Gillian Law

LUX_watertank-1024x587.jpgBy Gillian Law, technology writer

The LUX-ZEPLIN project is building the largest and most sensitive dark matter detector of its type ever constructed. The detector will be built a mile underground in the Sanford Underground Research Facility (SURF) in Lead, South Dakota and is due to go live in 2020.

Potential detector materials are currently being screened prior to their use in the experiment, and the results are collated and analysed using a 43-sheet Microsoft Excel spreadsheet. The spreadsheet has worked well to date, allowing researchers to share and view data, but moving to a more versatile and robust database solution will be very useful once the experiment begins, says Dr Alex Lindote, LZ Background Simulations project lead, who is based at Laboratory of Instrumentation and Experimental Particle Physics (LIP)-Coimbra, Portugal.

Lindote set up the spreadsheet in late 2015, bringing in data from a Google spreadsheet that had been set up by researchers to share their data.

“It was getting hard to track who was making changes and what was happening, so I was asked to start taking care of it. I decided to move it to an Excel file that I could control more easily,” Lindote says.

Once it became clear…

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9190581261_7cefddac29_z.jpgBy Gillian Law.

New Research Software Engineer (RSE) fellow Leila Mureşan will be using her microscopy image analysis skills to develop software for biologists, physicists and mathematicians as part of her RSE fellowship.

As a scientific software engineer at the University of Cambridge’s Cambridge Advanced Imaging Centre (CAIC) Mureşan designs and implements software to analyse imaging data. Computational microscopy uses software and computation to get around the limitations of optical systems, she says. Mureşan trained as a computer scientist in Romania, and went on to study the analysis of single molecule microscopy images with application to ultra-sensitive microarrays for her PhD at the Johannes Kepler University in Linz, Austria.  After doing post-doctoral research at the École Normale Supérieure in Paris and the Centre de Génétique Moléculaire at CNRS in Gif-sur-Yvette France she joined CAIC as it launched in 2014.

Mureşan has developed a particular interest in lightsheet microscopy imaging, which allows developmental biology scientists to follow the development of an embryo in a “fast and gentle” way over several days, she says. This process naturally produces an enormous amount of data, which requires software that can handle the analysis. Mureşan also works on super resolution microscopy, which increases resolution by an order of magnitude.

“I like this area a lot. The…

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5148710483_a9c0c77da4_z.jpgBy Gillian Law.

Joanna Leng is a computational scientist and visualisation expert who will focus her Research Software Engineer (RSE) fellowship on bringing research computing to imaging. She believes that some areas of the imaging community are failing to fully pick up on the potential of computing, and Leng hopes to transform the use of technology in the field to accelerate scientific discovery.  

Leng will develop software on campus at the University of Leeds for three new imaging techniques, collaborating with Sven Schroeder for spectral X-ray imaging, Rik Drummond-Brydson for spectral electron microscopy imaging and Michelle Peckham for super-resolution light microscopy, in partnership with Diamond Light Source, SuperSTEM and the SCI Institute in Utah, USA.

With 20 years of experience in imaging, visualisation and High Performance Computing (HPC), Leng brings a broad network of contacts to her fellowship, having been interested in imaging and visualisation since her undergraduate degree in biophysics at the University of Leeds. After university, she retrained in computer science, looking for a better paid career, only to “realise at the last minute that I couldn’t face working for one of the banks!” That moment of clarity “brought her to her senses”, and she moved to work in visualisation at the University of Manchester at the Computer Graphics Unit that shortly afterwards hosted an academic…

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8897696003_c549d5e58e_z.jpgBy Gillian Law.

Physicist and new RSE fellow Phil Hasnip specialises in software to predict materials properties, and in making that software accessible to all researchers.

Hasnip believes that most physics problems end up being materials problems. “You want a better battery? You need a better battery material. A better turbine? You need a stronger material for the blades. Wherever you look, materials are key.” says Hasnip. Running experiments on these potential new materials is expensive and difficult, so using computational methods to either predict what a material might do, or to explain what is going in on experiments, is incredibly useful.

