Software and research: the Institute's Blog

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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By Dominic Orchard, Research Associate, Digital Technology Group and Cambridge Programming Research Group, Computer Laboratory, University of Cambridge and Software Sustainability Institute Fellow.

Much like natural languages, programming languages evolve over time: a new feature is added, an existing feature is removed or modified, ambiguous parts of a specification are made clear, and so on. These evolutionary changes may be due to external factors such as new hardware, new theory or foundational research, trends or fashions in languages, and applications; internal factors such as deficiencies in a language, problems with existing features; or feedback from a community of users.

While the aim of evolution is to provide more effective languages, evolutionary changes frequently undermine the long-term sustainability of software. A change to the semantics of an existing language feature, or the removal of a feature altogether, is likely to modify the behaviour of some existing programs; other existing programs may not be compilable anymore. Therefore, an unmaintained piece of code might become increasingly unstable and unusable. Language evolution is…

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Tufte Collection by pseudoplacebo.By Larisa Blazic, Senior Lecturer - Faculty of Media, Arts and Design - University of Westminster.

Data visualisation, information design, infographics are forms of visual communication of data to educate, inform thus contributing to scientific discovery. A combination of basic graphics design elements, statistics and cognitive science, it functions as a translation of complex data sets into accessible, coherent and comprehensive narratives. In order to unpack how and why is this useful for scientific research and it's dissemination, it is probably best to start with Edward Tufte, an American statistician and artist, and Professor Emeritus of Political Science, Statistics, and Computer Science at Yale University.

Long before big data craze, in the late 20th century, he wrote, designed, and self-published The Visual Display of Quantitative Information and the two companion volumes Envisioning Information and Visual Explanations set to explain the fundamental principles of information displays, how to display data for precise, effective, quick analysis and how to communicate complex material by visual means.

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By Olivia Guest, Postdoctoral Researcher, Oxford BabyLab, Department of Experimental Psychology, University of Oxford and Software Sustainability Institute Fellow.

I signed up to go to PyData London for three reasons. Firstly, looking over the talks I noticed that a lot of them were about specific machine learning algorithms and libraries we (I and/or my lab use) in our research, e.g., gensim and theano. Specific emphasis was placed on artificial neural networks, a type of computational model I both teach to undergraduate students (part of a movement called connectionism) and use daily in my research. So I assumed that it would be a good opportunity to ask questions and meet the developers of some of the libraries and codebases we use.

Secondly, having been working in experimental psychology departments since 2009, it often requires a little more effort to stay in the loop so to speak when it comes to programming tools and trends. So while I know how to write a journal article and how to design experiments because I practise these in…

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