Breaking Software Barriers

key-concepts.pngBy Selina Aragon, Communications Officer, in conversation with Trung Dong Huynh, University of Southampton

This article is part of our series: Breaking Software Barriers, in which we investigate how our Research Software Group has helped projects improve their research software. If you would like help with your software, get in touch.

From concept to software

Provenance is traditionally the record of ownership of a work of art or an antique, used as a guide to authenticity or quality. Although mostly used to track the origins of a work of art, the term is now used in an array of fields ranging from palaeontology to science. It refers to having knowledge of all the steps involved in producing a scientific result, such as a figure, from experiment design through acquisition of raw data, and all the subsequent steps of data selection, analysis and visualisation. Such information is necessary for reproduction of a given result, and can serve to establish precedence. This concept also applies to the digital world; that is, data also originates from a particular point, and provenance provides evidence of its point of origin or discovery by establishing its ownership, custody, and transformations.

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By Steve Crouch, Research Software Group Leader, talking with Matt Gerring, Senior Software Developer at Diamond Light Source and Mark Basham, Software Sustainability Institute Fellow and Senior Software Scientist at Diamond Light Source.

This article is part of our series: Breaking Software Barriers, in which we investigate how our Research Software Group has helped projects improve their research software. If you would like help with your software, let us know.

Building a vibrant user and developer community around research software is often a challenge. But managing a large, successful community collaboration that is looking to grow presents its own challenges. The DAWN software supports a community of scientists who analyse and visualise experimental data from the Diamond Light Source. An assessment by the Institute has helped the team to not only attract new users and developers, but also increase DAWN’s standing within the Eclipse community.

The Diamond Light Source is the UK’s national synchrotron facility based at the Harwell Campus in Oxfordshire. By speeding up electrons to near light speed, they give off light that is 10 billion times brighter than the sun. Over 3000 scientists have used this light to study all kinds of matter, including new medicines and disease treatments, structural stresses in aircraft components, and fragments of ancient paintings, to name but a few.

Supporting and developing software for such a diverse community presents a number of challenges. The DAWN team already…

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By Alexander Hay, Policy & Communications Consultant, talking with Eric Rexstad, University of St. Andrews.

This article is part of our series: Breaking Software Barriers, in which we investigate how our Research Software Group has helped projects improve their research software. If you would like help with your software, let us know.

Abundance is a good thing not just for animals, but also for the researchers studying them. This study is, however, harder than it sounds, which is why it is an area of particular interest for Eric Rexstad, research fellow at the University of St. Andrews' Centre for Research into Ecological and Environmental Modelling

The exact term for this is Distance Sampling, where population numbers of a particular species in a certain area are estimated. For example, "how many harbour porpoises live in the North Sea?" as Eric puts it. Yet this leads onto more complex questions - in particular, how do animal populations react to perturbations or changes in the local environment, such as those caused by pollution or development?

Distance gets distant

One attempt to gauge this more complex picture is…

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By Alexander Hay, the Institute’s Policy & Communications Consultant, talking with Andreas Hegar, CGAT.

This article is part of our series: Breaking Software Barriers, in which Alexander Hay investigates how our Research Software Group has helped projects improve their research software. If you would like help with your software, let us know.

Life Sciences often suffer from a lack of programming skills. This isn’t always a problem – you don’t need to know how to code in order to gauge the diurnal eating habits of squirrels, for example – but it does become an issue when you need to work with large datasets.

This is a growing problem. Next Generation sequencing techniques produce vastly more data than ever before, and more people are needed to properly handle this and analyse it. Many life scientists do not need these skills, or at least, have not needed them until recently. The most sensible solution to this, then, is to train biologists these skills.

Enter CGAT

One solution to this problem is Computational Genomics: Analysis and Training, or CGAT, based at the MRC Functional Genomics Unit at the University of Oxford. This is run by a core staff of five, which includes Technical Director Dr Andreas Hegar, and was founded as a…

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By Gillian Law, TechLiterate, talking with Lee Margetts, University of Manchester.

This article is part of our series: Breaking Software Barriers, in which Gillian Law investigates how our Research Software Group has helped projects improve their research software. If you would like help with your software, let us know.

Software development for research into solid mechanics, particularly in High Performance Computing, has fallen behind other research areas such as fluid dynamics and chemistry, argues Lee Margetts, head of Synthetic Environments and Systems Simulation at the University of Manchester Aerospace Research Institute. It's time for some collaborative development to create some quality, shared code, he says.

"There's a lot of duplication of effort, and I think the field is held back by that. If you look at fields like computational chemistry, people are winning Nobel prizes! Lots of scientific disciplines where people share software are advancing better than solid mechanics, in my view."

In part, he admits this is due to differences in funding, as both computational chemistry and computational fluid dynamics have received funding…

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Shoot that poison arrow to my hearrrrr-rrrrt...By Gillian Law, TechLiterate, talking with Prashant Valluri, University of Edinburgh.

This article is part of our series: Breaking Software Barriers, in which Gillian Law investigates how our Research Software Group has helped projects improve their research software. If you would like help with your software, let us know.

There's a difference between writing code and writing good code, says Prashant Valluri, Lecturer at the University of Edinburgh's Institute for Materials and Processes, laughing as he describes how much he learned while working with the Software Sustainability Institute.

Valluri's team has developed code called TPLS (Two-Phase Level Set), for mathematically modelling complex fluid flows. The code aims to provide much more effective computational fluid dynamics (CFD) analysis for academia and industry, by providing efficient multi-phase models, better numerical resolution and efficient parallelisation.

TPLS uses an ultra-high resolution 3D Direct Numerical Simulation approach combined with the Level-Set method for tracking the developing interface between phases. It employs a 2D Message Passing Interface (MPI) process decomposition coupled with a hybrid OpenMP parallelisation scheme to allow scaling to thousands of CPU cores.

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By Gillian Law, TechLiterate, talking with Michael Chappell, University of Oxford.

This article is part of our series: Breaking Software Barriers, in which Gillian Law investigates how our Research Software Group has helped projects improve their research software. If you would like help with your software, let us know.

Sometimes you just have to recognise that you can’t do everything, acknowledge that someone else has more experience and skills than you do, and accept their help.

That’s what Michael Chappell, Associate Professor in Engineering Science at the University of Oxford’s Institute of Biomedical Engineering did, when he turned to the Software Sustainability Institute for a steer in how to take his software forward.

Professor Chappell had developed an excellent piece of software that did exactly what he set out to make it do: the C++ tool, FABBER, processes functional magnetic resonance imaging (fMRI) to recognise blood flow patterns in the brain and measure brain activity. It works well for the research group that Chappell currently leads, QuBIc, and many other developers in the field are also keen to create their own analysis models to work with it, but that’s where things begin to become problematic for Chappell.

"This bit of…

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Whether it's the people who invented Fortran, the challenges of polar exploration, the need for more women in software or anything you've ever wanted to Ask the Institute, our blog covers everything that's new and innovative about research software.

In addition to one-off posts, we run a number of blog series that investigate a specific concern or address a particular issue.

A day in the software life

Researchers from all disciplines talk about the software they use to make their research possible.

Desert Island Hard Disks

You find yourself stranded on a beautiful desert island. What software would you choose to bring with you and what luxury item would you take to make life easier?

Top tips

A quick introduction to a wide range of subjects related to software and research: everything from using Github to writing a press release.

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