As summer comes closer and the British weather becomes as unstable as usual, we can start enjoying face-to-face gatherings and events of all sorts without the barrier of facemaks. Some of us had not met in person for the last couple of years. Some of us had not met in person at all, and established a productive working or personal relationship entirely online! It is a strange feeling to realise that people in reality is 3D and have a height, dress in a variety of ways, and move around. I had never thought about it until now.
With the good (sigh) weather of late spring comes hayfever and lots of news, events and initiatives, from within Imperial, across London and the South East RS communities and beyond, so take some time to relax and read through all the things that this month’s newsletter brings you directly to your inbox.
After a break of more than two years, the RSLondonSouthEast 2022 workshop is back! It will take place On Monday 4th July 2022, at Imperial College London. Talks, posters and and a fantastic opportunity to mingle with the local/regional RSE community, all in one place! Registration will open after the bank holiday weekend.
The in-person RSE conference is returning for 2022! RSECon2022 will be held from 6th to 8th September 2022 in the Frederick Douglass Centre at Newcastle University. Keep an eye on the webpage for further announcements and the programme of this exciting event.
The next talk in the DiveRSE series on Equity, Diversity and Inclusion in Research Software Engineering will take place on on Monday 13th June, 2022 at 23:00 BST. Kelly Blincoe, PhD, University of Auckland, NZ will be talking about Reimagining software processes and practices for an inclusive RSE. You can find full details and registration information on the event page. A video will be made available after the event.
Nordic-RSE’s next online event, the Nordic-RSE online unconference 2022 will take place on the 16th-17th August 2022. Everyone interested can join & shape the agenda of the event - see the event page for details.
On Wednesday 1st June 2022 at 4PM BST / 5 PM CEST, the US-RSE Diversity, Equity, and Inclusion Working Group (DEI-WG) welcomes Alexander Serebrenik to present his talk Diversity in Open-source Software. Register on Zoom.
Continuing our series highlighting key members of the College community helping to provide, manage and support research computing and research software services, this month we have an introduction from Ryan Smith, Senior RSE within the RSE Team:
I joined the RSE team only 3 weeks ago (please come and say hello!), coming from a position as a senior scientist at a biotech company which specialised in cell signalling technology. Since graduating in Physics, I began to develop a strong appreciation for multidisciplinary research after embarking on a bioinformatics PhD in which it became evident that the skills I developed during my training as a physicist were very applicable to the sorts of problems that biologists were facing in quantitative proteomics. Consequently, I found myself in a position where my ability to translate research questions into software that scientists could use in their research was having an immediate and observable impact.
Although I did not know it at the time, the greatest satisfaction I got from my role as a scientist came from the activities which were aligned more with those of a Research Software Engineer, rather than those of the traditional career path of an academic. In subsequent roles after my PhD, I began to inadvertently focus my efforts on – and develop a great appreciation for - software development and its best practices. And so, when I came across the Research Software Engineering community and learned of its beliefs and the nature of its work, the decision to make a career switch to an RSE role seemed like a no-brainer.
I am particularly excited for the opportunity to continue to develop and diversify my skills within my new role as an RSE, and to help to broaden the engagement of Imperial’s central RSE team both with my existing network and by working with researchers across Imperial and beyond.
CHAMP is a HPC Access and Metadata Portal which provides an easy to use workflow for FAIR (Findable, Accessible, Interoperable, and Reusabe) data generation and publication. Created by the RSE Team member Chris Cave-Ayland as part of one of the projects of the team, CHAMP provides a web based interface allowing submission of HPC workloads and subsequent one-click publication of the results to data repositories such as Zenodo.
CHAMP is written in Python using Django and has been developed as a Passenger App within the Open OnDemand (OOD) framework. This approach allows the portal to be very simple but also portable across a wide range of HPC infrastructure. OOD provides a consistent programmatic interface for interacting with a number of popular HPC resource managers. It also supports a wide range of authentication mechanisms.
If you are a registered user of the Imperial College HPC Service, you can access CHAMP via OpenOnDemand and then going to Jobs and selecting CHAMP in the top menu.
RSE Code Clinics have arrived! The RSE Team is trialing at a low capacity this new service for the Imperial research community during June, so if you have an issue you want to discuss, book your appointment now for the 13th or 20th of June.
Contrary to the existing HPC Clinics, meant to provide immediate support in relation to the HPC and the RDS, the purpose of the RSE Code Clinics is to provide long-term impact for custom code bases. In particular, some of the topics the Code Clinics cover are:
For that reason, slots are booked, and the information related to the request (eg. link to software repository) sent between 1 and and 4 weeks in advance, so the RSE Team can review the material, prepare an appropriate response, and compile the resources that researchers can then use themselves to improve their software.
As this is a trial, your feedback will be invaluable to help shaping a useful service when Code Clinics are launched in full in July.
PyScript is out! Ever wanted to create interactive webpages without learning JavaScript - Now you can! PyScript is a framewok for creating and running Python applications that run in the browser, on the client side, like JavaScript. Check the keynote at PyCon US 2022 or see it in action in these examples.
It is true! Support for displaying math expressions has been a highly requested
feature for over 8 years. From May,
you can use the $ and $$ delimiters natively in Markdown on
GitHub to
insert math expressions in TeX and LaTeX style syntax.
No one likes to waste time doing the same thing again and again when setting up a new software repository. So, before embarking on a new adventure, check GitHub Templates! On this occasion, we bring you two templates created by the RSE Team with all the linters, code formaters and instructions on how to use them:
Please, use them, share them, provide feedback and contribute with your own templates!
Uncurled - everything I know and learned about running and maintaining Open Source projects for three decades - by Daniel Stenberg, is an absolutely brillaint book about do’s, don’ts and experiences on runing open source projects by the creator of curl, among many others. Highly recomended for those who are deciding about open sourcing their software.
Writing documentation can be both time consuming and easy to forget! A recent post on the Stack Overflow blog looks at Building a community of open-source documentation contributors
Citelang is the first markdown syntax for citing software. Here the author explains in more detail the idea and the usage.
All the 5 episodes of Season 2 of Lost Women of Science are available online, telling the story of Klára Dán von Neumann.
The latest episode in the Code for Thought podcast series is now available, intorducing two of the most recent Software Sustainability institute’s Fellows: James Byrne and Tom Russell.
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 our new AI/ML group. 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! rse-committee@imperial.ac.uk.
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 Diego Alonso Álvarez. All previous newsletters are available in our online archive.