Software and research: the Institute's Blog

By Olivia Guest, Postdoctoral Researcher, Oxford BabyLab, Department of Experimental Psychology, University of Oxford and Software Sustainability Institute Fellow.

I signed up to go to PyData London for three reasons. Firstly, looking over the talks I noticed that a lot of them were about specific machine learning algorithms and libraries we (I and/or my lab use) in our research, e.g., gensim and theano. Specific emphasis was placed on artificial neural networks, a type of computational model I both teach to undergraduate students (part of a movement called connectionism) and use daily in my research. So I assumed that it would be a good opportunity to ask questions and meet the developers of some of the libraries and codebases we use.

Secondly, having been working in experimental psychology departments since 2009, it often requires a little more effort to stay in the loop so to speak when it comes to programming tools and trends. So while I know how to write a journal article and how to design experiments because I practise these in…

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London symbols by Pavlina Jane.By Caitlin Bentley, Postgraduate research student, ICT4D Research Centre, Royal Holloway University of London.

This is the fifth in a series of articles by the Institute's Fellows, each covering an area of interest that relates directly both to their own work and the wider issue of software's role in research.

Information and communications technology for development (ICT4D) is a relatively contemporary multi-discipline, and continues to evolve. Generally, ICT4D comprises the application and development of ICTs to achieve social and economic development goals. Heeks (2010) wrote that ICT4D researchers need to approach research problems from a tri-disciplinary perspective: computer science, information systems and development studies. Additionally, ICT4D is fundamentally about human and sustainable development, and as Unwin (2009) has previously argued, researchers must prioritize the development needs and wants of the poor and marginalised people. ICTs are not a silver bullet by any means.

The roles of ICT4D researchers are to act as intermediaries, critics and advocates, and we draw ICTs from within our tool belts to engage in the politics of social, economic and sustainable development processes. Nevertheless, technological solutions to development problems can be beneficial if they are built upon existing…

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By Sarah Mount, Research Associate King’s College London and Institute Fellow

In many scientific disciplines, experimental methods are well established. Whether the methods in your field are simulations, lab work, ethnographic studies or some other form of testing, commonly accepted criteria for accepting a hypothesis are passed down through the academic generations, and form part of the culture of every discipline. Why then did the Software Sustainaiblity Institute and the Software Development Team feel the need to run #bench16, a one-day workshop on software benchmarking at King’s College London earlier this month?

Broadly accepted methods for establishing the running time of a piece of software (its latency) are not widespread in computer science, which often comes as a surprise to those working in other fields.

Unlike clinicians and ethnographers, computer scientists are in the enviable position of being in full control of their computers, but there are a still a large number of confounding variables which affect latency testing. These can come from the operating system, the programming language, the machine itself, or even from cosmic rays. The statistical…

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Typing BioJSby Manuel Corpas, Project Leader, ELIXIR-UK Technical Coordinator, CorpasLab, The Genome Analysis Centre (TGAC).

In this blog entry we discuss the outcomes of the recently held JavaScript for Visualisation Workshop, The Genome Analysis Centre (TGAC), Norwich, UK, April 21-22. This workshop brought 26 attendees from around the UK and the continent. The event was open to both core technical members and developers not currently involved in the BioJavaScript (BioJS) project. The workshop was facilitated by Software Sustainability Institute 2016 fellow Manuel Corpas to promote software best practices and the latest standards in JavaScript, inspiring the future technical roadmap for the BioJS community.

The Need for this Workshop

JavaScript has become the de facto language of the web. Console-like interactivity is now common place in most web applications and sites. Online collaboration plays an important role in research, enabling scientists to share and disseminate results regardless of geographical location. The data-intensive field of bioinformatics greatly benefits from JavaScript technologies applied to visualisation of biological datasets.…

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perito moreno by marc cornelis.By Allen Pope, a research associate at the National Snow and Ice Data Center and the Polar Science Center. He studies the Earth's frozen regions with satellite and airborne data, does fieldwork to make sure the satellites have it right, and shares his science with other people. He tweets @PopePolar.

This is the fourth in a series of articles by the Institute's Fellows, each covering an area of interest that relates directly both to their own work and the wider issue of software's role in research.

I love being outdoors. There is just something so viscerally engaging about exploring and studying the environment you’re standing in – all the better if it is a remote, snowy, beautiful location. But I spend significantly more time working at a computer than in the field, and I’m pretty happy about it, too. Why, though, if it was fieldwork which started me out?

