Steve Crouch

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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Annotate imageBy Devasena Inupakutika and Steve Crouch, Software Sustainability Institute.

The ability to add annotations is recognised as a good practice to enable collaboration around digital content. In a multimedia context, annotations prove to be important for effective search and organisation of document collections. Web-based multimedia annotation tool, Synote (Synchronised Annotation), meets the user need for making multimedia web resources such as podcasts, video lectures, and so on. It is also easier to access, search, manage and exploit through technologies that support creation of synchronised notes, bookmarks, tags, images and text captions.  The Software Sustainability Institute is working with Yunjia Li, Synote developer (Research Fellow), and Mike Wald, Professor at the University of Southampton, to help them overcome the barriers to the commercialisation of their software by investigating their current development processes and infrastructure, and help them develop general practice guidelines for development and deployment, and writing automated web-user interface testing.

These days multimedia is…

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By Devasena Inupakutika and Steve Crouch, Software Sustainability Institute, and Richard Bradshaw, University of Southampton.

As a part of their research, Jonathan Essex’s Research Group developed ProtoMS, a biomolecular simulation software that allows the simple development of methods for the calculation of relative protein/ligand binding free energies. The Software Sustainability Institute worked with them as part of an Open Call project to develop a test strategy and Python test suite, and to verify the operation of the ProtoMS software as an overall product. The great news is that the latest release now includes the test suite and has already found some interesting issues which have been resolved.

A firm and stable unit test suite is crucial for ongoing development in large projects. Writing unit tests adds value to a project while reducing the cost of code changes. With our aim to explore the software for its accessibility and usability and how to adopt a decentralised approach that can reduce strain on further development, we examined each unit of the ProtoMS Python code…

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By Steve Crouch, Research Software Group Lead.

This article was originally published on Jisc's Research Data Spring blog on 30 June 2016.

Sustainability is increasingly becoming recognised as a must-have goal in the development of research software. Earlier this year, I undertook a sustainability assessment of the projects that had reached the second phase of the Jisc's Research Data Spring. It is particularly heartening that Jisc has sustainability high on the agenda across its portfolio of software projects, and that the projects themselves are embracing this ideal with such enthusiasm.

The Institute’s Research Software Group has conducted over 60 consultancy activities with projects producing research software, and a part of that work often involves an assessment of the software's sustainability. Typically, this means taking an in-depth look at the software itself…

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By Vince Knight, Cardiff University, Olivia Wilson, University of Southampton, Shoaib Sufi, Software Sustainability Institute, Steve Crouch, Software Sustainability Institute, and Ian Gent, University of St Andrews.

A speed blog from the Collaborations Workshop 2016 (CW16).

"Congratulations Dr Smith"

The words every PhD student dreams of hearing, at least if your name is Smith. First from your examiners, and then soon afterwards from your supervisor. And then those words every PhD student dreads of hearing from your supervisor…

"Just before you go to your super-rich quant futures job on Wall Street, could you just …

…. hand over your code to my new PhD student please?"

You remember the same conversation three years ago, when you saw your predecessor Dr Jones stammer and make excuses, and promise to send their code to you "in a few weeks after I’ve tidied it up." You suppose technically that 156 weeks might be described as "a few weeks" but certainly you’ve never seen that software. Software that was good enough to get a PhD for Dr Jones, but not good enough to pass on to the next student. All you can say is

"No, I’m sorry Prof Patel, I can’t hand it on,... ".…

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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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By Steve Crouch, Research Software Group Lead.

During August, the Institute’s Research Software Group has helped developers in the areas of reflectance imaging and field theory to improve the usability and sustainability of their research software. We’ve also heard back from a previous project, where our work continues to realise a significant impact. Our Open Call is still open until 30 September - If you are looking for help with your own research software, why not submit an application?

Packaging imaging software for end-users

One of our collaborations is with the RTI-VIPSprogramme, which serves to provide solutions that employ Reflectance Transformation Imaging techniques. We’ve started work to help to improve the sustainability of the software and automate its installation for its end users, which include the British Museum, the Oxford Bodleian Libraryand the…

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By Steve Crouch, Research Software Group lead.

This is the first in a series of blog posts by the Institute's Team Leads to provide an insight into the day-to-day work of the Institute.

The Institute is once again holding its Open Call for Projects, and we're starting to see applications rolling in. So if your project develops research software and you'd like some free expert help, why not consider submitting an application? We work with projects from any discipline, and in the last two months we've helped two groups in the fields of biomolecular simulation and data provenance develop the means to test their software, and had a paper published with one of our projects in the area of biological data visualisation.

The Institute's Research Software Group holds its Open Call about twice a year, and we've just opened the latest round of the call which closes on 30 September 2015. Since 2010, we've worked with over 50 projects to help improve their research software.

Ensuring correctness in scientific codes

We're working with Jonathan Essex's Research Group at Southampton to develop an automated test suite to ensure the correctness of their…

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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 Devasena Inupakutika, Steve Crouch and Richard Bradshaw

Computer simulations are a good way to study molecular interactions. There have been striking advances in the application of computer simulation to innovative complex systems that have shed light on phenomena across the breadth of modern chemistry, biology, physics and drug design. ProtoMS (short for Prototype Molecular Simulation) is one such major piece of Monte Carlo biomolecular simulation software. The Software Sustainability Institute is working with ProtoMS developers to review and evaluate the software and its code, assess the usability, ease of installation and the long-term sustainability of ProtoMS by collating areas for improvement.

Simulating biomolecules is a particularly challenging problem and requires the use of specific computational techniques to perform experiments or study processes that cannot be investigated by any other methodology. The Essex Research Group of the…

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