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Software and research: the Institute's Blog

Latest version published on 6 October, 2016.

Fireworks.jpgToday, we start publishing blog posts from our new Agents. First up is Philippe Aeberhard, who takes a look at how software is helping investigate experiments that are difficult, dangerous and expensive to perform in the laboratory.

Fire, smoke and spectacular effects make up much of the fascination that led many chemistry students to their discipline. But it is these same aspects that can make everyday life for the (grown-up) chemical sciences researcher more difficult: considerations for workers' health and safety make experiments under harsh conditions cumbersome to carry out. Experiments involving very high pressure as encountered in geochemistry, or extremely high temperatures to which nuclear fusion materials are exposed, usually require expensive equipment. A research laboratory for conducting explosives research, for example, requires a sophisticated setup to prevent unwanted explosions and to protect workers. Similarly, the equipment for investigating the properties of materials under extremely high pressures like those found in the inner core of earth - more than 3,000 times higher than at the deepest point of the Oceans - presents a substantial cost.

Chemists focusing on materials and compounds under extreme conditions need not despair: a good part of the work can safely be conducted on a computer. In 2001, researchers concluded from atomic simulations that if titanium oxide, a very abundantly used semiconductor, is put under high…

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Latest version published on 30 September, 2016.

Security in complex systems is always a tricky business. Consider production Grid infrastructures as an example. The intricacies of establishing working trust relationships between the users and the infrastructure, and between the systems themselves, is a mammoth task. Solving problems with such systems is also very tricky, as I’ve previously found when developing EU-wide Grid interoperability demonstrators of open standards. They appear like dragons: huge, daunting, and difficult to defeat.

The UK National Grid Service asked Steve (well, the Institute really) to help them out with their SARoNGS system. Our arrangement was very effective. The Software Sustainability Institute provided development effort for the investigation, whilst the NGS fixed issues and offered the in-depth systems knowledge that only they could provide.

So what is SARoNGS all about? The Shibboleth Access to Resources on the NGS service greatly…

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Latest version published on 6 October, 2016.

wtfm.jpgIn the OGSA-DAI blog, Adrian Mouat wrote a blog post about code quality - illustrated by a rather accurate diagram from OSNews. We've kindly been allowed to repeat the post below.

As part of my work on the OGSA-DAI Visual Workbench project, I needed to evaluate the ADMIRE codebase. This led me to investigate the issue of how to define software code quality and how to assess it. Note that I wasn’t investigating the functional qualities of the code – whether or not it meets the user’s requirements – but how well written is the code itself? If you’ve done any research into this problem, you probably quickly realised that a lot of people have a lot of opinions, but it’s hard to point to a satisfying, objective description of code quality (in contrast to functional quality, which even has standards such as ISO 9126). It seems the most common definition is that shown in the comic strip to the right.

It appears facetious at first, but perhaps hints at a deeper truth: high-quality code should not surprise us; we should be able to quickly and easily discern the structure and intent of the code. But doesn’t this then place software quality in the eyes of the beholder? What if the person evaluating the code isn’t familiar with the patterns used by…

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Latest version published on 6 October, 2016.

UniversityOfGlasgow.jpgSince 2010, the University of Glasgow has been running primer courses to teach researchers simple coding. We asked Bill Wright, who runs the courses, to explain why Glasgow is investing time into teaching researchers about the benefits of, and methods for, coding.

There are few fields of research where IT does not play an important role: from researching prior work, data gathering, communication and presentation to performing sophisticated and complex analysis. Although third-party applications are the best software solution for many projects, a number of researchers find that they need to write, adapt or even commission bespoke code. Rather than performing the core analysis, this home-grown code is often used to test or assess data, to pre-process it for input to applications, or to post-process the output. The saving in time, effort and accuracy is often significant.

Writing bespoke code can be risky, especially if:

  • The amount of coding effort is underestimated
  • There is a lack of awareness about effort-saving programming techniques and facilities
  • Inadequate testing does not identify problems
  • A profusion of versions, patches and fixes resulting in confusion and uncertainty

And it is in countering these risks where some basic training in programming can pay off.

The courses being run at the University of Glasgow help to create awareness of what can be achieved by relatively simple and easy coding. The researchers use Python and are shown development environments, which offer…

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Latest version published on 6 October, 2016.

KneeXRay.jpgThere are over 300 different types of surgery for replacing knee joints, and each one of these procedures must be rigorously trialed to ensure that it meets health regulations. The VRIC team, with some help from the Software Sustainability Institute, has created software to help simplify the notoriously complex clinical-trial process, by integrating the processes and the information systems used in the trials (it's not exactly brain surgery...).

Orthopaedic research facilities support a hugely complex infrastructure that is needed to run clinical trials. To make matters worse, the infrastructure must also be shared by the partners involved in the trial: the medical research council and the National Health Service. It falls to the research facility to ensure that the right infrastructure is being used in the right way by the right partners - and that is a significant challenge.

The VRIC team, led by Dr Gary Wills at the University of Southampton, worked to improve software that was in use at the UCL Royal National Orthopaedic Hospital. This led to the creation of MyVric: software which helped clinicians to share results in a way that complied with the structure of the clinical trial.

Dr Wills knew that the MyVric software would be useful to other health organisations around the world. But before he distributed it, Dr Wills knew that an independent assessment of…

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