Having completed his PhD at the University of Cambridge followed by several post doc positions, Hasnip is now at the University of York where he is developing tools including the CASTEP program which uses quantum mechanics to compute the properties of materials and chemicals.

There is a constant tension in research between taking the time to improve the tools used and getting research results, Hasnip says, and he hopes to use his fellowship as an opportunity to focus on improving the tools available and making them more accessible to all researchers, rather than just those with computational skills. “Many of the tools being used aren’t really high enough quality. They’ve been developed by researchers who are good scientists…

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8523276256_b32bcc2df2_z.jpgBy Gillian Law

Research software ought to be easier to use, says newly appointed 2018 RSE Fellow Jeremy Cohen.

A computer scientist by background, Cohen has spent the bulk of his career to date in the Department of Computing at Imperial College London, supporting scientists in their research. “I’ve worked in a lot of domains, offering applied computing research to support scientists in various areas” he says. This has included using high-performance computing platforms and cloud-computing infrastructure.

“Of course, in general scientists tend to have some computing knowledge, but they often have very much a domain-focused view,” Cohen says. He aims to make their codes easier to access and use. Even if the scientist could do it themselves, they may end up doing it in a more complicated or inefficient way if they’re learning as they go along, “so I aim to make life simpler and let them focus on the science, not the computing.” Good code can also help scientists to make their modelling and simulation work more accessible to their broader team. “There’s often a lot of post processing needed on a model or simulation and so what I’m trying to do is bridge the gaps, or glue together different processes, and simplify complex things. Again, we’re working with people who are very experienced and they can do this work themselves, but we can help them to do it much more effectively.” That opens up the code to…

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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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By Gillian Law, Tech Literate.

Ashley Towers, Research Software Engineer at the University of Sheffield, explains why and how he won the job title he wanted. Job titles matter. Towers almost didn’t apply for his current job at the University of Sheffield – a job that he loves - because the title was all wrong.

"They advertised for a Computing Officer, and I probably wouldn't have paid any attention if I saw it on a job page, because it sounds like a IT Support, fixing-the-printers role. But I was fortunate in that my sister works for the University, and she sent me the advert."

The University was, in fact, looking for someone to buy or develop software for students in the School of Clinical Dentistry. Four years later, Towers has made the job his own, creating software that is vital to the dentistry students and brings great research possibilities – and has persuaded the School to change his job title to reflect it.

Towers is now a Research Software Engineer – a job title that the Software Sustainability Institute has been promoting since 2012.

"I’d never been a big fan of my job title, and it came up during my annual review. I had heard about the RSE community, and had a feeling it was a much better description of what I do. So I suggested it to my line manager, and he asked me to send him…

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Bits.jpgBy Gillian Law, Tech Literate, re-posted with permission from the _connect blog.

Creating software that actually does what the user needs it to do is a perennial challenge. There were some weary sighs of recognition from industry veterans in the recent Technology Strategy Board Multi-disciplinary Software Construction Workshop, as they recognised a topic that has been discussed for decades, but still needs to be addressed in the commercial sphere.

“We’ve been looking at this for 20 years,” said Professor Robin Williams, Director of the Institute for the Study of Science, Technology and Innovation at the University of Edinburgh.

“Edinburgh is actually very good at cross disciplinary work, and we aim for collaboration with social sciences, with business studies, with medicine – there are some difficult issues here, and they demand serious academic consideration.”

But however good the work at Edinburgh may have been, the need for better cross-pollination remains, he says. Today’s developers are tackling the same issues, often seemingly unaware of what has gone before.
The event, run by the Technology Strategy Board and sponsored by the ICT Knowledge Transfer Network, brought together academics, managers of small businesses, software developers and other interested parties to talk about how well-rounded…

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