October 2020 Newsletter

University of Sheffield Research Software Engineering Team Newsletter October 2020

This is the 4th monthly newsletter from the Research Software Engineering Team at Sheffield. We aim to share our experiences and information of other communities for those using software for research. This newsletter is a collection of interesting events and opportunities over the coming month. It also includes signposting to other resources that we have found beneficial or interesting. You may find the content within interest 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 BST (UTC+01)

Events

• Hacktoberfest 2020!: Series of online sessions hosted by the Sheffield RSE team to celebrate Hacktoberfest, a month long celebration of Open Source! See below more for details.
• JupyterCon Online
  • 12-16 October: Conference
  • 17th October: Sprints
• GovCamp North. 15th October 2020. The first unconference of it’s kind, bringing the people who work in and around the public sector together to share ideas and learn from each other how to make public services better.
• Research Reproducibility 2020: Educating for Reproducibility, December 2-3 2020, Abstract submissions by 15th October. Free conference bringing together experts and novices, researchers and educators, and students and administrators from multiple disciplines and institutions to explore best practices, innovations, policies, and new ideas for education around reproducibility, replicability, and rigour.
• 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:
  • 20th October Open Research with the Wellcome Trust: an online discussion of the Wellcome Trust’s new Open Access policy, with Hannah Hope, Anna Clements & Robert Smith.
  • 18th November Visualising CoVid-19 Data: a conversation about researchers’ experiences of visualising CoVid-19 data and the impact these are having on policy and society with James Wilsdon & Colin Angus.
  • 10th December Unpacking Open Monographs: a discussion about the opportunities and challenges in making monographs openly available with John Moreland & Kate Petherbridge.
  • 18th January 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

Hacktoberfest 2020!

It’s that time of the year again to brush up on our version control and online collaboration skills and carve some time out to learn more about and contribute to Open Source. Need more motivation? If you make 4 contributions to a participating project on GitHub you get an awesome limited edition t-shirt!

Contributing to open source can be fun and rewarding! It can also be daunting for new contributors, so the RSE team have put together a series of sessions to support folks new to open source and provide a space for folks to hack together. We kicked off Hacktoberfest on the 6th of October with an online session which included an introduction to open source and a practical exercise of making a pull request (contribution) using 3 different frameworks! (command, line, GitKraken, R & Rstudio). If you missed our session you can check out our online materials. We’ll then be hosting online hack sessions every Tuesday 2-4pm providing a space to hang out, hack together and get help if needed. Find our more details and register to get access to the hack room.

Lunchbytes

Lunch bytes #2: pros and cons of Jupyter Notebooks

The second edition of Lunchbytes was also a big success and focused on the pros and cons of Jupyter Notebooks! In particular, we hosted three short talks:

• (Mis)uses of notebooks as production tools in the financial industry. Fedor Gorokhovik, Man group slides

• Making the most out of notebooks John Charlton, Sheffield RSE Team Slides

• Pitfalls of Jupyter notebooks Richard Darst, Aalto Scientific Computing, Aalto University

The video recordings of the session are also now available.

Lunch bytes #1: writing safer (Python) code

The video recordings of the first Lunchbytes session are also now available.

Look out for our next LunchBytes session in December! Topic to be confirmed.

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.

• Two exciting new Research Software Engineering positions advertised at the Leiden Institute of Advanced Computer Science. The Dutch Language requirement is negotiable. https://www.universiteitleiden.nl/en/vacancies/2020/q3/20-432-research-software-engineers
• The Sheffield ReproducibiliTea network is looking for a new coordinator. ReproduciibiliTea 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

• A Recording of the Society of Research Software Engineering Annual General Meeting 2020 held on the 7th of September 2020 is now available.

• Sheffield RSE blog:
  • Our team member Bob Turner has been busy on our blog this month with, not one, but two new blog posts!
    • 2agile4academia: Chronicling the experiences of working in an agile manner with academics as part of the Scottish CoViD Response Consortium’s (SCRC) contribution to the Royal Society’s Rapid Assistance in Modelling the Pandemic (RAMP) initiative.
    • Open Source and Hacktoberfest: Some thoughts on Open Source and Hacktoberfest.
  • Team leader Will Furnass also discusses a recent talks he gave to introduce HPC to new PhD students
• RSE Stories Podcasts. Another bunch of excellent RSE Stories podcasts were released last month, including an interview with our very own RSE Anna Krystalli:
  • Publish Without Perish, Emmy Tsang
  • The Wisdom of the Systems Engineer, Bruce Wilson
  • R for Reproducibility, Anna Krystalli
  • Establish or Perish, Kenton McHenry
  • Pushing the bubble Mike Spencer
  • The Fortran Maestro, Damian Rouson

• Data deficits: why we need to monitor the demand and supply of information in real time Article about a project two members of the RSE team where involved in (Twin Karmakham and David Wilby) in collaboration with with GATE and FirstDraftNews. The project involves monitoring disinformation around COVID19, went live this month and includes a dashboard of live data and an analysis of fact checks over the first six months of the pandemic.

• More than 100 scientific journals have disappeared from the Internet: Researchers have identified dozens of open-access journals that went offline between 2000 and 2019, and hundreds more that could be at risk. Nature Article.
• Array programming with NumPy. Nature Article.
• Welcome to a new ERA of reproducible publishing. Blogpost on how new open-source technology lets eLife authors publish Executable Research Articles that treat live code and data as first-class citizens.
• COVID-19 data scandal prompts tweaks to elite journal’s review process. Science Article.
• How to digitize your lab notebooks. Converting paper records to digital formats provides secure back-ups that researchers can access from anywhere. Nature Article.

Software Updates

• GitHub CLI 1.0 is now available: GitHub recently announced the release of version 1.0 of GitHub CLI which brings GitHub to your terminal. Find out more on their blog.
• RStudio v1.4 Preview: Python Support: Find out about a number of features that will further improve the Python editing experience in Rstudio release 1.4.

Training Resources

• Hacktoberfest Introductory session materials: Learn about Open Source and how to collaborate through Git & GitHub using the command line, GitKraken or R & Rstudio!
• Reproducible Research Data & Project Management in R: Course materials developed for the ACCE DTP course. The course focuses on data and project management through R and Rstudio, introduces PhD students to best practice and aims to equip them with modern tools and techniques for managing data and computational workflows to their full potential.

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.