approach.
As a designer, coding skills are invaluable as they allow me to explain my designs and communicate with other stakeholders through tangible prototypes. Especially while building interactive devices, coding and creating mockups can help establish a common language and bridge the knowledge gap with a non-design audience. This is closely related to my research interest in creating boundary objects within interdisciplinary teams.
I am keen to be an active member of the Research Software Champions scheme as it presents a great opportunity to advocate for other design engineers like me who are not professionally trained in coding. There is much knowledge and many methods that non-coders are not aware of or do not have access to, which I believe can be made more transparent and available to my fellow PhD students at the Dyson School, enabling their creativity to be untethered by technical constraints.
This month, our Research Software of the Month is Bubble Analyser, developed in the Earth Science & Engineering Department.
Bubble Analyser was born out of very small and simple code made during an experimentalist’s PhD to measure bubble size in a flotation tank (mining/mineral processing). The goal was to have a user friendly, easy to use tool to analyse bubble size distribution (BSD), a factor that is well known for influencing the performance of many industrial processes, such as froth flotation. Other existing software was very expensive, obscure in the algorithms used, or are of general purpose and have many other applications and therefore was not tailored for this particular problem, making its use more complex.
Bubble Analyser is written in Matlab and features a graphical user interface to simplify its use. It includes a standard image processing algorithm that was tested against manually segmented images, showing errors under 5% in the calculation of the Sauter mean diameter, the most common descriptor of BSD. Additionally, Bubble Analyser has been designed to easily incorporate new segmentation algorithms developed by other researchers, in order to expand the software capabilities, allowing for algorithm comparisons, and fostering collaboration in research.
The development of the open-source code was an independent collaboration of Imperial early career researchers: Dr Diego Mesa, Dr Francisco Reyes, and Dr Paulina Quintanilla. Bubble Analyser is released under a GNU GPLv3 license and provides binary executables for Windows and macOS. It is also the awardee of the last edition of the Open-Source Booster programme, which will support its further development and flexibility in the future.
Numpy 2.0 has been released! While updates are a necessity, a major update on a library so widely used as Numpy is bound to make a lot of people nervous as it brings several breaking changes to the API. Have a look at the migration guide to find out what you need to change in your code in preparation to Numpy 2.0.
Staying with Python, it has just been advertised that from 2026 it will move to a year-based release. This means there will be no Python 3.15 in 2026 but rather it will be Python 3.26, clearly stating the year it was released.
The Centre for Scientific Collaboration and Community Engagement (CSCCE) are launching Birdaro, a new project that will provide support for open source scientific projects as they scale up. Read more about the project on the CSCCE blog.
Green DiSC is a new certification scheme which provides a roadmap for research groups and institutions who want to tackle the environmental impacts of their computing activities. Check out the Green DiSC page for full details! The next informative seission is on Thursday 18th July.
Finally, we have a rolling GTA opportunity here.
Continuous Integration (CI) via GitHub Actions is a key tool for supporting robust software development, but it is very easy to overuse it - or use it incorrectly - with negative consequences for the environment. In this blog post, Chris Cave-Ayland, Technical Lead of the RSE Team, discusses a few simple steps to make your CI workflows faster, more environmentally friendly and also reduce their cost.
On the topic of environmental computation, have a look at the Green Algorithms project, which contains calculators that researchers can use to estimate the carbon footprint of their projects, tips on how to be more environmentally friendly, training material, and other resources.
“Here’s why the Hidden REF is still needed”, an article by Gemma Derrick and Simon Hettrick recently published in ResearchProfessional News.
A new preprint from the team at the Netherlands eScience Center presents “RSMM: A Framework to Assess Maturity of Research Software Project”.
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.
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 Diego Alonso Álvarez. All previous newsletters are available in our online archive.