Software and research: the Institute's Blog

Google Glass in the operating theatre

By Shafi Ahmed, Colorectal Cancer Lead at Barts Health NHS Trust and Associate Dean at Queen Mary University of London.

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

Over the last few centuries, surgery has traditionally been taught as an apprenticeship with students clamouring around the operating table to glimpse a view of both surgical technique and clinical anatomy.

Not much as changed over this time, even now, medical students will be crowded in the operating theatre, sometimes stuck in the background and waiting for many hours to get a glimpse of theory being put into practice.

Thanks to the introduction of video imaging systems such as the laparoscope - as used in keyhole surgery - we have begun to visualise surgery in a much clearer and more accessible fashion for a larger number of students, and so this has become the benchmark for training in modern abdominal surgery.

First steps towards understanding the size of the research software community

By Simon Hettrick, Deputy Director.

In an earlier post, I discussed our plans for investigating the number of researchers who rely on software. We’ve spent the last month looking at the feasibility of some of our ideas. In this post, I’ll present our findings about one of these approaches and some of the problems that we’ve encountered. If you’ve ever wondered what happens when a clueless physicist starts to dabble in social science, then this is the post for you.

First of all, a quick recap. Anecdotally, it seems that the number of researchers who rely on software for their research is – pretty much – everyone. There are few researchers who don’t use software in some way, even when we discount things like word processing and other non-result-generating software. But without a study, we lack the evidence to make this case convincingly. And it’s not just about the size of the community, it’s also about demographics. Seemingly simply questions are unanswerable without knowing the make up of the research software community. How much EPSRC funding is spent on researchers who rely on software? Is that greater, proportionally speaking, than the AHRC?

The Reproducible Research Vibe from the Fellows 2014 summer meeting

Nine of this year’s Fellows met in sunny Southampton on June 23rd-24th 2014 to discuss various aspects of reproducible research and how it would shape future engagement with their research domains.

From the discussions that took place over the following two days, it became clear that the UK research community is focussing on Open Access, Open Science and Open Data, and that the time is ripe to build on these endeavours and promote the necessity and benefits of reproducible, computationally derived results. 

To do this, the Fellows agreed that targeting researchers who were unaware of reproducible research should be a priority for the Institute. This, of course, will require simple and convincing messages about the benefits and need of reproducibility for often time pressed but influential people such as Principal Investigators.

An open-source software package for single-molecule fluorescence: PyFRET

By Rebecca Murphy, a PhD student working for David Klenerman and Sophie Jackson at the Department of Chemistry, University of Cambridge.

Poor documentation, bugs, errors and spaghetti code: the problems in scientific software development are well known. My research field, single-molecule fluorescence (smFRET), faces an additional challenge: a complete lack of any standard software for data analysis. Each research group maintains their own code-base, with software written in programming languages from C++ to Labview.

Whenever methodological improvements are published, we scramble to implement our own versions, based on sketchy outlines crammed into the supplementary methods of high-profile papers. Without access to source code, it is hard to verify that published analyses perform as reported, or that our own attempted reimplementations behave as they should.

In the know about MICROSNOW

There's no business like snow business.By Dr Melody Sandells, Senior Research Fellow, Department of Meteorology, University of Reading.

Snow is cold, beautiful and incredibly important. More than a billion people need it for their water supply, and it also impacts lives elsewhere through its effect on weather patterns, transport. Its key recognisable feature – that it’s white - governs how much of the sun’s energy is absorbed by our planet.

So a pertinent question is how much has the snow cover changed with the changing climate, or if it has changed at all? We don’t yet know how much snow we have, let alone whether it has changed in volume, but we do have the potential to know.

Measurements of naturally emitted radiation at microwave frequencies have been made since the 70s. Scattering of this radiation depends on how much snow is on the ground, so a reduced signal means more snow. However, it is also sensitive to the size of the snow crystals - the small-scale structure of snow - and we are working towards an understanding of how to incorporate the physics of snow into our microwave models to make better satellite measurements of snow mass. Once we have all this figured out, we can apply the technique to the long-term dataset and see whether the snow distribution has changed.

Software Carpentry bootcamp in Pisa

By Aleksandra Pawlik, Training Leader.

This month, Software Carpentry didn’t quite support the leaning tower of Pisa, but it did the next best thing by helping students at the University of Pisa’s Istituto Nazionale di Fisica Nucleare become better coders. Running a bootcamp early June in Tuscany does have its perks. The memories of gelati and focaccine di ceci are still vivid. How could you not love being a Software Carpentry instructor?

The bootcamp kicked off with an introductory session and a lecture titled "Track trigger and applications beside particle physics." Then, in the afternoon, the students could review their computer settings with the instructors. This work, which took place before the bootcamp began helped make sure that everyone had the correct software installed, which saved us a lot of time over the next two days.

The Pisa bootcamp was not restricted to University of Pisa students, there were many others including one attendee who came all the way from Turin. Regardless of where they came from, all our participants had a good grasp of programming concepts and many had coded in more than one language.

International Women's Day and Engineering - A Great Mix!

By Devasena Inupakutika, Software Consultant.

This article is one of the articles in our series Women in Software, in which we hear perspectives on a range of issues related to women who study and work with computers and software.

“Using technology is cool, but I found out today that making it is simply awesome”  - these were the words of a 10 year old girl after she took part in the International Women's Day Robotics workshop, and followed a day of experimentation, learning and fun.

The event took place on March 7th at the University of Southampton’s School of Electronics and Computer Science, and was organised by Dr Reena Pau as part of our celebrations for International Women’s Day. The event was attended by 70 girls and young women from five schools, namely Park High (London), Testwood School (Southampton), St-Edmonds (Salisbury), ALNS (Portsmouth) and Sturnminster (Dorset).

The day started with welcome talks by Professor Michael Butler, and also Professor Dame Wendy Hall, who shared her experiences as a woman working in the computing field. Michael’s talk echoed Professor Karen Spark Jones’ maxim that “technology is too important to be left to men”.

Collaborations Workshop 2014 - outcomes and analysis

This year’s Collaborations Workshop was a great success, with a rich variety of outcomes and a great many things discussed around software in research and, in particular, reproducible research. 

CW14 took place at the Oxford e-Research Centre in March, with three days of events including talks, workshops, discussion sessions and keynotes from Institute co-investigator Carole Goble, Microsoft’s Kenji Takeda and Github’s Arfon Smith.

The final day was dedicated to a special CW Hackday where competing teams tried to develop their own software in a short space of time, and ended with prizes being given to the best coders.

#AskRobotics – the future of robots and us

By Dr Matthew Howard, Lecturer in Informatics at King’s College, London

Will the rise of machines threaten the human race? Are they truly capable of emotional intelligence? Will they put us all out of work? And more importantly, can they do the washing up?

Much of the public perception about robots is driven by Hollywood movies and alarmist or poorly informed media claims. People fear robots because they are portrayed with super-human capabilities, or because they worry about losing their jobs. Yet real robots are not like that. Robots are far less capable than humans or indeed many animals or insects, except when it comes to highly specialised tasks, and even then, there is always a human holding a big red emergency stop button.

Cloud computing resources available to help tackle climate change

By Kenji Takeda, Microsoft Research

The effects of climate change are moving from the realm of simulation to stark reality, with the most recent research showing how drier summers may also lead to more flash floods in the UK.

Understanding, managing and mitigating these effects is a critical endeavour for the global research community.

To support this effort, Microsoft Research is offering 40 Azure Awards, each with 180,000 core hours of cloud compute and 20 terabytes of cloud storage to help climate researchers.