October 2022 Newsletter

The University of Sheffield Research Software Engineering Community Newsletter October 2022

Welcome to this month’s newsletter for the research software community at The University of Sheffield, featuring news, opportunities, events and training for you.

It’s been an action packed month. Three new blog posts on the RSE Team website, two focussed on making quality code easy to achieve and one on valuing the outputs of RSEs and others. We’ve had the launch of the MATLAB User survey helping push forward better research practises in this vitally important language for research coders. The RSE Team has a new member, Edwin Brown, who will boost the teams capacity, particularly around AI and Machine Learning. And news that Paul Richmond is a winner of an award from the RSE Society recognising his contribution as president of the organisation.

Looking ahead to November, please come along to the next LunchBytes event on “Teaching Code”.

Bob

News, Web & Blogs

Blogs from the RSE Team:

• pre-commit : Protecting your future self Pre-commit is a powerful tool for executing a range of hooks prior to making commits to your Git history. This is useful because it means you can automatically run a range of linting tools on your code across an array of languages to ensure your code is up-to-scratch before you make the commit.
• Demonstrating Importance and Value in Research Software As research software engineers (RSEs) or researchers who develop software & code, at some point we will need to provide evidence that our software actually has some positive effect on the world. Whether this is for career progression, the REF, just for your own peace of mind…
• Writing better and more shareable code If you know how to write code, it’s not actually that hard to make it better! You just need to know how.

New LunchBytes recording online

• LunchBytes: From Eyes to Apps Our speaker this month was Dr Ilse Daly who told us about her journey from vision scientist to start-up founder at her company Blackdog Biomechanics.

Web and publications

• Introducing the FAIR Principles for research software Research software is a fundamental and vital part of research, yet significant challenges to discoverability, productivity, quality, reproducibility, and sustainability exist. Improving the practice of scholarship is a common goal of the open science, open source, and FAIR (Findable, Accessible, Interoperable and Reusable) communities and research software is now being understood as a type of digital object to which FAIR should be applied.
• Champions Program — A mentoring & training program for Scientific Open Source Champions Research software should serve everyone in our communities, which means it needs to be sustainable, open, and built by and for all groups. Currently, however, there is a dismaying lack of diversity in open source communities in general…
• Announcing the 2022 Table Contest This contest aims to highlight the many great ways people transform and present data.
• Best Practices for HPC Software Developers (Webinars) The HPC Best Practices webinars address issues faced by developers of computational science and engineering (CSE) software on high-performance computers (HPC). The sessions are independent, so join any or all.

Events

• Climate Justice and Open Research online event October 27th. In this session, TUoS researchers explore the value of open research practices in the response to climate challenges and inequalities.
• N8 CIR Machine Learning Theme Launch - 2022-11-01, The University of Leeds. Open to all researchers, PGRs and anyone involved in Machine Learning at an N8 institution, this event will bring the Machine Learning community from across N8 together to find out more about N8 CIR, plans for the theme and all-important networking opportunities.
• ODI Summit 2022: Data Decade Join the Summit virtually on 8 November 2022 from 10:00 – 22:00 GMT, where you will hear from world-leading data and AI experts, including the inventor of the World Wide Web, Sir Tim Berners-Lee and AI expert Sir Nigel Shadbolt addressing the data challenges we will face in the years ahead.
• NHS-R Community Conference 2022 16th and 17th November 2022. The main conference is a hybrid conference with the opportunity to join in person at Edgbaston Stadium, Birmingham or to join online via Zoom.
• LunchBytes Panel: Teaching Code As code and software become an ever bigger part of research (its likely that around 1/3 of researchers write code), coding and other digital skills become ever more important to researchers. In this online panel discussion, we will explore this with a few questions.
• Computing Insight UK 2022 Manchester Central Convention Complex on Thursday 1 and Friday 2 December. The theme for the conference this year is “Sustainable HPC” with sub-themes including “Sustainable Skills”, “Sustainable Funding” and “Net Zero Computing”.
• PyData Global 2022 - 2022-12-01 to 2022-12-03, Online. The PyData Global conference is an opportunity to listen, learn, and share knowledge about best practices, new approaches, and emerging technologies for data management, processing, analytics, and visualization.
• Reproducible Analytical Pipelines Webinar November 3rd. Join HDR UK and DNAnexus for a free webinar on reproducible analytical pipelines.
• UK National Open Hackathon 2023 Application Deadline January 16, 2023. Open Hackathons are multi-day intensive hands-on events designed to help computational scientists and researchers port and optimize their applications using GPUs.

Training

Research IT Training

Research IT is providing a place for beginners or advanced users to expand their knowledge of HPC and different programming languages. The courses are part of the Doctoral Development Programme. For more information please visit our training registration web page (via VPN): crs.shef.ac.uk.

