Hello and welcome to the August 2022 newsletter! I think we can all agree this summer has been an eventful one for the UK. From the record-breaking heatwave back in July to this month’s magnificent triumph of the Lionesses at the Euro 2022 finals, history has been made. But if you find yourself away from all this excitement coding away at your desk, know that you are also making history one commit at a time (pun intended).
In this edition of the newsletter we bring you a varied selection of events and interesting reads for your next coffee break. Is there an event, blog post or useful tutorial that you would like us to feature in the newsletter? Then drop us an email and let us know, or better yet, volunteer to join the College’s RSE Community Committee and help us edit future editions of this newsletter! You don’t need to be a software expert or hold a senior role to join.
SuperComputing22 (SC22) takes place in November in Dallas, TX. A small number of the workshops associated with SC22 have extended their submission deadlines into the start of September so there’s just time to get submissions in. Some workshops are also accepting extended abstract submissions for short presentations. Workshops still accepting submissions include the 9th International Workshop on HPC User Support Tools (HUST2022), deadline Thursday 1st September and Machine Learning in HPC Environments (MLHPC2022), deadline Friday 2nd September.
The next Imperial Research Software Community Seminar is taking place in person on Wednesday 14th September at 3pm. Maeg Doherty, a Software Sustainability Institute Fellow based at the National Institutes of Health in the US will join us to talk about her work on improving user experience in research software. Use this form to register your attendance.
EPSRC’s Access to HPC call is open. This call provides an opportunity for projects within EPSRC’s remit to apply for time on High Performance Computing (HPC) resources such as ARCHER2 and a group of Tier-2 HPC resources. The deadline for technical assessment submissions is 20th September 2022 (at 16:00) and the main application closing date is 18th October 2022 (at 16:00). See the call page for further information.
CodeRefinery is running an online workshop on tools and best practices for scientific software development. The workshop will take place on September 20-22 and 27-29. Visit the workshop website to register as an attendee or exercise leader.
CoSeC (the Computational Science Centre for Research Communities) have a call for presentations for their CoSeC Annual Conference 2022. The deadline for abstract submissions is Friday 30th September 2022. The conference takes place on 1st December as part of Computing Insight UK.
Registrations are open for the second Nordic-RSE online unconference which will take place on the 18th and 19th October 2022. Visit the conference website for more details and registration.
Our Research Software of the Month for August is DLTK, the deep learning toolkit for medical imaging.
DLTK is a neural networks toolkit written in Python that extends TensorFlow to enable deep learning on biomedical images. It provides specialty ops and functions for this domain out of the box. DLTK comes with introductory tutorials and basic sample applications, including scripts to download and pre-process the required data.
DLTK was developed by the Biomedical Image Analysis Group at Imperial College London. You can read a quick overview of the toolkit in this article from Medium’s TensorFlow blog.
DLTK is open source and available on GitHub at https://github.com/DLTK/DLTK.
Applications to the Software Sustainability Institute Fellowship Programme 2023 are now open. This programme provides an excellent opportunity to obtain some funding to support you in activities that you are keen to pursue and that are also in line with the SSI’s aims and goals. This may include things like attending conferences/workshops and running events.
Learn more about what the Software Sustainability Institute’s Fellows have been doing in the Fellows’ August 2022 Newsletter, including a report from our own community committee member Diego Alonso Álvarez.
Imperial’s guidance on open source software licences has just been updated. Take a look at the revised information for guidance on how to go about licensing your open source software. This is an area that can be complex and confusing for academic researchers and developers and this really useful resource takes a clear and pragmatic approach to offering help and advice.
GitHub Actions are now enabled on Imperial’s GitHub Enterprise Server - github.ic.ac.uk. There are no Runners enabled at this time but the service will allow users to add Actions to their repositories and configure their own Runners.
The RSE team’s Code Surgeries are continuing in September. If you have an issue you want to discuss, book an appointment with a member of the team.
Unlike the existing HPC Clinics, meant to provide immediate support in relation to the College HPC Service and the RDS, the purpose of these surgeries is to provide long-term impact for custom code bases. Topics that may be covered in these sessions include software development best practices (version control, testing, code architecture, continuous integration), code review, software optimisation, packaging, distribution and publication.
Imperial’s Research Software Community relies on its community committee to help keep these monthly newsletters appearing in your inbox, to run events and to advocate for the importance of good research software development practices across the College.
Some longstanding members of our committee are moving on due to work commitments and we’re looking for at least two new committee members to help with running the community.
Why join the committee? Joining the committee provides a great opportunity to get more involved with research software at Imperial, help to make new connections and to build your network across departments and faculties within the College. You’ll also have the chance to provide your thoughts and input on the type of events the community should be running, how we engage with the College’s research community and to get actively involved in event organisation and research software training.
What do we ask of you? As a voluntary role, we ask that you commit to help out with the running of the community on a best efforts basis, contributing time and input as and when you’re able to, around the constraints of your main role. We expect committee members to edit an edition of the newsletter at least twice a year and encourage you to engage with discussions in our community Slack workspace to help keep the community active. Other activities you might like to get involved with include event planning and organisation and keeping the website up to date. We also ask that you confirm with your supervisor/line manager that they’re happy for you to take on this role.
If you’re interested to join the committee or have questions, get in touch with Jeremy Cohen.
LunchBytes talks - A series of talks for and by the research community at The University of Sheffield on creating/maintaining/using/sharing research code, data and infrastructure. There are 13 episodes available online covering several aspects of software development for research.
A concise guide to reproducible MATLAB projects - A blog post by SSI fellow David Wilby on some tools and concepts that can improve the reproducibility of your MATLAB projects.
Are you a fellow author of C++ libraries? Then why not check out this tutorial on Modern CMake for C++ library developers.
Git’s database internals I: packed object store - The first installment of a five-part GitHub blog post series on the internals of Git.
The C Programming Language is a book that I am sure lives in many of our libraries. If the book has crossed your path then why not watch this cozy Youtube video of a chat with one its authors, Brian Kernighan.
Measure Thrice, Cut Once: A quick overview of application migration - an SSI blog post that outlines some of the key aspects to consider when migrating an application.
A new episode of the Code for Thought podcast was released this month. The episode features Gemma Derrick who is part of the organising committee for the Hidden REF, an initiative looking to recognise research outputs beyond publications and the people that make them possible.
RS Community coffee
…continues weekly via Teams - normally on Friday afternoons at 3pm but check our Slack workspace for exact times and connection details.
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 Computing Tips
See 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.
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! email@example.com.
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 Yasel Quintero. All previous newsletters are available in our online archive.