A very warm welcome to September’s Community Newsletter - especially to any first-time readers and newcomers to Imperial. This is the 21st edition… I can just about remember editing the first one back in January 2018. Since then, curating the newsletter has evolved from searching for relevant material to selecting content of particular interest. This is a nice problem to have: we have more news and achievements to report on than ever. Nevertheless, we rely entirely on your input so please do continue to contribute via email@example.com.
This month also marks the third birthday of the Research Software Engineering team in the Research Computing Service. As its founding member I’d like to take this opportunity to thank everyone who helped to establish the team, all the group leaders and others who have supported our efforts, and especially the members of the team who have done all the hard work to support so many researchers and projects since 2017. Long may it continue!
Finally, and as mentioned below, thanks to everyone who completed the recent Research Software Survey. We know that the Community and the RCS can do even more to support users and developers of research software across College, and we’re determined to deliver on that in the months and years to come.
In the meantime, here’s some topical reading material…
SORSE has a number of events in October, including talks on using containers to make research more FAIR (Findable, Accessible, Interoperable, and Reusable) and working as a self-employed RSE. As usual, there is also a monthly submission deadline: get your submissions in by the end of 30 September for the next review round.
JupyterCon 2020 will take place online on 5-16 October. Registration is now open.
In August’s newsletter we mentioned that the organisers of the Nordic-RSE conference were still hopeful of running the event in Stockholm on 1-2 December. It has now been postponed until May 2021, but will be replaced with a virtual Get together event on the original dates.
Computing Insight UK (CIUK) will be held virtually for the first time this year, on 3 December. Subscribe to their mailing list for registration details. The student poster competition is accepting submissions now.
Many thanks to everyone who contributed to the Research Software Survey. We have published an executive summary and the aggregated results (both links IC-only) and are now focused on improving how research software is supported across the College. We’re especially grateful for the detailed comments many of you took the time to submit.
Rich FitzJohn reports on the RESIDE team’s work to accelerate their COVID-19 transmission models at a GPU hackathon hosted by the University of Sheffield and NVIDIA. The resulting R code is accessible in a branch of
Rini Banerjee (MEng Mathematics and Computer Science student at Imperial) recently completed a internship documenting Devito using Jupyter Book
Diego Alonso Álvarez (Senior RSE in the Research Computing Service) led a team enhancing the Research References Tracking Tool (R2T2) at the recent eLife Innovation Sprint
Mark Woodbridge co-presented a SORSE session on the What, Why and How of Research Software Directories. Submissions to the Imperial RSD are always very welcome – Ed.
Hacktoberfest is coming soon. If you’re the maintainer of a software project hosted on GitHub and considering taking part (it can be a great way to attract new contributors) then please contact Rich FitzJohn firstname.lastname@example.org.
Challenge to scientists: does your ten-year-old code still run? This Technology Feature from Nature describes some of the challenges faced when attempting to reproduce experimental analyses published a decade ago - from using floppy disks to Windows 3.11 emulators. It also mentions some approaches that may future-proof your workflows via fully reproducible environments.
On the subject of containers: Docker have announced new usage policies for Docker Hub, automatically expiring images that are rarely accessed and rate-limiting image pulls. GitHub followed this announcement with one of their own: a public Container Registry with no such restrictions for public images. GitHub’s offering has the added advantage of working well with Actions - their increasingly-popular CI solution.
Array programming with NumPy is now the paper to cite if you’re a user
handcalcs is a package to render Python code symbolically in Jupyter (with some limitations)
Foam is a personal knowledge management tool “for organising your research, keeping re-discoverable notes, writing long-form content and, optionally, publishing it to the web”
CoCalc is a collaborative platform offering online Jupyter notebooks, a LaTeX editor and Linux terminal
Research in deep reinforcement learning is complex because experiments rely on many moving pieces. Tonic is a Python library that allows researchers to quickly implement new ideas and measure their importance by providing:
Tonic is a new project, developed by Fabio Pardo in the Robot Intelligence Lab in the Dyson School of Design Engineering. Fabio explains his motivation for the building the library:
While there are several existing libraries for deep reinforcement learning research, I have not been able to find one with enough simplicity, flexibility, and power to support rapid prototyping and benchmarking. I personally use it whenever I want to try something, and it usually takes only a few minutes or hours to get results. I hope that more people will contribute to the library in the future, adding new features and agents, making Tonic a popular choice for researchers to create their experiments and release their code.
You can see some animations of work carried out using Tonic on Fabio’s Twitter feed.
RS Community coffee continues weekly via Zoom - normally on Friday afternoons at 3pm but check our Slack workspace for exact times and connection details.
The Slack workspace also features an #OpenFOAM channel where regular code review sessions are announced (amongst other CFD-related discussions…)
Check the latest instalment of the Research Computing Service’s Research Computing Tips for some Best practices for job scripts.
That’s all for this month. Thanks to everyone who provided content for this edition.
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.
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This issue of the Research Software Community Newsletter was edited by Mark Woodbridge. All previous newsletters are available in our online archive.