Software and research: the Institute's Blog

Latest version published on 18 December, 2017.

Assigning fellows applicationsBy Raniere Silva, Community Officer

A few people have asked us how we run certain processes at the Institute. This time, we will look at how we assigned Fellowship programme 2018 applications to our reviewers.

Data repository

We used Google Forms to collect applications as, from experience in previous editions, we know that Google Spreadsheet works well for reviewers as they are familiar with the platform and usually have a Google account. Google Drive then allows us to share the data the reviewers need and use "Microsoft Excel programming language" to summarise the result of the reviews.

On the master spreadsheet each reviewer has a sheet with their initials, where they will find all the information needed to assess the candidates, with relevant columns to mark their thoughts. Data validation helps reviewers input correct values.

Sheet generation

To generate each of the reviewers’ sheet we use pandas and PuLP, both Python libraries. Pandas allows us to interact with raw data stored in a tabular form as a Google Spreadsheet and to create local CSV files. PuLP is a linear optimisation

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Latest version published on 14 December, 2017.

Motivate Better Practice in Research SoftwareBy James Grant, University of Bath, Andrew Washbrook, University of Edinburgh, Louise Brown, University of Nottingham, Niels Drost, Netherlands eScience Center, and Andrew Bennett, European Centre for Medium-range Weather Forecasts

What can be termed as "coding" is a subset of wider software engineering practices such as version control, continuous integration and good software design. Coding is prevalent in academia but practices that allow sustainable software to be produced are frequently overlooked.  Motivating the uptake of the approaches, methods and tools, and highlighting the benefit they deliver, by engaging with researchers who develop software is the first step in spreading best practice in our community.

In discussions with researchers, we find that the use of version control is often highlighted as the first methodology that they would like to introduce into their workflow. We would therefore like to 1) identify approaches that can promote the use of version control by reducing barriers from textbook to full integration and 2) highlight the wider benefits of the methods beyond traditional software development.

Software related courses at an undergraduate level tend to focus on code syntax and functionality with limited time spent covering software management practices.  By including the use of version control as part of these training programs we can avoid much…

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Latest version published on 13 December, 2017.

Good software development practiceBy Toby Hodges, EMBL, Roman Klapaukh, UCL, David McKain, University of Edinburgh, and Tobias Schlauch, DLR

WSSSPE members recognise the value of good practice in software development and the benefits of robust and reproducible code in research. The adoption of such practice requires an investment of time, energy, and money, and unfortunately it can be difficult to convince research scientists that this investment is worthwhile. Several initiatives already aim to encourage good practice in research software development, for example, Software Carpentry, the Software Sustainability Institute, the internal Software Engineering Initiative at the German Aerospace Center (DLR), and the Bio-IT project at EMBL. However, some research groups have remained difficult to reach.

Different approaches can be targeted at different levels and career stages. The majority of these share a common theme of support for the local research community.

For those at an early career stage, adoption of good practice can be encouraged by the availability of training, resources, and tools…

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Latest version published on 12 December, 2017.


Citation neededBy Stephan Druskat, Humboldt-Universität zu Berlin, Radovan Bast, University of Tromsø, Neil Chue Hong, Software Sustainability Institute, University of Edinburgh, Alexander Konovalov, University of St Andrews, Andrew Rowley, University of Manchester, and Raniere Silva, Software Sustainability Institute, University of Manchester

The citation of research software has a number of purposes, most importantly attribution and credit, but also the provision of impact metrics for funding proposals, job interviews, etc. Stringent software citation practices, as proposed by Katz et al. [1], therefore include the citation of a software version itself, rather than a paper about the software. Direct software citation also enables reproducibility of research results as the exact version can be retrieved from the citation. Unique digital object identifiers (DOIs) for software versions can already be reserved via providers such as Zenodo or figshare, but disseminating (and finding) citation information for software is still difficult…

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Latest version published on 11 December, 2017.

RSEsBy Caroline Jay, University of Manchester, Albert Solernou, University of Leeds, and Mark Woodbridge, Imperial College London

At present, few higher education institutions in the UK - or indeed internationally - employ a central team of dedicated research software engineers (RSEs) who sit outside of any specific academic department. The allocation of baseline funding to software developers is considered a risky activity when every member of staff represents a significant ongoing cost which has to be recovered. A cautious approach to employing people in what may be perceived as a completely new role is understandable, particularly in an uncertain financial climate.

Nevertheless, permanently employing RSEs has the potential to pay huge dividends, a fact borne out by the institutions who have established central pools, including the University of Manchester, UCL and the Turing Institute, and rapidly expanded their teams.

Institutional benefits of employing RSEs

A primary benefit of including software engineers on the baseline can be summed up by the Software Sustainability Institute mantra of “better software, better research”. Involving professional software engineers in research projects leads to better quality data, analysis and results, which has a direct impact on the scientific evidence base. Higher…

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