Software and research: the Institute's Blog

Free help to forge better software

By Steve Crouch, Consultancy Leader.

The Institute's Open Call provides developer expertise and effort - free of charge - to UK-based researchers. If your project develops research software and you'd like some expert help, you should submit an application to the Open Call.

We've just opened the latest round of the Open Call, which closes on 5 December 2014.

You can ask for our help to improve your research software, your development practices, or your community of users and contributors (or all three!). You may want to improve the sustainability or reproducibility of your software, and need an assessment to see what to do next, or perhaps you need guidance or development effort to help improve specific aspects or make better use of infrastructure. We want applications from any discipline in relation to software at any level of maturity.

From benign dictatorship to democratic association: the RSE AGM

By Simon Hettrick, Deputy Director.

If you don’t write papers, how should a university recognise your work? This and related topics were the focus of discussions at the first ever Annual General Meeting of Research Software Engineers, which took place on 15-16 September. The AGM was an important milestone in our campaign for Research Software Engineers: it marked the first formal meeting of the RSE community. 

Over fifty RSEs met at ORTUS, based in King’s College London to meet, collaborate and discuss work. The day kicked off with an overview of the RSE campaign from staunch RSE supporter, James Hetherington. This was followed by a talk from Kumar Jacob and Richard Dobson (respectively from Maudsley Digital and the NIHR BRC for Mental Health) about software use in mental health research. Maudsley Digital were the gold sponsor for the event, and were joined by our other sponsors NIHR BRC for Mental Health, GitHub, Microsoft Research and FitBit UK.

Fellowship - how it helped a digital humanites scholar.

By Stuart Dunn, lecturer at the Centre for e-Research, Kings's College London, and 2014 Institute Fellow.

One problem with being a digital humanities academic these days is the sheer volume of scholarly activity available – from seminars and workshops to conferences and symposia. In London alone, one could easily attend three or four such events every week, if not more.

My Fellowship has provided me with an excellent heuristic for selecting which events one goes to, and helped me to connect my participation in the community around how digital humanists approach and practice the sustainability of what they use and build.

Especially to one used to applying for research grants, the application process was extremely simple and lightweight. The focus was on your ideas and thinking, rather than just box-ticking. Even writing the application forced me to think succinctly about the challenges and questions facing the DH community in sustaining software. These include whether we are too reliant on proprietary software, what role crowdsourcing will play in the future and in what ways does the inherently collaborative nature of Digital Humanities impact in sustainability issues.

Fellowships - what's it like being a Fellow?

By Stephen Eglen, senior lecturer in Computational Biology at the University of Cambridge and 2014 Institute Fellow.

I first heard about the Software Sustainability Institute in 2013, when Laurent Gatto and I were planning an R programming bootcamp.

I have long been a believer in the open sharing of software, and so I was glad to read about many of the complementary issues that the Institute has promoted, both within the UK and worldwide. Another thing that convinced me to apply was that a respected colleague in the R community, Barry Rowlingson, was also a Fellow.

I found the application procedure refreshingly short and straightforward. The most useful thing in the process was to propose what I would do in the course of the Fellowship. I had been discussing with colleagues in the neuroscience community about ways in which we could encourage data and code sharing.

Top tips for software developers working with researchers

By Mike Jackson, Software Architect.

Working with researchers is something the Institute has been doing for many years now. So we thought it was about time to put together our top tips for software developers working with researchers, to help foster productive, and enjoyable, collaborations.

1. Remember they are not software developers

You may know the difference between centralised and distributed revision control, classes and objects, pass-by-value and pass-by-reference, upcasting and downcasting, coupling and cohesion, processes and threads, or a stack overflow and StackOverflow, but your researcher may not. Knowing how to knock together a few dozen lines of code does not make someone a software developer, as writing code is just a fraction of what a software developer does.

Reducing the Distance between theory and practice

Polar bears

By Mike Jackson, Software Architect.

Clever theory about how to estimate the density or abundance of wildlife is of limited value unless this theory can be readily exploited and applied by biologists and conservationists. Distance sampling is a widely-used methodology for estimating animal density or abundance and the Distance project provides software, Distance, for the design and analysis of distance sampling surveys of wildlife populations. Distance is used by biologists, students, and decision makers to better understand animal populations without the need for these users to have degrees in statistics or computer science. Distance places statistical theory into the hands of practitioners.

“Is this a good time?” – how ImprompDo can tell when you’re busy

By Liam Turner, PhD student at Cardiff School of Computer Science & Informatics.

This article is part of our series: a day in the software life, in which we ask researchers from all disciplines to discuss the tools that make their research possible.

Growth in smartphone technology has led to the traditional trawl for information to be devolved down to an individual level. This presents a challenge as traditional methods of making information available depend on when it is ready available, rather than when it is most convenient for a busy user.

Currently users have to work out the best way to get information while still managing their other commitments at the same time, but it would be more useful if this could be managed proactively. This predictive estimation would analyse and arrange itself around its user’s behaviour before it sent them the new information. This forms the backbone of our project in using the technical capabilities of the smartphone to infer interruptibility and so make a decision as to whether to deliver or delay.

What makes good code good at EMCSR 2014

By Steve Crouch.

On August 8th 2014, I attended the first Summer School in Experimental Methodology in Computational Research at the University of St. Andrews in Scotland. Run as a pilot for primarily computer scientists, it explored the latest methods and tools for enabling reproducible and recomputable research, and the aim is to build on this successful event and hold a bigger one next year.

The Institute already works with the Summer School organisers in a related project, recomputation.org. Led by Ian Gent, this project aims to allow the reproduction of scientific results generated using software by other researchers, by packaging up software and its dependencies into a virtual machine that others can easily download and run to reproduce those results.

Online psychological therapy for Bipolar Disorder

By nicholas [dot] todd [at] nhs [dot] net (Nicholas Todd), Psychologist in Clinical Training at Leeds Teaching Hospitals NHS Trust.

This article is part of our series: a day in the software life, in which we ask researchers from all disciplines to discuss the tools that make their research possible.

People with Bipolar Disorder often have problems gaining access to psychological therapy. Online interventions are an innovative solution to this accessibility problem and are recommended in clinical guidelines for mild to moderate anxiety and depression. These interventions provide round-the-clock, evidence based, self-directed support for a large number of people at a reduced cost to the NHS. 

The Living with Bipolar project was funded by Mersey Care NHS Trust and led by myself under the supervision of Professor Fiona Lobban and Professor Steven Jones, from the Spectrum Centre for Mental Health Research, Lancaster University. It was the first randomised controlled trial of an online psychological intervention for Bipolar Disorder to find preliminary evidence that the web-based treatment approach is feasible and potentially effective.

The Wild Man Game - bringing historic places to life

By Gavin Wood and Simon Bowen, Digital Interaction Group, Newcastle University.

This article is part of our series: a day in the software life, in which we ask researchers from all disciplines to discuss the tools that make their research possible.

Heritage organisations, such as museums, and managers of historic sites are increasingly interested in using mobile phones as a way of adding value to visits and directly connecting with the general public. App designers have responded by creating gamified digital experiences by borrowing game mechanics and game elements in an attempt to engage the user.

However, these experiences often fall short and we are given uninteresting treasure hunts that are often more about achieving goals and collecting rewards rather than thinking about and connecting with the heritage space itself. In response, we are exploring how digital play can bring our cherished cultural spaces to life, challenging the typical role for mobile phone apps in such contexts.