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?
The Cloud-SPAN project are running a two-week online course for UK-based researchers on “Metagenomics with High Performance Computing” between the 11th and 21st April 2023. This course may be of interest if you work in metagenomics or a closely-related area and are looking to develop the core skills to run pipelines on Imperial’s HPC platform or other high performance computing resources.
The Dutch Community for Research Software Engineers (NL-RSE) and the Health-RI Data Stewardship Community are organising an in-person meetup in Utrecht Netherlands titled Bugs in research data and software with Daniël Lakens. The event will be on Wed, 19 Apr 2023 and registrations are open… because we all make mistakes, and it is important to understand how they affect the data we use.
The Software Sustainability Institute (SSI) Collaborations Workshop (CW23) will take place on the 2nd-4th May 2023 in Manchester as a hybrid event. In person places are now full (a waiting list is in operation) but there are spaces available for online attendance.
The 8th EasyBuild User Meeting (EUM’23) will take place at Imperial on the 24th-26th April 2023. The deadline is approaching: if you are interested register before Sunday 2nd April 2023.
Related to EUM’23, the EasyBuild/EESSI UK workshop will take place at Imperial on the 27th and 28th April 2023. Attendance is free but registration is required and places are limited. The registration deadline is Sunday 9th April 2023. See the workshop webpages for further info. This is a great opportunity to learn about EasyBuild and to engage with the UK EasyBuild and EESSI communities.
JupyterCon 2023 will take place in Paris, France on 10th-12th May 2023. Conference registration is now open.
This June (2nd-4th) will see PyData London 2023, a fantastic opportunity to engage with the global community using and developing scientific tools for the Python ecosystem and beyond, also covering Julia, R, and others. The Call for Proposals is now open!
F1000Research has issued a call for papers for a new collection on Innovations in Research Assessment. The deadline for submissions is Friday 30th June 2023. You can also find further information in this short SSI post announcing the collection.
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.
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.
We have already met 3 of them in the “Research Computing at Imperial” section but our full cohort of Research Software Champions consists of 14 PhD students from departments across the College. The Champions will be undertaking their activities until the end of July and more information will appear on the Research Software Community web pages soon but, in the meantime, if you’d like to get in touch with a Champion working in your field you can contact Jeremy Cohen for more information.
Stanford University is again running the Code in Place course this year. Code in Place 2023 runs for 7 weeks from 24th April to 10th June 2023. This scheme provides you with a great opportunity to sign up as a Section Leader to teach Python to a small group of 10 learners who are assigned to you by the course organisers. The materials are based on the first half of Stanford’s Intro to Python course and look to support thousands of learners worldwide.
Are you getting a “WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED!” message when trying to connect to GitHub.com via SSH? Well, first of all: good! It means that all the checks are working. In fact, at approximately 05:00 UTC on March 24 GitHub replaced its RSA SSH host key. You can find details and what to do on the GitHub Blog. Please note that if you are using ECDSA or Ed25519 keys, you will not notice any change and no action is needed.
GitHub is testing out the capability to comment on files as a whole, not a specific line, in a pull request. This is useful for instance to comment on deleted files. The feature is currently in public beta. You can read more about it here.
In this blog post the authors spoke about the value of defining the roles of Research Software. It summarises the outcomes of the discussion started during The Future of Research Software international workshop and includes input from the community collected via social media.
There are a couple of new episodes available in the Code for Thought podcast series. One episode - Mind the Gap! - looks at research software training and features a panel discussion that includes Jeremy Cohen from our Imperial Research Software Community. Another episode reports on the recent German RSE conference held in Paderborn, Germany in February 2023, available in both English and German.
The team behind ARCHER2 is running a couple of webinars, based on their 2022 Image and Video Competition, where scientists present their competition submissions and talk through the science behind them. The first webinar took place on Wednesday 22nd March and the video is available on YouTube. The second webinar The Science behind the Image Competition - 2 will take place on Wednesday 5th April, 14:00-15:00. You can watch live online or check back on the event page for a link to the recording if you can’t make it for the live session.
For the US Women’s History Month, The International Conference for High Performance Computing, Networking, Storage, and Analysis is profiling over thirty-one women in HPC, in celebration of their contributions to the field of supercomputing. You can find some of them featured in these blog posts.
To return to the discussion about AI and how educators and students can adapt to it, check the episode Does your professor pass the Turing test? (Ep. 537) of the Overflow podcast.
Are you using Unix Shell to process your data? So maybe you are interested in a cheat sheet with 14 various set operations by using common command line utilities such as diff, comm, head, tail, grep, wc and others.
“Could you imagine one day having a dynamically evolving virtual replica of yourself that your doctor could use to drive personalized decisions to optimize your health and well-being?” This is an intriguing question to introduce the new webinar from the series Supercomputing Spotlights: Digital Twins: How High-Performance Computing is Personalizing the Future for Complex Systems Wed, April 19, 2:00-2:40 pm UTC. Participation is free, but registration is required.
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 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.
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! firstname.lastname@example.org.
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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.