April 2021 Newsletter

12 April 2021 12:00

University of Sheffield Research Software Engineering Team Newsletter April 2021

This is the 10th monthly newsletter from the Research Software Engineering Team at The University of Sheffield. We aim to share our experiences and information of other communities for those using software for research. This newsletter collects interesting events and opportunities over the coming month. It also signposts to other resources that we find beneficial or interesting. You may find the content interesting if you are someone in research using software, are a person paid to develop software (like a Research Software Engineer (RSE)). or are somewhere in-between (a research developer).

To receive this newsletter as an email each month, please sign up to our Google Group.

All times are BST (UTC+01)


New software TopoStats accelerates DNA discoveries

A new software package allowing scientists to quantify how small circles of DNA change their structure has been developed by researchers at universities in the UK and Germany.
Bob Turner of the UoS RSE team has been involved with this project.

Future events

GPU Technology Conference 2021, 12th - 16th April

The Spring 2021 edition of NVIDIA’s GPU Technology Conference is being held as an online event from the 12th to the 16th of April.

Registration for the event is free, providing access to live and recorded sessions, research posters, interactive panels, demos, podcasts, technical sessions, and more. DLI training workshops can be purchased for an additional fee.

Dr Paul Richmond of the UoS RSE team is presenting a session “Simulate the World and Everything in it: Complex Systems Simulations with FGPU2 [E31281] (Registration Required) at 9AM on Tuesday April 13th.

Register Online for free

Introduction to Deep Learning Course with Tensorflow Keras (in Python), 15th April

A one-day introduction to deep learning with practical labs using Tensorflow Keras in Python. The session is led by Twin Karmakharm.

Register with eventbrite

Software Sustainability in Practice, 20th April

This is an informal event by the Open Research Team at the University of York, aimed at getting researchers together to hear talks on and discuss the value of engaging in software sustainability practices. It’s quite short, and worth a listen in if you’re interested! There will be lots of overlap with stuff that has been discussed at Coding Club, but different perspectives being presented.

The host will be Emma Barnes (Research & High-performance Computing Team Leader), and the speakers are as follows:

  • Prof Simon Hettrick (Software Sustainability Institute Deputy Director)
  • Dr Jon Hill (SSI Fellow and Senior Lecturer in Environment and Geography)
  • Emma Rand (SSI Fellow and Senior Lecturer, Biology)
  • Dr Peter Hill (EPSRC RSE Fellow, York Plasma Institute, OUR VERY OWN) (reposted from N8 CIR list)

Register with eventbrite

Introduction to Deep Learning Course with Keras (in R), 22nd April

A one-day introduction to deep learning with practical labs using Keras (Tensorflow) in R. The session is led by Anna Krystalli.

Register with eventbrite

Open Research Conversations: Electronic Lab Notebooks, 22nd April

A session of talks and discussions about the use of electronic lab notebooks in the research process and beyond.

This is part of a series of Open Research Conversations facilitated by The University of Sheffield Library, which include talks from researchers and other experts to share their experiences, promote best practices and discuss the challenges they are facing.

Register with eventbrite

GUIs-for-RS: Workshop on Graphical User Interfaces for Research Software, 27th-29th April

Research software has been a driving force behind the birth and rapid growth of informatics, but it was the appearance of graphical user interfaces (GUI) in the 1980s that made computers accessible to everyone. A GUI helps to reduce the learning curve for using software, increases the base of potential users and can ultimately increase citations and impact. Moreover, a well-designed GUI can perform validation and increase the robustness and reproducibility of the results, productively decoupling developers from users.

The goal of these workshops is to help developers lose their fear - or reluctance - to invest time creating a GUI for their research software, and help them to give those first steps in the development of graphical user interfaces. The target audience is anyone who develops research software as part of their work, in any role, academic level and department.

This event is organised by the RSE team at Imperial College London.

Register with eventbrite

Upcoming ARCHER 2 training events:

  • Shared Memory programming with OpenMP, online self-service course.
  • Understanding Package Performance, 19th April
  • Efficient use of the HPE Cray EX Supercomputer ARCHER2, 20th - 22nd April
  • High Performance Containers?, 21st April

Details and registration for the courses can be found on their upcoming training page.

Upcoming N8 CIR training events:

  • Data Visualisation for Cultural Heritage Collections, 19th April. Registration closes on the 15th of April.

Details and registration for the courses and events can be found on their events page.

LunchBytes is a monthly series of short talks for those in the research community at TUOS who work with/write code, use/manage research data and use/manage research infrastructure. Through these talks we come together as a community to discuss best practices and useful methods/tools. If you’re interested in curating a session or giving a talk, get in touch at: lunchbytes-organisers-group@sheffield.ac.uk

The next LunchBytes event is scheduled for the 12th of May, with a provisional theme of Good practice in R. The exact date and details of talks will be advertised soon via the RSE team’s mailing list.

csv,conf,v6 May 4-5 2021

The 6th edition of csv,conf, a community conference for data makers everywhere, is being held online on the 4th and 5th of may.

Register with eventbrite

DAFNI (Data and Analytics Facility for National Infrastructure) Launch Event, 5th July

The Data and Analytics Facility for National Infrastructure (DAFNI) is recognised as a world leader in infrastructure system research. DAFNI is based in Rutherford Appleton Laboratory in Harwell, Oxfordshire. Using advanced computing, DAFNI provides world leading infrastructure systems research capabilities to collate infrastructure data from multiple sources, map and model it, and use advanced visualisations to demonstrate and explore scenarios.

Register with eventbrite

Previous events

A recording of the last LunchBytes event (Making GPU programming more accessible on 2021-01-13) is now available.

The Alan Turing Institute is starting to upload videos from its recent AI UK event on to its Youtube channel.

IBM Training For Bede During spring 2021 IBM delivered three training sessions on N8 CIR’s new high-performance computing platform Bede. Recordings and slides from these sessions can be found on the N8 CIR website.


SIGHPC Computational and Data Science Fellowships are now open

SIGHPC fellowships funds up to $15K per year for a student in a graduate (masters or PhD) program anywhere in the world. Nominations close April 30.

More information can be found on the Research IT News blogspot and from SIGHPC directly.

For RSE vacancies across the UK and elsewhere see the Society of RSE’s jobs board.

Web and Blogs

A Prime Case Study for Making MATLAB Code Go Faster.

Mike Croucher (A former member of RSE Sheffield) presents a case study improving the performance of a MATLAB code.

Software and Updates

Readme.so - The easiest way to create a README

A simple web-based editor which allows you to quickly add and customize all the sections you need for your project’s readme.


Need access to managed desktop software? The University provides a Find a pc website allowing students to remotely access PCs running University Desktop.

If you think there are other great training resources we should advertise, please get in contact (rse@sheffield.ac.uk).

RSE Sheffield’s Services

The RSE Sheffield team aims to collaborate with you to help improve your research software. We can provide dedicated staff to ensure that you can deliver excellent research software engineering on your research projects.

The RSE Sheffield team provides free Code Clinics (in collaboration with IT Services), plus paid services that allow us to collaborate longer term.

Contact Us

For queries relating to collaborating with the RSE team on projects: rse@sheffield.ac.uk

Information and access to JADE II and Bede.

Join our mailing list so as to be notified when we advertise talks and workshops by subscribing to this Google Group.

Queries regarding free research computing support/guidance should be raised via our Code clinic or directed to the University IT helpdesk.