Software and research: the Institute's Blog

Open source tomography training for Palaeontologists, Cardiff 2015

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.

Open source tomography training kicks off at Bristol

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 politics of instruments

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).

Programming language evolution and sustainable software

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.

Tufte and the art and science of effective data visualisation

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.

PyData London 2016

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.

Complexities of making software sustainability fit for purpose in ICT4D

London symbols by Pavlina Jane.By Caitlin Bentley, Postgraduate research student, ICT4D Research Centre, Royal Holloway University of London.

This is the fifth in a series of articles by the Institute's Fellows, each covering an area of interest that relates directly both to their own work and the wider issue of software's role in research.

Information and communications technology for development (ICT4D) is a relatively contemporary multi-discipline, and continues to evolve. Generally, ICT4D comprises the application and development of ICTs to achieve social and economic development goals. Heeks (2010) wrote that ICT4D researchers need to approach research problems from a tri-disciplinary perspective: computer science, information systems and development studies. Additionally, ICT4D is fundamentally about human and sustainable development, and as Unwin (2009) has previously argued, researchers must prioritize the development needs and wants of the poor and marginalised people. ICTs are not a silver bullet by any means.

Workshop sets new Benchmarks

By Sarah Mount, Research Associate King’s College London and Institute Fellow

In many scientific disciplines, experimental methods are well established. Whether the methods in your field are simulations, lab work, ethnographic studies or some other form of testing, commonly accepted criteria for accepting a hypothesis are passed down through the academic generations, and form part of the culture of every discipline. Why then did the Software Sustainaiblity Institute and the Software Development Team feel the need to run #bench16, a one-day workshop on software benchmarking at King’s College London earlier this month?

Outcomes for the JavaScript Visualisation Workshop

Typing BioJSby Manuel Corpas, Project Leader, ELIXIR-UK Technical Coordinator, CorpasLab, The Genome Analysis Centre (TGAC).

In this blog entry we discuss the outcomes of the recently held JavaScript for Visualisation Workshop, The Genome Analysis Centre (TGAC), Norwich, UK, April 21-22. This workshop brought 26 attendees from around the UK and the continent. The event was open to both core technical members and developers not currently involved in the BioJavaScript (BioJS) project. The workshop was facilitated by Software Sustainability Institute 2016 fellow Manuel Corpas to promote software best practices and the latest standards in JavaScript, inspiring the future technical roadmap for the BioJS community.

The Coding Scientist I Never Thought I Would Be

perito moreno by marc cornelis.By Allen Pope, a research associate at the National Snow and Ice Data Center and the Polar Science Center. He studies the Earth's frozen regions with satellite and airborne data, does fieldwork to make sure the satellites have it right, and shares his science with other people. He tweets @PopePolar.

This is the fourth in a series of articles by the Institute's Fellows, each covering an area of interest that relates directly both to their own work and the wider issue of software's role in research.

I love being outdoors. There is just something so viscerally engaging about exploring and studying the environment you’re standing in – all the better if it is a remote, snowy, beautiful location. But I spend significantly more time working at a computer than in the field, and I’m pretty happy about it, too. Why, though, if it was fieldwork which started me out?