August 2022 Newsletter

The University of Sheffield Research Software Engineering Community Newsletter August 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

• ‘The entire protein universe’: AI predicts shape of nearly every known protein (Nature) - DeepMind’s AlphaFold tool has determined the structures of around 200 million proteins.
• How to create a Python package in 2022 - Useful tutorial/blog summarising the current state of python packaging, using Poetry.
• Welcome to Quarto Workshop - 2hr webcast walking you through Quarto, the evolution of RMarkdown, supporting Python, Julia and much, much more.
• Code for Thought Podcast
  • Code for Thought is going Live - Peter Schmidt reflects on the progress of the Code for Thought podcast and its future development.
  • Drones, shrubs and ecology Listen to SSI Fellow Isla Myers-Smiths who tells us how they measure climate change in arctic ecosystems and the technical challenges involved.
  • Open Science and Research Software Teresa Gomez-Diaz from the University Gustave Eiffel in Paris takes us through open science, open software and the importance of software licensing (often forgotten by engineers).

Events

• Research Software Hour weekly, Thursdays 19:30 UK time / 20:30 Oslo time / 21:30 Helsinki time - Hosted by members of the Nordic-RSE community, this continues weekly on Twitch. Research Software Hour is an online stream/show about scientific computing and research software. It is designed to provide the skills typically picked up via informal networks; each week, they do some combination of exploring new tools, analyzing and improving someone’s research code, and discussion. Watchers can take part and contribute code to us which they analyze and discuss on stream.
• RSECon22 6-8th September - The annual UK conference is hosted in Newcastle this year, registration is closed.
• Digital Humanities Congress 2022 8-10th September - This Sheffield conference aims to promote the sharing of knowledge, ideas and techniques within the digital humanities, registration for attendees closes 31st August.
• Sheffield DevOps Meetup 8th September - Speaker: Tom Hoyland with Metaphors, Monitoring and Metrics: How a Platform Team changed the way they communicated to change the way they delivered products and services.
• Write the Docs 2022 11-13 September 2022 - Write the Docs brings everyone who writes the docs together in the same room: Programmers, Tech Writers, Support, Designers, Developer Advocates, and more. We all have things to learn from each other, and there’s no better way than sitting together and talking. We invite you to join 300 other folks in our event to explore the art and science of documentation.
• OpenFest 2022 14-15th September - The University library is hosting this conference on the topic of open research practices. Programme Here - Register Here
• GitKon 2022 11-13th October - GitKraken is hosting an online conference filled with sessions on everything important to Git users.
• 1st International Conference on FAIR Digital Objects 26-28 October
• Computing Insight UK 2022 1-2nd December - A HPC focused conference in Manchester, this year’s key theme is Sustainable HPC, abstract submission closes 16th September.

Training

Introduction to Deep Learning with Tensorflow in Python

14 September 2022 - 09:00-17:00

Details: https://rse.shef.ac.uk/training/workshop/2022-09-14-deep-learning-with-tensorflow-in-python

Recent advances in deep neural networks coupled with an increasing amount and complexity of scientific data collected in a wide array of domains provide many exciting opportunities for deep learning applications in scientific settings. Furthermore, libraries such as Google’s Tensorflow python library have made building deep learning models more accessible through common tools, freely available to researchers.

In this course, we’ll introduce some basic neural network and deep learning theory and give participants practical experience in some popular deep learning models and techniques.

Content includes:

• Introduction to Regression and Classification using neural networks
• Image classification with Convolutional neural networks
• Speeding up the training process of your own models using existing neural network

Register via eventbrite: https://www.eventbrite.co.uk/e/introduction-to-deep-learning-with-tensorflow-in-python-tickets-304788559787

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): https://crs.shef.ac.uk.

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

This highly popular workshop will run again in September, October and November. Join the RSE mailing list to be the first to get the details.

Opportunities

Funding

• Software Sustainability Institute Fellowships - 2023 applications now open! The Institute’s Fellowship Programme provides funding for individuals who want to improve how research software is done in their domains, fields and/or areas of work. Being a Fellow also helps individuals develop skills and knowledge in their area of software sustainability, empowers them to speak about software sustainability issues and network with like-minded individuals from a wide variety of backgrounds. See here for more details! Deadline 3rd October.
• Sony Research Award Program - The Sony Research Award Program provides funding for cutting-edge academic research and helps build a collaborative relationship between faculty and Sony researchers. Application deadline 15th September.
• 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. The deadline for submitting your application is Friday 16 September 2022. Applications received after this date will be reviewed in the next round. Find out more about this opportunity at: https://rse.shef.ac.uk/collaboration/tier2/

Jobs

• 2 RSE Roles at University of Exeter - Closes 17th August
• CTO at Beautiful Canoe, Aston University spinout - closes 19th August
• UK Gov Knowledge Transfer Partnerships (KTP): 2022 to 2023 Round 3 Funding Competition - Closes 14th September

LunchBytes: Workflow Managers

The recording from last month’s LunchBytes session on workflow managers is now available on the event’s webpage.

Featuring:

• Will Furnass: The Trouble with Scripts - setting the scene by showing us how, without workflow management, stitching several pieces of software together can present some challenges.
• Magda Dabrowska: Nextflow - a relatively new workflow manager which allows for writing scalable computational pipelines.
• Ian Sudbery: Ruffus - one of the oldest of the modern style workflow management systems. Ruffus pipelines consist of a series of python functions that are linked together using a python feature known as decorators.
• Joe Heffer: Common Workflow Language - an open standard for describing how to run command line tools and connect them to create workflows.

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.