Software and research: the Institute's Blog

 

Digital History, Humanities, data structuresBy Melodee Beals, Digital Historian at Loughborough University and Software Sustainability Institute fellow

Originally posted at mhbeals.com

Historians appear to be quite happy with tables. Tables are neat, orderly repositories of information. Rank and file, we input our names, dates, and other titbits of historical data. Rank and file, we organise our world into an unending supply of lists — lists providing the relevant percentages, absolute enumerations or qualitative descriptions of anything we can imagine. Over the years, of course, our tables have evolved from mere typographical conventions to function-laden spreadsheets, capable of statistical and algebraic functions, textual concatenation, and a host of other minor miracles. Yet, for all the seeming convenience of Microsoft Excel (and its ilk), we pay a hefty price — our time and sanity. “Hyperbole!” I hear you shout. “Nonsense!” I hear you cry. And, when these initial protestations fade, we are left with the ever popular: “I have a system.”

The best laid plans

I’m sure you do; I did. For a very long time, I thought it was an…

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RSE State of the NationBy Simon Hettrick, Deputy Director.

The first State of the Nation Report for Research Software Engineers provides a history of the RSE campaign and a snapshot of the RSE community as it stands today. If you want to know how a name coined during one of our workshops turned into an 800 strong community which is gathering interest from around the world, then the report is a good place to start.

Most research would be impossible without software, and this reliance is forcing a rethink of the skills needed in a traditional research group. With the emergence of software as the pre-eminent research tool used across all disciplines, comes the realisation that a significant majority of results are based, ultimately, on the skill of the experts who design and build that software.

The UK has led the world in supporting a new role in academia: the Research Software Engineer (RSE). This report describes the new expert community that has flourished in UK research, details the successes that have been achieved, and the barriers that prevent further progress.\

The report is available for download from Zenodo: 10.5281/zenodo.495360.

Software and decision-making, oncologyBy Jakob Nikolas Kather, MD, MSc, National Center for Tumor Diseases (NCT), Heidelberg, Germany.

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

Diagnosis and treatments in oncology

Cancer is a common disease and one of the leading causes of death. If detected at an early stage, some types of cancer can be cured by surgery, but often a tumour is detected at an advanced stage, and its cells have already spread throughout the body. Although many of these patients cannot be completely healed, several different treatment options are available. These treatments make a difference for cancer patients: they can significantly prolong life and often reduce symptoms as well. For each patient, we face the question: which treatment option is optimal at the current point of the disease? Clinical trials in the last decades are providing us with guidance in many situations. Often, there is an established "state of the art" for a treatment that has been shown to be superior to other options. However, as the arsenal of treatment options keeps growing, it is increasingly difficult to compare all options under all circumstances. Also, on the other hand, novel and more…

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Interpretative research

By Heather Ford, University of Leeds.

My research involves the study of the emerging relationships between data and society that is encapsulated by the fields of software studies, critical data studies and infrastructure studies, among others. These fields of research are primarily aimed at interpretive investigations into how software, algorithms and code have become embedded into everyday life, and how this has resulted in new power formations, new inequalities, new authorities of knowledge [1]. Some of the subjects of this research include the ways in which Facebook’s News Feed algorithm influences the visibility and power of different users and news sources (Bucher, 2012), how Wikipedia delegates editorial decision-making and moral agency to bots (Geiger and Ribes, 2010), or the effects of Google’s Knowledge Graph on people’s ability to control facts about the places where they live (Ford and Graham, 2016).

As the only Software Sustainability Institute fellow working in this area, I set myself the goal of investigating what tools, methods and infrastructure researchers working in…

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citing softwareBy Will Usher, Senior Researcher: Infrastructure Systems Modeller, University of Oxford

Plagiarism is a serious issue, and we are all familiar with the horror stories of students unceremoniously ejected from courses for copying essays. Any undergraduate degree worth its salt teaches students how to cite work correctly, acceptable bounds on quotation and how to attribute ideas and concepts to their sources. But in the growing world of open-source research software, best practices have yet to be universally understood, as I recently found out.

During my PhD at University College London, I became involved in the heady enthusiasm of the Research Software Programming group, attending and then helping out at Software Carpentry workshops. As a consequence, I was keen to apply my new knowledge of Python, version control and software development to my research. As luck would have it, I discovered an existing Python library on Github, which implemented several Global Sensitivity Analysis routines I could make use of. As I used the library, I started adding bits and pieces, and so by the end of the PhD I had made a considerable contribution to the package.

It's probably safe to say that SALib (sensitivity analysis library) is the go-to Python library for the unfortunately still-far-too-niche use of global sensitivity analysis in modelling, and our…

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