Research Software Group

Research Software Engineer

James is a Research Software Engineer at the Software Sustainability Institute.  He received an MChem in Chemistry for Drug Discovery from the University of Bath, before joining the Institute for Complex Systems Simulation PhD programme in 2013. He joined the SSI in September of 2017.

During his PhD studies James worked on a number of software projects, including the Monte-Carlo simulation package ProtoMS.  ProtoMS was successful in an SSI Open Call and received assistance in developing a test suite to ensure correctness of the core Fortran component.  His role in this project was in further development of the test suite, both code and infrastructure, and in ensuring the reproducibility of simulation across a range of platforms and compilers.
 

MONC By Selina Aragon, Communications Officer, in conversation with Adrian Hill, Met Office

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.

Adrian Hill, the project’s primary contact, talked to us about the usefulness of the Institute’s collaboration with the Met Office and EPCC to promote the uptake and development of MONC. Adrian especially highlighted the invaluable help he received from Mike Jackson, Research Software Engineer, in setting up the basis for what has progressed into successful software with unexpected benefits and long-term value, used by researchers as well as PhD and masters' students.

Collaborative efforts

In collaboration with EPCC (Edinburgh Parallel Computing Centre) and the Met Office, the Institute provided help to rewrite the Large Eddy simulation model (LEM) as its successor, the Met Office NERC cloud (MONC). MONC is a complete re-engineering of LEM, which preserves LEM's underlying science. MONC has been developed to provide a flexible community model that can exploit modern supercomputers…

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The Research Software Group and the Software Sustainability have organised a Data Carpentry workshop, which will take place on 1st & 2nd August 2017 at the University of Southampton.

The course will cover data organisation in spreadsheets and OpenRefine, SQL for data management, and an introduction to R for data analysis. By the end of the workshop, learners will be able to more effectively analyse and manage their data to aid reproducibilty and  to increase their chances of furthering their research.

For further information and registration, please visit the event page.

Data Carpentry is an international movement to teach researchers better software skills. For more information about Data Carpentry, visit their website.

Constructive Code CritiqueBy Nicolas Gruel, University of Manchester, Andrew Walker, University of Leeds, Vince Knight, Cardiff University, and Mike Jackson, University of Edinburgh.

This post is part of the Collaborations Workshops 2017 speed blogging series.

Code review is accepted as a key process in the creation of maintainable software with a low defect rate. Wilson et al. recommend code reviews as one of their Best Practices for Scientific Computing. The value of code review is beginning to be recognised in the development of research software, for example, in…

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Newcastle University are seeking to recruit a researcher with experience in the development of optimised high performance computing software to join a large multi-disciplinary team of researchers on an ambitious research project. The researcher will be expected to extend and develop a large scale biological simulation model built around LAMMPS. The initial focus for this work will be on parallelising extensions to the LAMMPS codebase which simulate microbial cells using an Individual Based Model. 


This post will be based within the Large Scale Modelling Team of the NUFEB project at Newcastle University. For more information about the project please see the NUFEB website http://research.ncl.ac.uk/nufeb

The closing date for applications is 26 April 2017. Further details can be found at: http://bit.ly/2mZHkBN or contact Steve McGough.

Weather forecastingBy Malcolm Illingworth, Software Consultant, Software Sustainability Institute

The Software Sustainability Institute have been working with the Institute of Climate and Atmospheric Science (ICAS) at the University of Leeds, to help improve the sustainability of their GLOMAP software suite. Kirsty Pringle of ICAS applied for consultancy from the Institute via the Open Call.

One of the biggest challenges in our ability to understand and predict climate change is learning about the role played by tiny particles, such as dust or soot. These aerosol particles are known to influence our climate in complex ways, but how this interaction works is an open area of research.

The Institute of Climate and Atmospheric Science (ICAS) at the University of Leeds  seeks to improve our understanding of how these aerosol particles affect our climate. Their research uses both computer-based climate models and uncertainty analysis to quantify the role that natural aerosols play in climate change. As part of this research, ICAS have developed the GLOMAP model, a flexible…

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Photo of inflatable Santa by Bart FieldsEveryone at the Software Sustainability Institute would like to wish our friends and colleagues all the best for the holiday season.

After a busy year, including the first Conference of Research Software Engineers, the announcement of a wonderful new set of Fellows, and even more eventsSoftware and Data Carpentry workshops, and Open Call projects, we need a little break to get ready for everything we've planned in 2017. So please excuse us while we switch off our email from the 23rd December to the 2nd January, and enjoy the festive season (responsibly)!

View of the 260 tonne water tank that will house the LZ experiment
View of the 260 tonne water tank that will house the LZ
experiment, located 1 mile underground in Davis Cavern of
the Sanford Underground Research Facility, South Dakota.
Credit: Carlos Faham, Berkeley Lab.

By Mike Jackson, Software Sustainability Institute

85% of the mass of the Universe is made up of dark matter. Despite indirect evidence of the existence of dark matter, going all the way back to the early 20th century, there has, so far, been no direct measurement of dark matter interacting with a detector here on Earth. Not yet at least, for the LUX-ZEPLIN (LZ) project are building the largest and most sensitive dark matter detector of its type ever constructed. I will be providing consultancy to LZ’s researchers at University College London on migrating LZ’s data storage and analysis software from Microsoft Excel to a database-centred solution.

The LUX-ZEPLIN project is a consortium of 230 scientists in 37 institutions in the U.S., U.K., Portugal, Russia, and Korea and is joint-funded by the US Department of Energy and the UK Science and Technologies Facilities Council (STFC). LZ are building their dark matter detector a mile underground in the…

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Grassroot mappingBy Karen Anderson, University of Exeter, and David Griffiths, FoAM Kernow

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

Smartphones have emerged as powerful research tools for collecting scientific data because they are equipped with a broad suite of sensors (e.g. cameras, microphones, light sensors, accelerometer, compass, gyroscope, and GPS) and on-board microcomputers and are widely used globally. Many smartphones are designed to service the information requirements of multinational developers—they are location-aware—, and applications downloaded by users can transmit information back to providers. This capability can be exploited through the programmable nature of smartphones: sensors developed to supply  location-based services to providers can now be hacked using readily available computing resources. One such opportunity that remains untapped is the smartphone as a remote sensing imaging device that can be deployed in conjunction with rapidly developing lightweight drone technology.

We undertook a short project to explore the…

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Automated assembly line

By Mike Jackson, Software Sustainability Institute

Continuous integration frameworks build and test our software, so we don't have too (well, we do, but they do it too!) As part of my work on automated testing to boost recipy's confidence, I've had my first experience of AppVeyor, a continuous integration service for Windows, and it was good!

Growing up in Scotland, I endured an oft-repeated peak and trough of emotion when watching BBC television. A new drama or comedy would be trailed by an enthusiastic announcer, anticipation would rise at the forthcoming delights, only to be dashed upon the rocks of the announcer's concluding words "...except for viewers in Scotland". I've noticed a similar trait in the world of research software where phrases such as "...except for Windows" or "...except for Internet Explorer" occur frequently enough to be noticeable, along with their fellow "works on Linux/UNIX", leaving "Windows" unsaid. So, having used Travis CI, a deservedly-popular Linux-based open source continuous integration framework for projects hosted on GitHub, it was refreshing to see that there's a similar service for Windows, AppVeyor.

I'd first used Travis CI when…

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