Software and research: the Institute's Blog

Collage fellows By Shoaib Sufi, Community Lead, Software Sustainability Institute

Our Fellowship Programme 2017 offers £3000 funding for conference visits, running workshops, and other domain or institutional events. If you would like your work supported and you are keen on improving and promoting best practice in research software, then the Fellowship Programme is for you. The Programme allows individuals to gain credibility for the promotion of best practice, network with like-minded people, and learn new skills.

Apply to become a Software Sustainability Fellow and join a network of over 70 Fellows that represent the physical sciences, medicine, biological sciences, mathematics, computer science, social science, creative arts and historical studies, research software engineering, and more.

Our Fellows have a standing in the community, a passion for promoting better computational practice and a social personality to make it all happen. If you’re a researcher who understands the value of software in research, an advocate for the adoption of software skills, or someone who codes to help support research, then this is the right programme for you.

As well as attending conferences and workshops, Fellows run training events for their…

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dorchard2_0.pngBy Dominic Orchard, Research Associate, Computer Laboratory, University of Cambridge and Institute Fellow.

The need for more rigorous software verification in science is well known. The presence of software errors can seriously undermine results leading to paper retractions, bad policy decisions, and even catastrophic technological failures.  Often the responsibility is placed on the programmer, but simply trying to be more careful is not enough. There is a wealth of research in computer science aimed at automating testing and verification, yet little of this has crossed over into practice in the sciences. In April 2016, we held a meeting in Cambridge on Testing and Verification for Computational Science to bridge the gap between computer scientists and natural scientists concerned with software correctness.

Before computer science became a discipline, computing existed mainly as a service to science, providing fast and accurate calculation. As computer science developed, it pulled in philosophy, logic, mathematics, semantics, and engineering but has largely moved away from its roots in science. This has lead to a gulf between computer science and the natural and physical sciences. While there have been many advances in program verification, little of this is applied to address the correctness of scientific software. This meeting was organised…

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By Simon Hettrick, Deputy Director.

I’m a lazy writer, so when it comes to summarising last week’s RSE Conference, I will defer instead to the genius of Adrian Jackson’s tweet:

With all the excitement about RSEs over the last couple of years, we knew it was the right time to run a conference to bring them together. We’ve had workshops and AGMs, but this was going to be bigger, better and way more intense. The thing that impressed me most was the buzz. We attracted a lot of new people, but they were interacting like old friends. We worked hard to have an inclusive event, but I think this is also representative of people feeling a part of the community. As one of the emails we received said:

“This might have been my 30th conference but it was the first where I felt thematically 100% at home and understood”.

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IHUB_2.pngBy Toni Collis, Applications Consultant

The Ionomics Hub (iHUB), a collaborative international network for ionomics, is a science community web portal that promotes knowledge extraction and reuse of ionomic data. The iHUB contains ionomic information on over 300,000 plant and yeast samples. Ionomics is the measurement of the total elemental composition of an organism which coupled to genetics provides a powerful tool to understand important biological processes and problems. A better understanding of the mechanisms regulating the ionome offers potentially new approaches to manipulate such agriculturally important traits as salinity tolerance and mineral nutrient efficiency to develop crop varieties that are more resilient to the predicted impacts of climate change on soil fertility. Further, it will allow improvement in crop yields in a more sustainable manner to deliver the yield gains required to meet future population growth. Together with the Software Sustainability Institute, David E Salt, the Director of iHUB and Professor of Genome-Enabled Biology in the Division of Plant and Crop Science based at the University of Nottingham wants to ensure that this valuable resource continues to operate and is maintained for years to come.

A major challenge to the reproducibility of science is the provenance of data. Sharing this data also…

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3D Reconstruction of NeuronsBy Paul Graham, EPCC and Software Sustainability Institute.

The Software Sustainability Institute have started a new project working with Colin Davis, Professor of Cognitive Psychology at the University of Bristol, and James Adelman, Associate Professor of Psychology at the University of Warwick, and their software easyNet. This is a computational modelling software package for cognitive science. It is a research tool used to better understand the mechanisms and codes underlying human cognition. By running of simulations of computational models, it is possible to generate predictions that can then be tested in behavioural experiments. So far the main interest has been in understanding reading, but research has also been conducted in speech perception and production, spatial cognition, memory and social cognition.

Computational modelling has played a critical role in the advancement of theory in cognitive science. However, the rate of theoretical progress has been hampered by a number of systemic issues relating to low levels of transparency, reusability, accessibility and reproducibility. The cognitive psychology research community is composed largely of non-modellers who refer to published models in their own empirical work, but do not directly…

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