February 2021 Newsletter

10 February 2021 16:00

University of Sheffield Research Software Engineering Team Newsletter February 2021

This is the 8th 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 GMT (UTC+00)

News

An International Council of RSE Associations has been founded to help the various existing national RSE associations work better together and to help develop new national RSE associations. The UK Society of Research Software Engineering is one of the founding member organisations. There will be other exciting announcements from the Society of RSE in the coming days; follow @researchsofteng to find out more.


On 2021-01-27 the UK national supercomputer ARCHER was switched off after seven years of service. EPCC, who have provided the ARCHER service over that period, have been reflecting on its impact and the resources it provided. ARCHER has been superseded by ARCHER2.


Our local chapter of the UK Reproducibility Network (UKRN) is being rebranded the Open Research Working Group and will be run by new leads (Claudia von Bastian and Jim Utley). Through this group members will share good practice, events and facilitating conversation about open research.


Stanford have conducted a survey on the use and creation of research software; see the results here. The RSE Sheffield team conducted a similar survey at TUOS recently and will be sharing the results soon.


The Research IT team in IT Services are now on Twitter (@RIT_Sheffield). Follow them for news regarding new resources and training.

Future events

The RSE Sheffield team is running an event to provide information about the team, our projects and how to collaborate with us.

The latest UK Research and Development Roadmap places increasing emphasis on open research. In this information session you can learn about why Research Software Engineering is vital to reproducible research. You will hear about how the funding agencies are increasingly looking at how software is developed and used when assessing your funding applications. You will also find out about how you can embed Research Software Engineers within your research projects as well as examples of collaborations which the RSE team has been involved in.

Register via EventBrite.


The RSE Sheffield team is running two full-day practical workshops on Deep Learning, focussing on the use of TensorFlow with Python in one workshop and R (plus Keras) in the other. 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 for the R and Keras event on 2021-02-18.

The Deep Learning with Tensorflow in Python (2021-02-11) has now sold out, but we hope to run it again in future.


12-week course on parallel computing with GPUs starting 2021-02-07. The course has been designed as an undergraduate 4th year module for the Dept of Computer Science but is available to staff and PhD Students (as part of the DDP program) and regularly has staff and PhD student enrollment. The first 3 weeks are focused on teaching C and OpenMP followed by GPU programming with CUDA C. Lectures are provided as pre-recorded mini lectures and there are 2 hours of scheduled support per week to undertake practical lab classes. Assessment is not required for DDP or staff participants. If you are interested in enrolling as a PhD student then please do so via DDP. You will need to contact the DDP team to enroll. Staff interested in enrolling for the module should contact p.richmondsheffield.ac.uk.


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 will be in early to mid March, with a provisional theme of Making GPU programming more accessible. The exact date and details of talks will be advertised soon via the RSE team’s mailing list.


ITS have announced 2021 dates for lots more Linux, shell scripting, HPC and numerous Python workshops. Follow the link for dates and registration info.


The Software Sustainability Institute (SSI) will host its first online Research Software Camp on research accessibility from Monday 22 February to Friday 5 March 2021. This is a free online event encompassing live sessions, web resources and social media activities. It will focus on different aspects of research accessibility, ranging from making tools, techniques, datasets, software and protocols used in research reproducible, open and sustainable, to exploring formats and tools to facilitate and improve accessibility for people with disabilities. They welcome anyone involved with research and research software from all career stages to attend any or all of the live sessions, and take part in the SSI’s social media and website activities.

Chris Hartgerink, from Liberate Science, will deliver a pre-recorded keynote talk on “Social Models of Inaccessibility” which will become available first thing on Monday 22 February, followed by a live Q&A session with Chris on 24 February at 3:30pm GMT via Zoom. This will allow participants to ask questions and start conversations around Chris’ talk. Register for free live Q&A with Chris.


If you are part of a team that already or wants to accelerate some software using GPU programming (e.g. CUDA, Sykl, rocM, OpenCL) then you may be interested in a GPU hackathon being organised by EPCC at which you could get support from experienced, knowledgeable mentors. This is the successor to the GPU hackathon held in Sheffield in recent years. See these blog posts for what a GPU hackathon can offer. Application deadline: 2021-02-19. Event itself: 2021-04-19, 2021-04-26, 2021-04-27, 2021-04-28.


External workshop on Sustainable Software Development for Researchers: at this workshop, attendees will learn about the basic steps to prepare code for sharing with others and for citing in a research paper.

This workshop is run by Carina Haupt, Head of Group Software at the German Aerospace Centre. It consists of two sessions, one on 2021-02-25 13:00 - 17:00 GMT and 2021-02-26 09:00 to 12:30 GMT, with participants needing to attend both sessions. Register on Eventbrite.


External workshop on Boosting your research reproducibility with Binder: during this free workshop, the instructors will discuss reproducible computing environments and why they’re important, show examples of others’ projects in mybinder.org and help attendees learn how to prepare a Binder-ready project. The workshop is run by The Turing Way, and will take place on 2021-03-03 from 10:00 to 16:30 GMT. Register on Eventbrite.


