Software and research: the Institute's Blog

Latest version published on 5 February, 2018.

3857596_b61f5c8d78_z.jpgBy Sammie Buzzard, University College London; Martin Donnelly, University of Edinburgh.

Introduction or why does this matter?

Whether our involvement in software is in developing it from scratch, building upon existing code, reusing or repurposing someone else’s work, or preserving it (for ten years or until the end of the world, whichever comes first), good software practices benefit us all. This could range from basic version control for an undergraduate’s first coding project to passing well-documented software from one research project to its successor, but the best way to motivate people to improve their practices will be highly dependent on the individual and their circumstances and drivers.

Additionally, appealing to the individual is effective but it doesn’t scale—there are simply too many people involved in research software for a small community of advocates to reach on an individual basis. There are also more wide-ranging actions that could be taken, for example by journals and funding bodies, that could catalyse change within the research software community as a whole. Like any bridge, it is  a good idea to start building from both ends...

So what can we do at an individual level?

In common with most other…

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Latest version published on 2 February, 2018.

LUX_watertank-1024x587.jpgBy Gillian Law, technology writer

The LUX-ZEPLIN project is building the largest and most sensitive dark matter detector of its type ever constructed. The detector will be built a mile underground in the Sanford Underground Research Facility (SURF) in Lead, South Dakota and is due to go live in 2020.

Potential detector materials are currently being screened prior to their use in the experiment, and the results are collated and analysed using a 43-sheet Microsoft Excel spreadsheet. The spreadsheet has worked well to date, allowing researchers to share and view data, but moving to a more versatile and robust database solution will be very useful once the experiment begins, says Dr Alex Lindote, LZ Background Simulations project lead, who is based at Laboratory of Instrumentation and Experimental Particle Physics (LIP)-Coimbra, Portugal.

Lindote set up the spreadsheet in late 2015, bringing in data from a Google spreadsheet that had been set up by researchers to share their data.

“It was getting hard to track who was making changes and what was happening, so I was asked to start taking care of it. I decided to move it to an Excel file that I could control more easily,” Lindote says.

Once it became clear…

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Latest version published on 1 February, 2018.

raniere.pngBy Raniere Silva, Software Sustainability Institute.

In early 2017, NumFOCUS received a grant from the Gordon and Betty Moore Foundation that helps fund a variety of diversity and inclusion initiatives, including the Diversity & Inclusion in Scientific Computing Unconference during PyData New York City 2017. NumFOCUS is publishing notes about the Unconference at their blog.

This wasn't my first time attending a event label as a unconference, I attended Google Summer of Code Mentor Summit, Mozilla Festival and, of course, Collaborations Workshop, and because of this I had my own fantasy of how the event would be: diverse and amazing group of attendees, infinite number of breakout rooms—you can fit as many breakout rooms as…

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Latest version published on 30 January, 2018.

life-sciences-fair.pngBy Justin Clark-Casey, Research Software Engineer, Department of Genetics, University of Cambridge.

InterMine is an open-source life sciences data integration platform created at the University of Cambridge in the UK. It takes biological data from many sources and combines it into a unified whole, adding visualisations and search facilities that aim to provide insights for scientists and engineers that can accelerate research and the growth of the bioeconomy. Over the next three years, through a grant from the UK Government’s BBSRC funding agency, the InterMine team is going to be making sure that the data it makes available is as findable, accessible, interoperable and reusable—”FAIR”, for short—as possible. Keep reading to find out why we believe that making the world of data a “FAIRer” place is so important.

The Oxford Dictionaries define data as the “facts and statistics collected together for reference or analysis.”. We’re gathering ever more of it every year, and it’s no wonder that The Economist, for one, calls it “a driver of growth and change”, creating “new infrastructure, new businesses, new monopolies, new politics…

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Latest version published on 29 January, 2018.

andysouth.pngBy Andy South, Software Sustainability Institute fellow

Back in July, 2017 I attended the annual R users conference (useR! 2017) in Brussels and gave a lightning talk about my thoughts on the sustainability of releasing a small R package.

I love the diversity of domains at useR and the mix of interesting use cases and useful code ideas. This was the second time that I attended useR!. The first time was in 2013 when the conference was hosted in Spain. This year, there were 1100 attendees from 54 countries. For me, the diversity of domains makes it a very accessible event. It's OK to express ignorance of what your neighbour in the coffee queue is doing. I talked to an engineer analysing measurements collected every second for hundreds of power stations across Europe, a physiotherapy student automating sending injury questionnaires to sports teams, a statistics lecturer creating a new teaching platform and running a controlled test on two groups of students. Seeing this large number of people in a conference venue is a reminder of the size and diversity of the R community, that I mostly just experience online.

The Software Sustainability Institute funded my attendance out of my fellowship fund. I've been freelance for a few years and the cost on top of the time makes it difficult to justify attending conferences. I learnt a lot, met some nice people and hope to attend again when useR! is…

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