RSE Team: Git & GitHub through GitKraken workshop - from Zero to Hero!

This is an introductory course, teaching the git and GitHub skills required to manage research code over it’s development lifecycle. These skills are essential for collaborative research teams.

This two half-day course is being run multiple times in the coming months:

• 31 October 2022 and 1 November 2022 “sold out”
• 28 November 2022 and 29 November 2022

If a course is “sold out” please join the wait list - we regularly email people to encourage those that can no longer attend to cancel.

RSE Team: Introduction to Deep Learning Course with Tensorflow Keras (in Python)

A one-day introduction to deep learning with practical labs using Tensorflow in Python:

• 16 November 2022
• 18 January 2023

If a course is “sold out” please join the wait list - we regularly email people to encourage those that can no longer attend to cancel.

Bioinformatics Training

• Introduction to RNA-seq analysis in R Monday 12th December 13:00 - 16:00, Wednesday 14th December 13:00 - 16:00, Friday 16th December 13:00 - 16:00

Opportunities

Funding

• Get up to 12 days of software engineering support for your HPC/ML/GPU project. The Research Software Engineering team is offering to support researchers with the use of High Performance Computing (HPC), Machine Learning (ML) and Graphics Processors (GPUs) in their research projects. All researchers at our University can receive up to £5,000 of support time, or roughly 12 days of support, provided by a Research Software Engineer (RSE). This call aims to increase the uptake of the University’s Tier 2 HPC resources, which are national facilities available to researchers in all faculties. This is an open call and applications are considered on a first-come-first-served basis. There is no current deadline and applications will be reviewed on an ongoing basis.
• ARCHER2 Embedded CSE (eCSE) Support Call. The ARCHER2 eCSE call provides funding for up to 18 person months of an RSE/PDRA to work on codes to run on ARCHER2. The deadline for submitting documents for technical evaluations is 2022-10-04 16:00 BST with a final proposal deadline of 2022-10-25 16:00 BST.
• Digital Infrastructure Incubator Deadline December 2, 2022. Code for Science & Society (CS&S) solicits expressions of interest from open source digital infrastructure teams to participate in the second cohort of the Digital Infrastructure Incubator (DII).
• CHIST-ERA Open & Re-usable Research Data & Software. This call tackles the challenge of open research data and software from the perspective of their possible reuse. The objective is to create the conditions for research in any domain based on open or shared data and software. Call deadline: 2022-12-14 17:00 CET
• Oracle for Research Project Awards Oracle Research (this years sponsors of the RSE conference) have an open grants program to sponsor research projects with free cloud credits to tackle computational challenges. The majority of cloud providers no longer offer free credits however Oracle grants include access to a variety of Oracle Cloud technologies including compute, GPUs, and HPC. In addition to cloud credits, they also provide researchers and supporting RSEs with technical cloud support to transition and optimize their workflows on an Oracle Cloud environment. If interested then apply directly.

LunchBytes

LunchBytes are a monthly series of short talks from the research community on research software, data, and infrastructure. November’s LunchBytes (24 November 2022 - 12:00-13:00), will be a panel discussion on “Teaching Code”.

LunchBytes needs YOU!

LunchBytes are organised by and for the research software community at The University of Sheffield. If you’d like to curate a session on a topic or present something, get in touch by emailing lunchbytes-organisers-group@sheffield.ac.uk - Or suggest topics on the jamboard.

Support

Code Clinics

Why not come to a Code Clinic? We’re keen to hear from you.

Code Clinics are fortnightly supported sessions run by the RSE team and IT Services’ Research and Innovation IT (ITS R&I) team. They are open to anyone at TUoS writing code for research to get help with programming problems and general advice on best practices.

At each session, members of the RSE and/or ITS R&I teams will be available to review code, advise, troubleshoot, and suggest ways to improve your computational workflows.

Research IT HPC Drop In

HPC Drop-In sessions are providing assistance with HPC related user issues such as challenges in scaling an application from desktop to supercomputer. We are considering extending the number of our sessions to two or three weekly. These interactive sessions could provide a better interface with our users than our non-interactive ticketing system. These sessions are advertised on the HPC mailing list.

Research IT Consultations

Alongside the HPC Drop-In sessions, Research IT are also running one to one consultations to solve in depth user specific problems. These consultations can be booked via our webpage. If you are interested please visit the following link: https://students.sheffield.ac.uk/it-services/research/support.

Sheffield RSE Team

The Sheffield RSE Team aims to collaborate with you to help improve your research software.

They can provide dedicated staff to ensure that you can deliver excellent research software engineering on your research projects.

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

Research IT

The Research and Innovation Team within IT directly supports research, both academic and commercial. We provide large scale HPC systems, advice on everything from statistics to ML to data pipelines and training for both students and staff. Working with academics, our staff are embedded within research groups on both long and short term engagements.