Imperial College Research Software Community Newsletter - March 2023

Greetings Research Software Community!

It is spring already. Although the weather might not be feeling too vernal just yet. Despite that, what better time to look for new things, start new projects, try new tools?

For this newsletter’s issue I have done my little experiment with AI. I have asked ChatGPT how to create the perfect newsletter and it seems that we are already ticking all the boxes: from “Include relevant news and updates” to “Highlight community members”, from “Offer helpful resources” to “Include a call to action”. What the AI seems to miss is that you also need a great community. And the response to our initiatives shows that clearly. Consider, for instance, the PhD students that are now Research Software Champions here to help colleagues involved in software development for research at Imperial. We are growing together, and this is great.

And you? Are you using large language models in your research? Why not share your experiences in our community’s Slack workspace?

Happy reading!

Dates for your diary

Research Computing at Imperial

For our Research Computing at Imperial feature this month, we’ll be introducing three of our new Research Software Champions. As part of a project on enhancing research software culture and developing an updated Research Software Directory to promote the software that is developed at Imperial, we have a group of 14 Champions from across all 4 Imperial Faculties. The Champions will be working within their local research communities to understand more about how software is used, what challenges are faced and how we can support an enhanced culture around the use of best practices for building research software at Imperial. You’ll be hearing from some of our other Champions in the coming months but this month, we begin by introducing Metin Bicer, Sneha Jha, Leandro Perao.

Metin Bicer: I’m a Civil and Environmental Engineering PhD researcher specialising in collecting and analysing human movement data. My research focuses on developing predictive models to estimate biomechanical variables in human walking using a single sensor worn at the lower back. I have published two papers in the field of biomechanics, including one that involved generating synthetic data to enhance existing datasets. Currently, my work involves generating human movement data based on various physical attributes. I joined the Research Software Champions scheme because I believe in the importance of reproducibility of scientific articles and open access to software and data in scientific research. I am passionate about delivering information about best practices for writing research software to my department to create a culture of open-source research software development practices.

Sneha Jha: I am a postgraduate researcher working across the Dept of Mathematics and the Dept of Surgery and Cancer. I am member of the Translational Data Analytics and Informatics In Healthcare group and the iCARE group under the NIHR Imperial BRC. I am a computer scientist by training and prior to Imperial College, I received a graduate degree in computer science and worked as a research scientist in the United States. I was also a software developer and consultant in what seems like a past life now. My research interests are in machine learning and natural language processing with a focus on solving problems in health care. I am also interested in the overlap of technology with policy, law and ethics. The interdisciplinary nature of my research is fertile ground for adapting tools and techniques across subfields. As a research software champion, I hope to expand and share that experience with the larger community at Imperial.

Leandro Perao: I am a 4th Year PhD Student in the Mechanical Engineering Department, where I undertake research on multiphase flow within nozzles using Computational Fluid Dynamics (CFD) tools. I began working with research software when trying to use OpenFOAM, an advanced open source CFD package, but after experiencing difficulties with this, I then switched to do moving mesh simulations using Ansys Fluent, a commercial software package for fluid simulation. As someone working on software-related activities, I somehow overlooked for a good period of time the role of the Research Computing Service (RCS) in supporting such work at Imperial. Once I discovered the RCS, they were very helpful in offering advice and support with technical challenges I was having. I joined the Research Software Champions scheme hoping to improve awareness in the Mech. Eng. community about the many channels that exist to support their software research from the first steps. My work will include talking to the community to find out their needs for tackling computing research challenges.

Research Software of the Month

Our Research Software of the Month for March 2023 is Far INfrarEd Spectrometer for Surface Emissivity (FINESSE), because software is often used to control hardware in research:

FINESSE is open-source graphical software to control a spectrometer system developed at Imperial College’s Space and Atmospheric Physics group.

Emissivity of the Earth’s different surface types helps determine the efficiency with which the planet radiatively cools to space and is a critical variable in climate models. However, to date, most measurements of surface emissivity have been made in the mid-infrared. The FINESSE project is novel in employing a ground-based system capable of extending these datasets into the Far-infrared. The system is tuned in particular for targeting ice and snow, as the response of the climate to global warming is observed to be most rapid in Arctic regions. Far-infrared emissivity data provided by FINESSE will inform climate modelling studies seeking to better understand this rapid change. They will also help to validate emissivity retrievals from upcoming satellite instruments focusing on the far-infrared which will be deployed by ESA (FORUM) and NASA (PREFIRE).

The software was developed by Imperial’s RSE team. It is written in Python and uses the PySide6 Qt bindings for the GUI components. It provides a convenient interface for controlling the various hardware components and viewing data produced, including a Bruker EM27 spectrometer, a stepper motor for controlling the mirror, two temperature controllers and a separate temperature monitoring array.

In the future, this software will be adapted as part of a second project to deploy a modified version of the equipment on the UK’s Facility for Airborne Atmospheric Measurements aircraft.

RSE Bytes


Blog posts, tools & more

Some reminders…

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 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.

Research Software Engineering support

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:

HPC documentation and tips

All the documentation, tutorials and howtos for using Imperial’s HPC are available in the HPC Wiki pages. 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.

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!

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This issue of the Research Software Community Newsletter was edited by Stefano Galvan. All previous newsletters are available in our online archive.