Software and research: the Institute's Blog

3D archaeology - now low-cost, high-volume and crowd-sourced

By Andrew Bevan, Senior Lecturer, UCL Institute of Archaeology.

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.

Archaeologists have long had a taste for computer-based methods, not least because of their need to organise large datasets of sites and finds, search for statistical patterns and map out the results geographically. Digital technologies have been important in fieldwork for at least two decades and increasingly important for sharing archaeology with a wider public online. However, the last decade of advances in computer vision now means that the future of archaeological recording – from whole landscapes of past human activity to archaeological sites to museum objects – is increasingly digital, 3D and citizen-led.

Structure-from-motion and multi-view stereo constitute a bundle of ‘computer vision’ methods (‘SfM’). They are a form of flexible photogrammetry (the latter being a science with a much older pedigree) in which software is able to automatically identify small features in a digital photograph and then match these across large sets of heavily-overlapping images in order to reconstruct the camera positions from which these photographs were taken.

Automatic performance tuning and reproducibility as a side effect

By Grigori Furisin, President and CTO of international cTuning foundation.

Computer systems' users are always eager to have faster, smaller, cheaper, more reliable and power efficient computer systems either to improve their everyday tasks or to continue innovation in science and technology. However, designing and optimising such systems is becoming excessively time consuming, costly and error prone due to an enormous number of available design and optimisation choices and complex interactions between all software and hardware components. Furthermore, multiple characteristics have to be carefully balanced at the same time including execution time, code size, compilation time, power consumption and reliability using a growing number of incompatible tools and techniques with many ad-hoc, intuition based heuristics.

During the EU FP6 MILEPOST project in 2006-2009, we attempted to solve the above issues by combining empirical performance auto-tuning with machine learning. We wanted to be able to automatically and adaptively explore and model large design and optimisation spaces. This, in turn, could allow us to quickly predict better program optimisations and hardware designs to minimise execution time, power consumption, code size, compilation time and other important characteristics. However, during this project, we faced multiple problems.

A look at FORTRAN unit test frameworks

StrawberriesBy Mike Jackson, Software Architect.

As part of our open call collaboration with TPLS I was to develop a suite of unit tests. TPLS is written in FORTRAN and while there are de-facto standard unit test frameworks for Java (JUnit) or Python (PyUnit), for FORTRAN there are none. In this blog post I look at the test frameworks that are available for FORTRAN, compare two, FRUIT and pFUnit, and explain why I opted to use FRUIT for TPLS.

Venerable beads – tracing the origins of ancient jewellery

By Beatrice Demarchi, Research Fellow at the Department of Archaeology, and Dr Julie Wilson, Lecturer at the Department of Chemistry. University of York.

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.

Interdisciplinary research between fields as diverse as biochemistry, physics and archaeology can help us decipher the most amazing things, for example the choices that our ancestors made thousands of years ago when deciding how to adorn their dead.

People have been using personal ornaments (jewellery) for tens of thousands of years to demonstrate their status in a group or society. If we are lucky, we may find these ornaments in graves or caves and can speculate as to their meaning and provenance. Were these “jewels” made with local raw materials? Or were they traded in exchange for exotic goods? Each of these possibilities tells us something about the environment that people lived in and how they chose to exploit it. However it is often very difficult to identify the raw material when the ornaments are both sculpted and also found in a degraded state.

Smart Glasses – a new vision for the visually impaired

By Dr Stuart Golodetz, Postdoctoral Research Associate at the Nuffield Department of Clinical Neurosciences, University of Oxford, and head of object detection and tracking for the Smart Glasses Project.

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.

People who are visually-impaired face numerous daily challenges, from how to find where to go and the best way to avoid obstacles on the way, to how best to locate, recognise and interact with other people and objects. This can have a significant impact on their independence, confidence and overall quality of life. However, although visual impairments can prevent people from making use of visual signals from the world around them, only a small percentage of visually-impaired people are completely blind in the sense that they receive no useful visual inputs at all.

It is far more common instead for people to retain some level of residual vision, whether that amounts to small regions of their visual field in which they can see, or the more limited ability to distinguish between light and dark. In some cases, the real issue is one of visual signals being drowned out by ‘noise’, and by boosting the signal-to-noise ratio in those regions it is sometimes possible to provide people with at least some ability to perceive what they are looking at.

I'd never been to a programming conference before - I wish I hadn't

By April Wright, Graduate Student, University of Texas at Austin.

This post is reproduced from the original by kind permission of the author. Following the original post, April received a number of messages of support, which can be viewed on Storify.

I went to SciPy this week. I'd never been to a programming conference before, and they featured a lot of education talks.

I wish I hadn't.

Last night, at the Software Carpentry mixer, a grand total of five men shook my husband's hand and ignored mine. My total of new people met is a dismal ten. Compare it to the Evolution meetings, which is my meeting, where I met upwards of forty new people, had a blast, and was treated by all participants like a member of the community.

I was reminded of a question my friend Steve Young asked me a while back: "What makes some women stick it out and be awesome [in tech]?" I'm going to turn the question around a bit. It's easy to be awesome. Lots of women are doing awesome things. But I could have sat in my office and worked all week, rather than attending this meeting. I could have done far more awesome alone, and I wouldn't have had my face rubbed in the fact that I'm different. I'd feel a lot less alone had I spent the week hanging out alone.

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.