Hello RSEs! Like in a weird time machine, we are finally experiencing suspended events from the past: Euro 2020 now and soon Olympics 2020. For tennis lovers, Wimbledon is finally happening. So, a great time for sports. And a great time for practising them as well. It is a pity that we are not also able to enjoy the weather from summer 2020 that I’m sure all of us remember as much better than the current one. But probably it is just a false biased memory… ;)
In any case, let’s enjoy this summer as much as possible, staying active, meeting friends and relatives, and having some good times. And when meteorology fails us, we can find shelter in our RSE newsletter, with many events, blog posts and videos to keep us busy and entertained.
In this month’s newsletter:
Monday 28 June-Friday 2 July University of Exeter wants to celebrate the best of Data Science and AI with seminars, workshops, presentations and training opportunities. Registration is essential.
The launch event for our new Imperial Research Software Community DeepLearners group (#deeplearners Slack channel) will take place on Monday 5th July 16:00-17:00. You can sign up to join the session via this form: https://forms.office.com/r/D9bihQGRjG (IC login required).
The deadline is approaching to submit an abstract for an article in PeerJ Computer Science’s upcoming Special Issue on Software Citation, Indexing, and Discoverability. See the call for papers for further details. The abstract submission deadline is 16th July 2021.
The sktime community (sktime is a unified framework for machine learning with time series) of the Alan Turing Institute is organising the 2021 summer programme, held virtually. It consists of events and activities which can be joined separately, from May to August.
The Early Career Program (part of the SC21 conference), will be held virtually this year. It “is a series of workshop-style sessions intended to help guide early-career researchers within the first five years of a permanent position in navigating a successful career path”. Applications close July 31, 2021.
Also in the remit of SC21, the PAW-ATM workshop “aims to serve as a forum for exhibiting parallel applications developed using high-level parallel programming models that serve as alternatives to MPI+X-based programming”. Submissions deadline: July 23, 2021.
Another run of the “Reproducible computational environments using containers - Introduction to Docker and Singularity” course will be taking place on the 28th/29th July 2021. Registration is open.
The “Research Software Engineers in HPC (RSE-HPC-2021)” workshop will take place again this year as part of SuperComputing (SC21). We had a submission from our community accepted at last year’s RSE-HPC workshop. If you’re working with or building research software that runs on or has links with HPC infrastructure, do consider submitting something to this workshop. The call for papers is currently open and the submission deadline is 6th August 2021.
Imperial College is seeking to make appointments to the below research computing-related posts from within the College’s community. The advertisements are now live internally on the College website, which can be seen at the following links (IC login required):
Director of Research Data Strategy
Director of Research Software Engineering (RSE) Strategy
Director of User Engagement
Closing date for submission is Monday 5th July 2021 by 17.00 hours.
The Call for new Imperial RS Community committee members is still open, so consider volunteering and helping to shape the role of research software at Imperial. Committee members help to organise and run a range of research software events and training courses, maintain our website and promote the importance of maintainable, sustainable, robust research software across the College. Contact Jeremy Cohen if you’d like to volunteer as a committee member or you have any questions about what’s involved.
If you are organising events and initiatives focused on Research Software Engineering, you can get some financial support (generally up to £1000) from the Society of Research Software Engineering. A policy for event and initiative funding is now online, providing all the details.
A short blog post by Dan Katz on “Scalable Computational Reproducibility”.
“The people who build software in the land of dataspeak”, a blog post by the Netherlands e-Science Center CEO, Prof. Joris van Eijnatten.
A new self-service course on Message-Passing Programming with MPI has been launched by the ARCHER2 team.
Some concepts are harder than others to explain/understand. Quantum computing is among the most difficult, so some inventive approaches are helpful. The Stack Overflow blog has a post with a quite unorthodox way to explain it.
Have you ever discovered that the amazing documentation of your project’s repository has some spelling errors just after pushing it? Maybe an automated spell checker integrated in your CI pipeline is the right solution.
The Software Sustainability Institute posted on its YouTube channel the recording of the talks of the Collaborations Workshop 2021 that took place online from Tuesday, 30 March to Thursday, 1 April 2021. They cover several topics (FAIR Research Software, Diversity and Inclusion, Software Sustainability).
If you are wondering how different RSE groups are managed, you can read NL-RSE’s blog post that summarises the conversations with two RSEs from different institutions that took place as part of the April 2021 NL-RSE meetup.
Have you been taking yourself on an adventure through the magical kingdom of shell scripting (possibly after attending one of the great Software Carpentry courses recently)?! This website provides quick access to interactive help/man descriptions for complex shell commands, while this page summarises some gotchas of coreutils command you are likely to use in a script.
We have many powerful tools and APIs to exploit parallelism, but the simplest solution is to run several instances of the same command/programs at the same time: GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
Two new inspiring RSE Stories were released on 3rd and 17th of June 2021. “Dinosaur” is an interview with the RSE and founder of the RSE stories podcast Vanessa Sochat, while “Going in with enthusiasm” tells how Kate Court made the exciting journey from Arts and Humanities to Computer Science.
Reach out for the Code for Thought podcast if you want to hear about software architectures in a (at least for now) 3-part series of episodes.
This month the spotlight is on DeepMedic, an efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans developed within the BioMedIA group and listed in Imperial’s Research Software Directory. The research was initially presented in the article “Efficient Multi-Scale 3D CNN with Fully Connected CRF for Accurate Brain Lesion Segmentation” and ranked first at the Ischemic Stroke Lesion Segmentation (ISLES) challenge for the sub-acute ischemic stroke lesion segmentation (SISS) category, MICCAI 2015.
DeepMedic can process NIfTI images, a very common neuroimaging file format, to detect and segment structures. It uses 3D Convolutional Neural Networks that can be created and trained with custom data by providing properly labelled examples. It is available Open Source and the GitHub repository contains clear instructions on how to setup DeepMedic (including NVIDIA CUDA) and datasets that can be used to check the correct behaviour of the system.
A specific section provides information about the steps required to run DeepMedic with other data.
RS Community coffee continues weekly via Teams - normally on Friday afternoons at 3pm but check our Slack workspace for exact times and connection details.
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.
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.