Software and research: the Institute's Blog

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.

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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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Dagsthul Perspectives WorkshopBy Carole Goble, Manchester Principal Investigator at the Software Sustainability Institute, and Mike Croucher, Robert Haines, and Caroline Jay, Fellows at the Software Sustainability Institute.

How should we build the research software of the future? This was the question under consideration at the Dagstuhl Perspective’s Workshop ‘Engineering Academic Software’, co-organised by the Software Sustainability Institute’s Manchester PI Carole Goble. Experts in the area from across the world spent an intensive week presenting, discussing, debating and writing, to define current problems in the field and determine how we could address them.

The Institute was out in force, with fellows Mike Croucher, Robert Haines and Caroline Jay offering their thoughts on the present and future states of application…

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The detailed MRI maps of the pigeon beak did not show magnetic nerves by UCL News.By Russell Garwood, Lecturer at the University of Manchester and Software Sustainability Institute Fellow.

The Software Sustainability Institute sponsored a training course introducing the tomographic software suite SPIERS in Cardiff at the 2015 Annual Meeting of the Palaeontological Association. Organised by Institute fellow Russell Garwood, and colleagues Mark Sutton and Imran Rahman, by the end of the morning session palaeontologists were studying wasps in amber in 3D.

As outlined in a previous blog post, computerised tomography (CT) scanning is an increasingly common approach in many different fields for characterising objects in three dimensions. Scanners are cheap and accessible, but the software used to create digital visualisation can be very expensive. Freely available software for this does exist, and accessible training in these programs can stop software prices becoming a barrier to widespread adoption of micro-CT, especially where funding is limited. To this end, Institute fellow, Russell Garwood and colleagues Mark Sutton (Imperial College, London) and Imran Rahman (University of Bristol) offered a training session funded by the Software Sustainability Institute at the start of…

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123D Catch obelisk 3D scan (Slottsmöllan - Sweden) by Creative Tools.By Russell Garwood, Software Sustainability Institute Fellow and 1851 Research Fellow/Lecturer at the University of Manchester.

The 10th and 11th of February 2015 saw two days of training on using software for tomographic reconstruction for earth scientists at the University of Bristol. Software Sustainability Institute fellow Russell Garwood outlines the rationale behind the meeting and reports from the Institute-sponsored training courses.

The world of computerised tomography (CT) scanning is an exciting place to be. The advent of microtomography, a high-resolution form of scanning, allows researchers to look non-destructively inside an enormous variety of objects. From materials science and medicine to engineering and Egyptology, micro-CT is opening new avenues of research of which scientists could only have dreamed a few decades ago. Such scanners only provide grayscale slice images that show the cross-section of an object; however, these slices are relatively rarely the end of the line in any given study.

Usually, digital visualisation and/or quantification of the datasets are required. For this, software provides the primary tools. Many packages for visualising CT data exist, but most of the widely-used software packages are very expensive. This is at odds with increasingly cheap and accessible CT scanners, and free (…

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Streams of Consciousness: Data, Cognition and Intelligent Devices Conference 2016

By Heather Ford, University Academic Fellow, University of Leeds School of Media and Communication and Software Sustainability Institute Fellow.

What are the politics of instruments? Researchers are using new tools to harness collective intelligence in the form of vast quantities of digital data that we parse and find patterns in using algorithms. We use these new data sources and tools to discover security threats and to understand epidemics, to predict and to control. To what extent are we using new tools to help us think through important questions about the world, or are the tools using us? This was one of the key questions posed at the Streams of Consciousness: Data, Cognition and Intelligent Devices Conference at the University of Warwick that I attended last month (21st & 22nd April 2016).

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