Research Software Group

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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Gaia artist's impresion
Gaia artist's impression. Credits: ESA/ATG MEDIALAB;
Background Image: ESO/S. Brunier, June 2013

By Francesca De Angeli, in collaboration with Marco Riello, Gregory Holland, Patrick Burgess and Paul Osborne.

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.

On 19 December 2013, at 09:12:19 UTC, a spacecraft containing the Gaia satellite was launched from Europe's Spaceport in French Guiana. The Gaia satellite reached its stable operational orbit around L2 (approximately 1.5 million km from the Earth) about one month later. Since then, a continuous stream of data has been downloaded for further processing on ground. This data includes broad-band photometry and low-resolution spectra for all sources brighter than magnitude 20 and high-resolution spectra for sources brighter than magnitude 16.

The Gaia focal-plane assembly is the largest ever developed for a space application, with…

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Instructor TrainingBy Steve Crouch, Software Sustainability Institute, with Karin Lagesen, University of Oslo, and Laurent Gatto, University of Cambridge.

Last month, we held a Software and Data Carpentry Instructor Training workshop at the University of Cambridge, sponsored by the R Consortium. The demand for Carpentry events in the UK, and trained instructors to facilitate them, has always been very high, and I found this to be a very enjoyable event to increase the instructor pool in the UK.

The main organiser of the event was Laurent Gatto, a Software Sustainability Institute Fellow who has delivered numerous Carpentry courses since becoming a certified instructor in 2014. We also had the able helping hands of Paul Judge and Gabriella Rustici from the University of Cambridge Bioinformatics Training facility, who assisted greatly with the event and helped us make great use of the sophisticated presentation systems present in the training room.

The workshop was held on 19th and 20th of September, with myself and Karin Lagesen as instructors. We were delighted with the very high level of engagement from the 25 trainees - this was very much the kind of group we hope…

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Figure 1: Inspect your raw mass spectra and run tools from within the OpenMS visualisation tool TOPPView
Figure 1: Inspect your raw mass spectra and run tools
from within the OpenMS visualisation tool TOPPView

By Timo Sachsenberg and Oliver Kohlbacher, University of Tübingen

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.

High-throughput mass spectrometry has become a versatile technique to tackle a large range of questions in the life sciences. Being able to quantify diverse classes of biomolecules opens the way for improved disease diagnostics, elucidation of molecular structure and investigation of cellular pathways. In an interplay with other open-source software, OpenMS enables powerful workflows to transform biological data into meaningful knowledge.

In recent years, mass spectrometry has gained significant attention in the life sciences. The mass spectrometer determines the…

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Root-knot nematodes affect cropsBy Malcom Illingworth, Research Software Engineer.

The Software Sustainability Institute has been working with the School of Biological, Biomedical and Environmental Sciences at the University Of Hull to help improve the sustainability of their ReproPhylo software suite. The ReproPhylo developers applied for consultancy from the Institute via the Open Call.

Root-knot nematodes are parasitic roundworms whose larvae infect plant roots. These tiny parasites have a devastating impact on agriculture, causing 5% of crops to be lost worldwide each year. The Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, The University of Hull studies the genomes of these root-knot nematodes to understand how they have evolved and continue to evolve, their diversity, and the threat they pose to crops. This research involves applying both large-scale comparative genomics—comparing the genomes of different organisms—and phylogenomics—analysing genome data and evolutionary relationships. As part of their research, the group has developed ReproPhylo, a phylogenomics pipeline written…

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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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