Hello again, and welcome to our October newsletter, coming to you this month from the Faculty of Medicine.
So Hallowe’en is almost upon us, and this year we don’t need to look far for horror stories to provide the thrills of the season. Where even to begin? How about the recent loss of thousands of patients from the government’s Covid “database” which won’t have come as a surprise to RSEs wearily debugging yet another Excel import. What can we say except that solid research software skills have never looked so relevant, or necessary. “If there were health and safety rules for software, Excel would be up there with radium cigarettes and arsenic gobstoppers”. (Although, hoping for a similar frisson of superiority from this article on Matlab and its impact on public health, I was sadly disappointed.)
26th October: The Research Data Alliance is running an introduction to itself and next years’ plenary here: What is RDA and Why Should I Attend Plenary 17?.
29th October: The Wellcome Trust continues a series of online talks to celebrate 20 years of the Human Genome Project.
11th November: If you haven’t yet had your fill of “digitally-delivered interactive experiences” then the DSI is heralding A New Era of Experiential Medicine in this seminar with Dr Adam Gazzaley, who I have on independent authority is an engaging speaker.
7th December: Registration opens for the Software Sustainability Institute’s annual Fellowship Programme. “Fellows come from a wide variety of backgrounds, experience and career stages. What they have in common is a passion for their area, the ability to communicate their ideas effectively, and a real interest in the role of software in research.” Fellows are awarded £3000 to spend over 15 months on a variety of possible activities. Our own community committee member Diego Alonso-Alvarez is a current SSI Fellow and if you’re interested in applying you are welcome to get in touch with him.
NVIDIA are setting up a supercomputing facility in Cambridge for medical research.
Wellcome are running a survey for researchers who use health data.
The US National Cancer Institute has launched the Imaging Data Commons, providing DICOM images, annotations and analysis results, linked to proteomics and genomics datasets. “As a centralized resource for imaging data, IDC will offer documented provenance, search and visualization capabilities, harmonization, standardization, and quality control.”
Shift a paradigm in your lunch break with this surprisingly readable article on The future of digital health with federated learning.
Altogether now: “That’s my code, so name me on your paper!” How should we celebrate the research excellence obscured by the REF? The case of the Research Software Engineer.
Better Scientific Software (BSSw) presents articles from expert community members on topics related to software productivity and sustainability.
Another introduction to scientific computing with Python.
Build a global, scalable, low-latency, and secure machine learning medical imaging analysis platform on AWS with the Radboud University Medical Center, who have thusly deployed their Grand Challenge platform for biomedical image analysis.
Start learning about HPC programming at RookieHPC.
Check your production servers for accidentally deployed Git artefacts with Gitjacker.
Check out the new features in Python 3.9, including enhanced timezone support and two new operators for dictionaries.
Spend a day replicating research into what you do all day, if that isn’t all a bit too meta.
We’ve talked about Streamlit for Python UI apps in a previous newsletter, but one interesting new development described in this article is a facility to share apps without having to deploy them to your own server.
October’s research software of the month comes from a recent Imperial PhD, Kai Arulkumaran:
FGLab is a computational science dashboard, designed to make prototyping experiments easier. Experiment details and results are sent to a database, which allows analytics to be performed after their completion. The server is FGLab, and the clients are FGMachines.
FGLab suits a different kind of workflow to Jupyter notebooks/CodaLab worksheets. The latter are ideal for presenting a single working experiment along with data, live code, explanatory text and visualisations. On the other hand, FGLab decouples code from the dashboard, with the results of a series of experiments with different hyperparameters being stored in a database. Prototyping experiments often involves small code changes that are not worth committing - these can qualitatively be captured in the notes interface that accompanies each experiment, much like with a physical lab notebook.
See further details on FGLab.
Each month we highlight a piece of research software that is being used or developed at Imperial. If you have a suggestion of some software that you’d like to see us feature, please email email@example.com.
RS Community coffee continues weekly via Zoom - normally on Friday afternoons at 3pm but check our Slack workspace for exact times and connection details.
Check the latest installment of the Research Computing Service’s Research Computing Tips.
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! firstname.lastname@example.org.
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This issue of the Research Software Community Newsletter was edited by Jazz Mack Smith. All previous newsletters are available in our online archive.