Software and research: the Institute's Blog

RSEHistory1.jpgBy Simon Hettrick, Deputy Director 

On a beautifully sunny day in March 2012, a small group met at Queen’s College Oxford and challenged a long-standing problem: why is there no career for software developers in academia? They didn’t know it at the time, but this meeting led to a nationwide campaign that created a vibrant and rapidly growing community, and established a new role in research: the Research Software Engineer.

The lack of a career path for academic software developers wasn’t new back in 2012, but it had gone largely unchallenged. Many academics were aware of the importance of software to research; they could see that the people who created this software went largely unrecognised, and they were beginning to worry about the consequences of this oversight. What happens when something is so vital to research, yet overlooked and severely under-resourced? Concerns like these were raised at our Collaborations Workshop, and this led the group to meet and challenge them.

A new role is born

The group that rose to the challenge consisted of Rob Baxter, Ian Bush, Dan Emmerson, Robert Haines, Neil Chue Hong, Dirk Gorissen, James Hetherington and Ilian Todorov (I missed this now-historic moment because I was running the conference). They realised that software developers lacked something more fundamental than just recognition—they lacked a name. In a short study in 2014, we investigated…

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Research Data Visualisation WorkshopBy Raniere Silva, Community Officer, Olivia Guest, University of Oxford, Vincent Knight,Cardiff University, Christina Bergmann, Ecole Normale Supérieure.

The Institute’s Research Data Visualisation Workshop took place on the 28th of July 2016 at the University of Manchester. Raniere Silva’s warm welcome was followed by Prof. Jessie Kennedy’s, from the Institute for Informatics and Digital Innovation at Edinburgh Napier University, keynote talk. Jessie spoke about the miscommunication of data due to poor visualisation techniques and how to avoid it. With over 50 attendees, the workshop provided an environment for learning and sharing. In the following sections, we will cover the events that took place during the workshop.

The Keynote

RDVW keynote

The Research Data Visualisation keynote talk was titled: ‘…

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BW1.jpgDr Becca Wilson, Software Sustainability Institute Fellow, Research Fellow, Data 2 Knowledge Research Group, University of Bristol

I attended the 2016 UseR conference at Stanford University 27th–30th June 2016. This year’s UseR Conference was of particular importance as it coincided with the 40th anniversary of the S statistical programming language (the precursor to R) and the 75th birthday of Professor John Chambers—a co-creator of S.  The conference was highly attended, with around 900 registered delegates split 50:50 across academia and industry.  Those unable to attend could follow #useR2016 on twitter and watch the stream from keynote talks live, all talks were recorded and are available online.

The opening keynote Forty years of S by Rick Becker, co-creator of S at Bell Labs in the 1970’s, was a nostalgic look back at the origins of the ‘S’ statistical language. Rick highlighted how far analytic processing has come—when in the 1970s batch computing was done via punch cards, processing for a regression analysis took two hours and then you had to wade through pages of print out to identify the solution. Ultimately R was released as an open source alternative to the licensed S, with much of its functionality retained from S including the use…

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recipy.jpg By Mike Jackson, Software Architect

A major challenge to reproducibility in computational science is the effort that is required to keep track of provenance and to make research that relies upon code more reproducible. recipy provides an almost effortless way to track provenance in Python. I am working with recipy’s developers—Software Sustainability Institute fellow Robin Wilson and Janneke van der Zwaan of Geography and Environment at the University of Southampton—to develop an automated test suite for recipy as a precursor to expanding the development of recipy and promoting recipy more widely.

recipy is an open source Python module package hosted on GitHub and released under the open source Apache License Version 2.0. It is available via this repository or as a Python package that can be installed via Python’s pip package manager. Once a researcher has installed recipy, all they have to do is add “import recipy” at the top of their Python scripts, and all of…

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A word cloud of the software used in researchBy Simon Hettrick, Deputy Director.

Over the last couple of years, we’ve had occasion to ask people about the software they use in their research. We’re about to start a long-running survey to collect this information properly, but I thought it might be fun to take a rough look at the data we’ve collected from a few different surveys.

It would be easy to survey people if there existed a super-list of all possible research software from which people could choose. But no such list exists. This raises the question of how many different types of software do we expect to see in research? Hundreds, thousands, more? The lack of this list is rather annoying, because it means we have to collect freeform text rather than ask people to choose from a drop-down list. Free-form text is the bane of anyone who collects survey data, because it takes so much effort to clean. It is truly amazing how many different ways people can find to say the same thing!

