Software and research: the Institute's Blog

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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Square at Raniere Silva, Software Sustainability Institute.

When EuroSciPy 2016 was announced, I told to myself that I need to attend it. The first reason was to compare it with SciPy Latin America 2016, whose organisation I helped with last March, and be able to provide suggestions to both events in 2017.

Both conferences are about the use of Python in science and received between 100 and 200 attendees from different countries. SciPy Latin America 2016 attendees complained about the four tutorial parallel track and I believe that, for a conference of this size, having only beginner and intermediate tutorial tracks, as done by EuroSciPy, is the right choice. EuroSciPy had the last day reserved for sprints, something that was cut from SciPy Latin America—and that can be improved if the organizers provide an agenda for it. SciPy Latin America had some swags for the attendees that I really missed on EuroSciPy.

Another reason that I wanted to attend EuroScipy 2016 was to promote the Software Sustainability Institute, Software Carpentry and Data Carpentry. I taught a Git Tutorial based on Software Carpentry material on the second day. The organisers told me that they received positive comments about the Git Tutorial—which made me happy! EuroSciPy also had some lightning talk…

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RSEHistory1.jpgBy Simon Hettrick, Deputy Director 

On a beautifully sunny day in March 2012, a small group met at Queen’s College Oxford and challenged a long-standing problem: why is there no career for software developers in academia? They didn’t know it at the time, but this meeting led to a nationwide campaign that created a vibrant and rapidly growing community, and established a new role in research: the Research Software Engineer.

The lack of a career path for academic software developers wasn’t new back in 2012, but it had gone largely unchallenged. Many academics were aware of the importance of software to research; they could see that the people who created this software went largely unrecognised, and they were beginning to worry about the consequences of this oversight. What happens when something is so vital to research, yet overlooked and severely under-resourced? Concerns like these were raised at our Collaborations Workshop, and this led the group to meet and challenge them.

A new role is born

The group that rose to the challenge consisted of Rob Baxter, Ian Bush, Dan Emmerson, Robert Haines, Neil Chue Hong, Dirk Gorissen, James Hetherington and Ilian Todorov (I missed this now-historic moment because I was running the conference). They realised that software developers lacked something more fundamental than just recognition—they lacked a name…

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Research Data Visualisation WorkshopBy Raniere Silva, Community Officer, Olivia Guest, University of Oxford, Vincent Knight,Cardiff University, Christina Bergmann, Ecole Normale Supérieure.

The Institute’s Research Data Visualisation Workshop took place on the 28th of July 2016 at the University of Manchester. Raniere Silva’s warm welcome was followed by Prof. Jessie Kennedy’s, from the Institute for Informatics and Digital Innovation at Edinburgh Napier University, keynote talk. Jessie spoke about the miscommunication of data due to poor visualisation techniques and how to avoid it. With over 50 attendees, the workshop provided an environment for learning and sharing. In the following sections, we will cover the events that took place during the workshop.

The Keynote

RDVW keynote

The Research Data Visualisation keynote talk was titled: ‘…

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