November 2022 Newsletter

The University of Sheffield Research Software Engineering Community Newsletter November 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.

News, Web & Blogs

New LunchBytes recording online

• 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. Questions around teaching code were put to an online panel. The panel included Emma Norling (Director of Learning and Teaching in the Department of Computer Science at the University of Sheffield), Shangshang Gu (School of Health and Related Research, University of Sheffield), Ashley Cadby who plays a key role in teaching code in the Department of Physics and Astronomy at the University of Sheffield and Norbert Gyenge (IT Services) with expertise in shorter courses. Thanks to Bob for organising the event!

Web and Publications

• RSE mentoring scheme - Registration deadline is 30th November.
• 15 new Fellows to start training in data stewardship and management - 15 Fellows are joining the fellowship of the ELIXIR-UK DaSH project to seed local data steward communities across the UK. Fellows will work with ELIXIR-UK to produce and deliver training in Research Data Management (RDM) within their host Universities and Institutes.
• Amsterdam Declaration on Funding Research Software Sustainability - The Research Software Alliance (ReSA) and the Netherlands eScience Center hosted a two-day international workshop in Amsterdam (the Netherlands) on 8-9 November 2023 to set the future agenda for national and international funders to support sustainable research software. As the importance of software in research has become increasingly apparent, so has the urgent need to sustain it.
• Ten simple rules for funding scientific open source software - Scientific research increasingly relies on open source software (OSS). Funding OSS development requires intentional focus on issues of scholarly credit, unique forms of labor, maintenance, governance, and inclusive community-building. Such issues cut across different scientific disciplines that make them of interest to a variety of funders and institutions but may present challenges in understanding generalized needs. Here we present 10 simple rules for investing in scientific OSS and the teams who build and maintain it.
• Case study: Asynchronous task scheduling for the Music #AI project - Research Innovation and IT have been working on an exciting project with researchers from the Department of Computer Science. The goal of this project was to improve the existing music AI web application in terms of usability, maintainability, and scalability.
• Code Reproducibility Training initiative - The Code Reproducibility Training initiative which is part of the ELIXIR-CONVERGE WP2 project, aims to create training materials to learn how to develop sustainable and reproducible code.
• I-X Centre for AI in Science - Imperial’s I-X Centre for AI in Science. I-X is Imperial’s flagship AI initiative bringing AI together with interdisciplinarity and grand challenges. Our centre is dedicated to using AI to disrupt and advance Science, Engineering and Mathematics and is underpinned by core support from Schmidt Futures.

Events

• R course for Digital Humanities - 2022-11-29 and 2022-1-06, Online. Following a similar format to the 2021 workshop, the course is a gentle introduction to R for text analysis. Over the course of two sessions you will be taught the basics of the powerful programming language before being provided with hands-on experience analysing long-form text in the RStudio development environment.
• Computing Insight UK 2022 - 2022-12-01 to 2022-12-02, Manchester Central Convention Complex. 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.
• Free ARCHER2 course at Newcastle University covering Docker and Singularity - 2022-12-07 to 2022-12-08, Newcastle University. This course is a run of the Docker and Singularity lessons in the Carpentries Incubator.

• University of Sheffield Inaugural Annual Open Research Lecture - 2022-12-09, The Diamond, Lecture Theatre 5. Lecture given by Dr Tom Stafford titled ‘Wide Open?’. Dr Tom Stafford will review concerns about Open Research practices: that they are unnecessary, performative, exclusive, neocolonial, a distracting example of data positivism, undermine scholarly societies, slow down research, generate confidentiality risks, amongst others.

• Lab Notebooks for Computational Mathematics, Sciences & Engineering Wednesday - 2022-12-14, Online. The HPC Best Practices webinars address issues faced by developers of computational science and engineering (CSE) software on high-performance computers (HPC).

• UK National Open Hackathon 2023 - Application Deadline 2023-01-16, Online. Open Hackathons are multi-day intensive hands-on events designed to help computational scientists and researchers port and optimize their applications using GPUs.

• Intermediate Software Development Skills for Earth and Environmental Scientists: Reproducible Research through Reusable, Reliable Code in Python - 2023-03-27 to 2023-03-31, University of Manchester. Fancy improving your research techniques within the Earth, atmospheric and oceanic sciences? For any questions about the course and application, please contact Anja Le Blanc via e-mail at anja.leblanc@manchester.ac.uk.

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.

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

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:

• 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.

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.

Please keep an eye out for new dates being released shortly via our mailing list!

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.

Opportunities

Funding

• Digital Infrastructure Incubator Deadline 2022-12-02. 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. Deadline 2022-12-14. 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.
• Wellcome PhD studentships. Deadline 2022-12-16. Training the next generation of researchers in high-quality research of complex multi-component public health interventions and policies to reduce non-communicable or chronic diseases.
• PhD at University of Bristol: Open spectroscopy in Environmental Sciences: Machine-learningaugmented analysis and interpretation - Deadline 2023-01-23. PhD that is associated with the Bristol RSE group. The project title is “Open spectroscopy in Environmental Sciences: Machine-learning- augmented analysis and interpretation”. The aim is to help develop machine learning models and software that can aid in the interpretation of spectra. Analysis of this data seeks to address specific environmental questions, such as how soil bacteria are connected to the release of greenhouse gases, or how changes in geochemistry influences the release of pollutants into drinking water.
• Artificial intelligence hubs for real data and for scientific and engineering research - Deadline 2023-02-09. Apply for funding for a research hub in either artificial intelligence (AI) for real data or AI for scientific and engineering research.
• Mathematical and computational foundations of artificial intelligence - Deadline 2023-02-09. Apply for funding to advance the fundamental mathematical, statistical, and computational concepts that underpin artificial intelligence (AI).
• Get up to 12 days of software engineering support for your HPC/ML/GPU project. Deadline N/A. 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.
• Oracle for Research Project Awards - Deadline N/A. 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.

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.