Software and research: the Institute's Blog

By Stephan Lautenschlager, Fellow and PhD Candidate at the University of Bristol

Palaeontology, the study of fossils and extinct organisms, has a reputation for being a very traditional and dusty discipline. Partly influenced by Palaeontologists’ portrayal in the media, the public imagines them roaming the badlands in the search for new fossils. Alternatively, they are seen as ivory tower scientists, spending most of their time in museum collections studying the bones of long extinct animals. Although both images hold a partial truth, palaeontology has experienced a tremendous paradigm shift in the last decade and has evolved into a multi-disciplinary science. Advances in hardware and software, and their wide and comparably inexpensive availability have led to a surge of computational methods to study fossils.

By Alexander Hay.

What is the best open-source software? This is a question I decided to answer, and so began a long and no doubt eventful journey of discovery. One of my first destinations was at an open-source break out session, which took place last month at the Collaborations Workshop 2013. Cue much debate.

It's not possible (and probably not helpful) to decide on the best software overall, so instead I have focussed on open-source software that is exemplary in certain areas. Here follows the first three examples of this software and why we chose them. In future posts, I will work through the other examples on our list.

By Simon Hettrick.

This article about the EGI Community Forum was originally posted on the Gridcast blog.

In his keynote address at the EGI Community Forum, Peter Coveney described the need to combat the fragmentation of e-Infrastructure. Unlike other talks I have seen on this subject, Peter’s focus went beyond the hardware "it’s not just the tin and iron boxes but the software and - most importantly - the people". It is the human capital, the well informed and correctly trained researchers, that we need to make the most of e-Infrastructure.

By Mike Jackson.

After last week's EGI Forum, I returned to The University of Manchester where I led a Software Carpentry boot camp alongside my Institute colleague Aleksandra Pawlik, and David Jones from the Climate Code Foundation. Both Aleksandra and David, who helped out at the Edinburgh boot camp in December, made their instructor debuts.

By Mike Jackson.

At last week's EGI Community Forum, we hosted a day of Software Carpentry boot camp highlights. These were taster sessions drawn from Software Carpentry's highly successful boot camps, which are for researchers who want to learn software development skills to do more in less time, and with less pain.

• Using version control to record provenance and collaborate more easily.
• Using testing to help ensure your software, and results, are correct.
• Data management using a NoSQL database to manage your data more easily.

By Charis Cook, GARNet.

GARNet is the UK Arabidopsis research network. You can be forgiven for not having heard of Arabidopsis thaliana (pictured right) before, as it is a weedy relative of mustard, also known as the humble thale cress.

So why, why, is there a network for A. thaliana researchers? Well, in practice we work with plant scientists of all kinds – but of course there is a reason why we still focus on this one little plant.

By Alexander Hay

Anxiously we have waited, fingers crossed as the total finally reaches the magic mark… nails chewed, coffee drunk – all the while, waiting. And then, the moment of final apotheosis, the ascension we have waited so long for…

Yes, dear friends, we now have 1000 Twitter followers.

By Neil Chue Hong.

One of the biggest challenges for researchers is understanding which software they should choose to reuse or modify for their own work. The diversity and variety of software used in a research environment means that personal recommendations and demonstrations at conferences are often the only way to get a sense of the reusability of the software.

Software reusability is important not just for correctness: it enables improved efficiency and productivity, ability to link related outputs, and a more sustainable research software ecosystem. What is required is a simple way of understanding and assessing the reusability and maintainability of a piece of research software.

By Robin Wilson, Fellow and postgraduate at the University of Southampton. Reposted from Robin's Blog.

This is a first of a number of posts based upon discussions I had while at the Collaborations Workshop 2013 (#CollabW13 on Twitter) in Oxford last week. During one of the sessions I described a simple technique that I try and use to increase the sustainability, reproducibility and releasability of code that I write, data I collect and the results of my work – and people thought this idea was great, and that I should blog about it…

So, what is this wonderful technique?

By Simon Hettrick.

Spam is annoying. That's hardly news, but it's not until you run a website with a commenting system that you realise just how expensive spam can be. We want an accessible commenting system that allows people to get involved with the topics discussed in our blog, but the ceaseless deluge of spam is making it difficult. Things have got to change (and we'd like your help)!

Our old commenting system allowed anyone to comment, but all comments were moderated. This was a source of some contention, because when you're motivated to comment on a blog, you want to see your response instantly. Allowing anyone to comment also means that the spammers can go crazy, and they continue to do so even though all spam comments are deleted and never published. Just like a never-ending lunch party at your grandmother's, the spam just keeps coming.