Open Call

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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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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Cuneiform tabletWe are working with the RTI-VIPS project to simplify the deployment process for their Reflectance Transformation Imaging software, packaging these complex components into an installer designed for use by researchers in the humanities. This will help to overcome a key deployment barrier faced by the software's users, including researchers from the British Museum and the Louvre.

The RTI-VIPS programme serves to provide solutions that employ Reflectance Transformation Imaging techniques to capture the reflectance properties of a given surface. Multiple captures are taken with varying light sources to construct an interactive relit record of the material sampled. Cultural heritage examples of the technology include work on cuneiform tablets, numismatic archives, manuscripts, rock art and lithic artifacts.

Simplicity!

The RTI-VIPS software is comprised of a number of software packages that handle the acquisition and viewing of images, the calculation of reflectance properties, and camera management and calibration.

The software developers, based within the Web and Internet Science Research Group at the University of Southampton, want to investigate more convenient methods to deploy the software components required to operate the system. Currently the installation process is manual and comprises numerous steps…

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CloudsBy Mike Jackson, Software Architect.

We're helping EPCC and the Met Office promote the uptake, and ongoing development, of the Met Office NERC cloud (MONC) model within the atmospheric sciences community. We're assessing how easy it is to deploy MONC, helping set up a MONC virtual machine and advising on setting up resources for engaging with and supporting researchers.

At the Met Office weather and climate are predicted using numerical models, in particular, the Unified Model (UM). The UM is run on super-computers to produce high spatial resolution forecasts (1 km) for the UK. The details of forecasts are valuable for many public institutions and companies.

A vital tool for the development and testing of the UM is the Met Office Large Eddy simulation model (LEM). The LEM is used to simulate atmospheric phenomena, such as fog, clouds and deep convection at very high resolutions (10 to 100 s metres). The LEM was first developed in the early 90s and parallelised in the mid-1990s. While it can be argued that science undertaken with the LEM underpins many of the atmospheric parameterisations in the UM, the LEM can no longer capitalise on supercomputer enhancements, as the code structure and…

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Clouds We're helping EPCC and the Met Office promote the uptake, and ongoing development, of the Met Office NERC cloud (MONC) model within the atmospheric sciences community. We're assessing how easy it is to deploy MONC, helping set up a MONC virtual machine and advising on setting up resources for engaging with and supporting researchers.

Modelling clouds for weather forecasting

The UK Met Office uses software to create its weather forecasts. This software simulates the behaviour of weather using complex mathematical models. These models can use information about past weather to forecast future weather. The Met Office's best known weather model is the Unified Model (UM), which generates national and international forecasts down to a scale of 1 kilometre. The Met Office also has a number of other models that concentrate on specific aspects of weather. One of these is the Large Eddy Simulation model (LEM) which models clouds, atmospheric flows and turbulence.

The LEM has been developed over the past 30 years. But, it is now showing its age and LEM's performance does not significantly improve if run on more than 512 processes whereas many modern super-computers have tens of thousands of processors. A consequence of this limitation is that the UK atmospheric sciences community relies on…

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The Institute's Open Call provides the opportunity for UK researchers to gain software development expertise and effort - for free.

The latest round of the Call has just opened, and we invite research projects from any discipline who would like help with the development of their software to make a submission, and are particularly keen to attract applications from BBSRC and ESRC funding areas. The deadline for submissions is April 29th 2016.

For more information on the Open Call and to submit an application, please visit the Open Call page. You can also find out more about our current and past projects.

By Paul Graham, EPCC and Software Sustainability Institute.

We've been working with Professor Paul Burton and Dr Becca Wilson of the School of Social and Community Medicine, University of Bristol and their software DataSHIELD (Data Aggregation Through Anonymous Summary-statistics from Harmonized Individual levEL Databases). This is a suite of software that enables remote and non-disclosive analysis of sensitive research data. Data providers can use it to make their datasets available for use in analysis without disclosing individual level data itself, and researchers can thus gain access to the data without risk of disclosing participants. DataSHIELD is used principally in the biomedical field, but the technology used has universal application wherever sensitive individual level data needs to be protected, but also usefully analysed.

DataSHIELD provides a novel technological solution that can circumvent some of the most basic challenges in facilitating the access of researchers and other healthcare professionals to analysis of individual level data. There are a number of challenges to be overcome. Individual-level data is not allowed to be released. Many of the datasets are considered as intellectual property and this means they can be made available for analysis but cannot be physically shared with other organisations. Finally, the quantity of data can be problematic. Many of the datasets are image-based or involve genomic data (potentially millions of variables…

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Boxes with TEST printed on them

By Mike Jackson, Software Architect.

In August I completed an open call project with Trung Dong Huynh, Luc Moreau and Danius Michaelides of Electronics and Computer Science at the University of Southampton. As part of their research into provenance, they have developed the Southampton Provenance Tool Suite, a suite of software, libraries and services to capture, store and visualise provenance compliant with the World Wide Web Consortium (W3C) PROV standards. I developed a test framework in Python, which tests Provenance Tool Suite toolkits and services operating collectively. Dong, Luc and Danius contacted me with their experiences on using the test framework to date...

The Provenance Research Team had populated a small repository of five test cases (sets of semantically-equivalent PROV documents) I had created, with over 470 more test cases. From these, the test framework is now used to create and run over 7,500 individual tests. The team had used the framework's extensibility points, and…

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By Steve Crouch, Research Software Group lead

With Autumn just around the corner, September has seen some exciting activities within the Institute’s Research Software Group. We’re helping improve the testing of Grid accounting software used by the Large Hadron Collider, we’re assessing the sustainability of a web service that supports greater fitness, and we’ve had a record number of applications into the recently closed Open Call!

The Open Call

The sixth and latest round of the Institute’s Open Call closed at the end of September, and despite the usual slow summer months we received a total of 23 applications this time - a new record! We’re reviewing these applications now, and we’ll be letting applicants know the result of this review by the end of October.

So if you didn’t manage to get an application in this time, the good news is that another next round of the Open Call is planned to open in January 2016. We’ll keep you updated with details!

Integration testing Grid accounting software

We’re often asked how to improve the testing of software, and we’re working with the Research Infrastructure Group, based at Daresbury Laboratory and Rutherford…

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The Institute's Open Call provides the opportunity for UK researchers to gain software development expertise and effort - for free. The submissions deadline for this round of the Open Call is next week, Wednesday, 30 September 2015.

We invite research projects from any discipline who would like help with the development of their software to make a submission. For more information on the Open Call and to submit an application, please visit the Open Call page. You can also find out more about our current and past projects.

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