I collected together five of our surveys from 2014 to 2016, which relates to 1261 survey participants. From these, we collected 2958 different responses to the question “What software do you use in your research?”, but after a few hours of fairly laborious data cleaning (using Open Refine to make things easier) these were boiled…

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Cloud computing proposals wanted for Internet of Things research

By Kenji Takeda, Microsoft Research

We are in the midst of an invisible revolution with the promise of ubiquitous and pervasive computing; not a dream, but a newly emerging reality. The nexus of cheap and capable devices, connectivity and cloud computing is rapidly giving shape to the Internet of Things (IoT). Microsoft is delighted to offer cloud computing resources to IoT researchers around the world through a special Azure for Research IoT call for proposals — next deadline is 15th August 2016.

“To maximise the economic and societal benefits of IoT, Social and Physical Scientists, working together, must anticipate and remove barriers to adoption. It also raises the bar on addressing 21st century technological challenges using innovative, collaborative and interdisciplinary research methods. IoT works alongside technologies like cloud analytics, such as Microsoft’s Azure platform, to revolutionise the application of IoT data streams,” explains Professor Jeremy Watson, University College London, who leads the PETRAS Research Hub, launched earlier this year with the aim of developing and deploying a safe and secure IoT.

The Azure IoT Suite provides an easy-to-use platform to connect devices to the cloud, allowing…

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By Mike Croucher, SSI Fellow, Research Software Engineer and author of Walking Randomly.

William Stein, lead developer of the computer algebra system, Sage, and its cloud-based spin-off, SageMathCloud, recently announced that he was quitting academia to go and form a company. In his talk, William says "I can’t figure out how to create Sage in academia. The money isn’t there. The mathematical community doesn’t care enough. The only option left is for me to build a company."

His talk is linked below and his slides are also available.

“Every great open source math library is built on the ashes of someone’s academic career.”

William’s departure is not unique. Here’s a tweet from Wes Mckinney, creator of pandas, one of the essential data science tools for Python.

Contact us

We are looking for similar stories: good research software people who felt that they had to leave academia because there wasn’t enough support, recognition…

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By Devasena Inupakutika and Steve Crouch, Software Sustainability Institute, and Richard Bradshaw, University of Southampton.

As a part of their research, Jonathan Essex’s Research Group developed ProtoMS, a biomolecular simulation software that allows the simple development of methods for the calculation of relative protein/ligand binding free energies. The Software Sustainability Institute worked with them as part of an Open Call project to develop a test strategy and Python test suite, and to verify the operation of the ProtoMS software as an overall product. The great news is that the latest release now includes the test suite and has already found some interesting issues which have been resolved.

A firm and stable unit test suite is crucial for ongoing development in large projects. Writing unit tests adds value to a project while reducing the cost of code changes. With our aim to explore the software for its accessibility and usability and how to adopt a decentralised approach that can reduce strain on further development, we examined each unit of the ProtoMS Python code…

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By Steve Crouch, Research Software Group Lead.

This article was originally published on Jisc's Research Data Spring blog on 30 June 2016.

Sustainability is increasingly becoming recognised as a must-have goal in the development of research software. Earlier this year, I undertook a sustainability assessment of the projects that had reached the second phase of the Jisc's Research Data Spring. It is particularly heartening that Jisc has sustainability high on the agenda across its portfolio of software projects, and that the projects themselves are embracing this ideal with such enthusiasm.

The Institute’s Research Software Group has conducted over 60 consultancy activities with projects producing research software, and a part of that work often involves an assessment of the software's sustainability. Typically, this means taking an in-depth look at the software itself…

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By Larisa BlazicSenior Lecturer, Faculty of Media, Arts and Design, University of Westminster

The Libre Graphics Meeting (LGM) is a meeting about free and open source software for graphics such as raster graphics editor Gimp, vector graphics editor Inkscape, desktop publishing software Scribus, free sketching and painting program Krita, 3D creation Blender, among many other amazing projects. Held yearly since 2006 and hosted by a different institution each year, LGM attracts developers, artists, and professionals who use and help improve free and open source software graphics applications. Unlike many events devoted to free and libre open source software, LGM has always had a strong artistic focus, with designers and artists showcasing their work alongside the work of software developers. It is one of the best examples of community and cross-disciplinary engagement in the world of free software graphics.  

From 15th–18th April 2016, Westminster School of Media Arts & Design (WSMAD) at the University of Westminster (London) hosted the 11th edition of the Libre…

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