SORSE (Series of Online Research Software Events) run talks/workshops for the international RSE community. Their most recent talk was on creating web apps with Python. See this YouTube channel for recordings of past events and the SORSE site for info on upcoming events (inc several on community building).


Dates and deadlines for Supercomputing 2021, the world’s biggest conference on high-performance computing, have been announced. The organisers currently appear to be planning for an in-person event.


TIER, the Sheffield Methods Institute and the UK Reproducibility Network are co-organising a symposium across Fridays in March entitled Instruction in Reproducible Research: Educational Outcomes Background, schedule and registration info.


People involved in DAFNI, including several from Sheffield, are giving talks on the National Digital Twin project at an event on 2021-02-26. DAFNI is a national project to provide a platform for securely storing data and running models, primarily using high-performance computing hardware. More info including registration.


The Library are running an event on Electronic Lab Notebooks on the 2021-04-22.

Previous events

A recording of the last LunchBytes event (Beyond Static Data Visualisations on 2021-01-13) and slides for most talks are now available.

At the event we had talks on plotting data in time using video, the use of Shiny to develop interactive web interfaces to represent datasets or support data manipulation, a consideration of the problem data visualisation solves and a look at the alternative tools in the toolbox, plus an overview of a interactive data visualisation tool written in C++.

Information on all previous LunchBytes sessions (including links to slides/video where available) can be found on our site.


In January Tom Stafford and Anna Krystalli presented at a TUOS Open Research Conversations event on future directions of reproducible research advocacy at TUOS and on some of the technical challenges. Slides from the event are now available here: DOI:10.15131/shef.data.13516274.


FOSDEM, one of the biggest conferences on Free and Open-Source software happened on 2021-02-06 / 2021-02-07. There were lots of talks on a great variety of topics, including a high-performance computing track. Recordings of many of the talks will no doubt end up on YouTube soon.

Opportunities

Applications for the Software Sustainability Institute’s 2021 fellowship programme closed on 2021-02-07. Good luck to anyone who applied!


If you are interested in open-source community building and mentoring then check out this Twitter thread by Yo Yehudi (Tech lead at the Wellcome Trust, Open Life Science co-founder and Software Sustainability Institute Fellow) on opportunities relating to the Google Summer of Code programme and to Outreachy (Internships Supporting Diversity in Tech).


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

Web and Blogs

A post from UKRI chief executive Professor Dame Ottoline Leyser on why research’s ‘lone genius’ image is unhelpful: good research is often facilitated by teams of people with complementary backgrounds and expertise. Dame Leyser is collaborating with “Minister for Science Research and Innovation, Amanda Solloway, to find 101 people, doing 101 different jobs that make major contributions to research and innovation, but who are not researchers and innovators.”


HPCWire featured an article on the Julia programming language, which it argues could now be a serious challenger to Python, R and MATLAB given performance features provided by the language itself plus its expanding array of libraries (with the lack of libraries in its early days having limited adoption then).


A new paper in the EMBO Journal (molecular and cell biology) entitled Reproducible image handling and analysis looks at common problems with image data and analysis in the biosciences, suggests protocols that help avoid these issues and provides guidance to journal editors on how to facilitate the submission of reproducible methods. DOI:10.15252/embj.2020105889.


A blog post on what someone learned when porting some code from MATLAB to Python, including the importance of version control, packaging and documentation.


A Nature article on Five reasons why researchers should learn to love the command line: DOI:10.1038/d41586-021-00263-0.


A post arguing for all software projects to have easily discoverable guides to the software’s architecture. (Editor: I’m very much in favour of this; such guides are a massive help when trying to familiarise oneself with someone else’s code and a lack of architectural information might result in an open-source software project stagnating through a lack of contribution).

Software and Updates

Exciting new things in MATLAB: Mike Croucher (RSE Sheffield alumnus) took up a new post at Mathworks at the start of 2021 so we’ve been learning about developments in the world of MATLAB:


Support for Python 2 has been dropped in the newest version of Pip (the most common tool for installing (pure) Python packages). This is another reminder that Python 2 in general is no longer supported and people should migrate to Python 3.x if possible.

Resources

Code for Thought is a new podcast on software, engineering, research and anything in between. The most recent episode was on the challenges of funding research software engineering. The podcast is run by Peter Schmidt, a Senior Research Software Developer at UCL.

If that floats your boat you may also be interested in:

  • the more established RSE Stories podcast, run by the super-prolific Vanessa Sochat.
  • the back catalogue of the (seemingly now defunct) RCECast podcast, which is largely focussed on high-performance computing technologies.

Online, self-paced MATLAB training is available to all at TUOS via the MATLAB Academy. There are courses on more specific topics such as image processing and deep learning in addition to the fundamentals of MATLAB.


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

To contact the RSE team about seminars, training or JADE: rse-team-group@sheffield.ac.uk

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 University central IT support.