December 2020 Newsletter

3 December 2020 12:00

University of Sheffield Research Software Engineering Team Newsletter December 2020

Before you read the rest of the newsletter, I’d like to point out our own Lunch bytes talks on Dec 9. This month’s theme is Accelerated Machine Learning, and we have short talks from NAG and NVIDIA.

One item, the call for the NVIDIA GPU Technology Conference, closes tomorrow, so this is a final reminder to press submit if you already have a proposal in draft form.

This is the 6th 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: such as researchers, research developers, or people paid to develop software like Research Software Engineers (RSEs).

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

All dates and times are in GMT (UTC+00)

News

We don’t do a comprehensive survey of the journals, but we keep an eye out for relevant published articles. We have:

Events

  • Advent of Code — Dec 2020 05:00 — Advent of Code has started already, but it’s never too late to start, and you can proceed at your own pace. A month of advent-themed coding challenges throughout December! If you fancy making your Advent of Code social, join the #adventofcode channel on our Slack.
  • NVIDIA GPU Technology Conference — Call for poster and talk submissions, deadline Fri 4th Dec 2020 — The NVIDIA GTC brings together a broad community of developers, researchers, engineers, and innovators with the common goal of sharing their achievements while discovering new technologies and tools that drive change around the globe
  • PyJamas Conf 2020 — 5th Dec 2020, online, beginng 08:00 UTC — 24 hours streaming of talks about Python and connecting with Python communities around the world that you can access at home, in your PJs.
  • GitHub Universe — 8–10th Dec 2020, online — Join GitHub team leaders, industry icons, and artists inspired by code for three days of live interactive sessions as we explore the future of software for developers, enterprises, and students.
  • Cloud-powered academic research — Dec 9th 09:00–10:45, online — Microsoft Azure bring together Researchers and Research Technology Professionals to discuss how Cloud can accelerate your time to insights and breakthrough discoveries.
  • Virtual Data Analysis in Atomic Force Microscopy Meeting — 10th Dec 2020, online — This event aims to bring together the AFM community to tackle the lack of consensus across the field regarding data analysis and availability.
  • The Scholarly Communications team at TUoS Library are hosting Open Research Conversations, a series of online discussions on Open Research Practices. Sessions will include talks from researchers who have made their research open and other experts sharing their experiences, promoting best practices and discussing the challenges they are facing:
    • 10th December Unpacking Open Monographs: a discussion about the opportunities and challenges in making monographs openly available with John Moreland & Kate Petherbridge.
    • 18th January 2021 Reproducibility in Practice: a discussion on the importance of reproducibility and the challenges faced when attempting to reproduce others’ research with Tom Stafford & Anna Krystalli
  • Christmas in the Cloud — 10-11th Dec 2020, online — University of Bristol RSE Team will host a free 2-day workshop in partnership with AWS aimed at researchers and research software engineers with the goals of: learning how to port and optimise applications for the cloud, using portable cloud technologies, such as terraform, to configure and deploy infrastructure-as-code applications, and gaining real hands-on experience of developing cloud applications in partnership with experienced RSEs and AWS solutions architects
  • Joint Roadmap for Open Science Tools 2020 Conference — 14–16 Dec 2020, online — a virtual event designed to hold space for the community of practitioners building, maintaining, and advocating for open tools to support research and collaboration.
  • Research IT Forum — 16th Dec 2020, 15:00–16:30, Blackboard Collaborate — save the date! — The Research IT team will be holding its next Research IT forum event on the 16th of December from 3–4:30pm. These quarterly events will celebrate research at Sheffield. This December’s event will be dedicated to showcasing machine learning at Sheffield. You can expect to hear about the statistics behind machine learning and the use of machine learning in medical imaging. You’ll also hear about two new high performance computing resources that will soon be available to users here at the University of Sheffield.

SORSE

A Series of Online Research Software Events (SORSE) is organized by volunteers from the international Research Software Engineers community — an international answer to the COVID-19-induced cancellation of many national RSE conferences.

Upcoming SORSE events

Lunch bytes

Lunch bytes 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

Upcoming Lunch bytes
  • Lunch bytes #3: Accelerated Machine Learning — 12:00 Wednesday 9th December, online Google meet. We have short talks from NAG and NVIDIA covering Accelerated Machine Learning using cloud computing, and how accelerated machine learning can be used to tackle simulation in physics and engineering. There will be opportunity for discussion and questions too!
  • Lunch bytes #4: Data Visualisation — 12:00 Wednesday 13th January
Previous LunchBytes

Video recordings and slides from previous LunchBytes sessions are available via the RSE Sheffield website

Puzzle Corner

Are you looking for a fun programming based set of puzzles to while away those long (boreal) winter nights? You might like to try Project Euler which is a series of problems that are designed to be solved with the aid of a computer (no particular programming language is recommended).

Euler Problem 1―Multiples of 3 and 5―is:

If we list all the natural numbers below 10 that are multiples of 3 or 5, we get 3, 5, 6 and 9. The sum of these multiples is 23.

Find the sum of all the multiples of 3 or 5 below 1000.

Opportunities

  • Exciting new opportunities for EPSRC funded fellowships with opportunity for early career stage onwards applicants to focus on innovation, instrumentation/technique development or software engineering or to include non‐technical elements to create positive change in the research community.
  • The Sheffield ReproducibiliTea network is looking for a new coordinator. ReproducibiliTea is a peer-led journal club formed to help early-career researchers improve Open Science. There are groups all around the world. Would suit early-career researcher, including PhD candidates. Join the Google Group to start a discussion: https://groups.google.com/a/sheffield.ac.uk/g/reproducibilitea”

Web and Blogs

Software and Updates

  • GitHub on nbdev GitHub have a nice blog article about their collaboration with fastai to bring nbdev to GitHub’s web-offering (in preview only at the moment). Definitely one to keep an eye on.
  • RStudio v1.4 Preview: Python Support: The RStudio preview has had a minor update, so might be worth a look if you haven’t tried it yet. Find out about a number of features that will further improve the Python editing experience in Rstudio release 1.4.
  • Tool of the month — dot from graphviz
    A 4 layer graph with a K<sub>2,2</sub> in the
middle My pick for ancient Unix tool of the month is the venerable dot from graphviz. I have recently been using this to draw graph networks from git repos. dot converts a simple text representation of a graph network into a PNG file or other graphic format. The shell script to generate the network graphic:

      dot -Tpng > graph.png <<EOF
      digraph G {
        a -> {b1 b2} -> {c1 c2} -> d
      }
      EOF
    

Resources

If you think there are other great training resources we should advertise, please get in contact.

Sheffield RSE Team Services

The RSE 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 team provides free Code clinics and paid services allowing 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.