I’m…

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Airplane by Tracy Hunter.By Robin Wilson, Geography and Environment & Institute for Complex Systems Simulation, University of Southampton.

This is the third in a series of articles by the Institute's Fellows, each covering an area of interest that relates directly both to their own work and the wider issue of software's role in research.

1. What is remote sensing?

Remote sensing broadly refers to the acquisition of information about an object remotely (that is, with no physical contact). The academic field of remote sensing, however, is generally focused on acquiring information about the Earth (or other planetary bodies) using measurements of electromagnetic radiation taken from airborne or satellite sensors. These measurements are usually acquired in the form of large images, often containing measurements in a number of different parts of the electromagnetic spectrum (for example, in the blue, green, red and near-infrared), known as wavebands. These images can be processed to generate…

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Snow Flake by Dave Dugdale.By Melody Sandells, Research Fellow, Environmental Systems Science Centre, University of Reading.

This is the second in a series of articles by the Institute's Fellows, each covering an area of interest that relates directly both to their own work and the wider issue of software's role in research.

My research is about the physics of snow, and how to retrieve snow information from satellite data. Things have moved on a lot since I was an undergraduate where the concept of email was new to the masses, the introduction of the web blew our minds and Windows 3.11 on a 486 was amazing. In the old days, you would read a paper and if it was of sufficient interest, you would go away and code it for your own purposes - in my case it was state-of-the-art Fortran90. Things aren't like that anymore - why recode stuff that has already been done previously for the paper? Yet, for me, the urge to recode just won't go away.

My first foray into snow modelling…

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By Toni Collis, Director - Women in HPC.

"What is a good (or bad) percentage of female users of a scientific computing facility?"

In this article, originally published to accompany a talk given at the recent public opening of Grace, UCL's new computing facility, Toni Collis uses this question to look at the diversity of the community in general, focussing on the High Performance Computing (HPC) community that represents the large-scale use of scientific computing. By looking at other studies, including analysing data collected by the Institute about research software use and development in the UK, Toni calls out the things we still need to be aware of if we are to continue to honour the work of pioneering computer scientist Grace Hopper, inventor of the first compiler for a computer programming language.  

Toni Collis is Director of Women in HPC, and works with the Institute's Policy team as a collaborator on…

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By Shoaib Sufi, Community Lead, Software Sustainability Institute.

The Institute’s Collaborations Workshop 2016 (CW16) took place from 21-23 March 2016 at the Royal College of Surgeons of Edinburgh. The opening slide set the scene displaying a weighted representation of which software the people attending used in their daily work. Shoaib Sufi’s welcome to attendees was followed by an introduction from the Institute Director, Neil Chue Hong. Neil spoke about the work of the Institute and how to get the most out of a Collaborations Workshop (CW). The clue was very much in the name, the main idea was to meet people, people you may not have met before, thus widening your network of potential collaborators. With over 80 attending it made for a real opportunity to learn and share. We cover how the workshop unfolded below.

Lightning talks

We moved quickly onto lightning talks; these gave attendees 2 minutes to talk about aspects of their work and how this related to the theme and sub-themes of the workshop: Software & Credit, Reproducible Research, Collaborative working, code/data sharing and data science. We had almost…

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By Aleksandra Pawlik, Training Leader

Last week the Institute in collaboration with the North West UniversityCape Town University and Talarify helped run the first face-to-face Software and Data Carpentry Instructor Training. 23 new instructors from South Africa, Namibia, Zimbabwe and Kenya attended the event. After the workshop the Institute's work was also presented at the Association of South African University Directors of Information Technology (ASAUDIT) Autumn General Institutional Meeting. 

The Instructor Training started off on Sunday, 17th April in the evening with a short ice-breaking session of lightning talks during which the participants talked about "The coolest thing about their job" for 2 minutes. The experience in chairing similar sessions during the Institute's Collaborations Workshop turned out to be invaluable!

On Monday we introduced the participants to the Mozilla Science Lab Study Groups. The goal of this session was to create foundations for collaborative, peer-to-peer environments in which researchers can share their knowledge and skills.  After lunch we moved on to the Instructor Training curriculum. All participants were very engaged during the group exercises and were eager to discuss effective approaches to teaching and the practical applications of educational psychology theories. One of the most…

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