Software and research: the Institute's Blog

Is software a method?

By Philip Fowler, Software Sustainability Institute Fellow and postdoctoral researcher at the Department of Biochemistry at the University of Oxford.

Last month I attended the 59th annual meeting of the US Biophysical Society. It's the sixth time I've been but the first time I've gone really thinking about how our community treats software under my remit as a Software Sustainability Institute Fellow. I was also chosen as a guest blogger and you can see my posts on my blog or on the Biophysical Society blog.

Wait... what is biophysics?

It is the application of physical methods (and to a lesser extent, theories) to biology, focusing mainly at the molecular level. This includes determining the structure of proteins (and more famously, DNA) by illuminating a protein crystal with X-rays, recording the diffraction pattern and then inferring the complex 3D structure that would be responsible for that pattern. It is a mature discipline: the first conference of the society was in the 1950s and now it attracts over 6,000 scientists every year.

Software Management Plan Service prototype live

Software management plan guide and service

By Mike Jackson, Software Architect.

Software management plans set down goals and processes that ensure software is accessible and reusable throughout a project and beyond. To complement our guide on Writing and using a software management plan we have now developed a prototype software management plan service, powered by the Digital Curation Centre's data management plan service, DMPonline.

Releasing data service software as free open source software

Reflections of the same thing

By Mike Jackson, Software Architect.

Linked data is a way of representing and joining information from a variety of sources to allow it to be accessed, browsed, searched and used as easily as one would browse the web. One of the principles of linked data is that URIs are used to name things whether these be people, places, books, software, magazines, departments, machines and so on.

As anyone can develop their own linked data sets, and propose their own URIs, many URIs may be created for the same thing. sameAs.org is a service offered by Seme4 Limited that allows users to find out which URIs refer to the same thing. sameAs Lite is a refactored, open source, version of the software that powers sameAs.org. We are providing consultancy to Seme4 on how to improve sameAs Lite for deployers and developers and to promote community engagement.

Google Code is shutting down - what should you do next?

By Neil Chue Hong, Director of the Software Sustainability Institute.

Google announced today that their open source project hosting site, Google Code, is to close. The site has disabled the creation of new projects, will turn read-only on 24 August 2015, and will close on 25 January 2016. In the announcement.

Google's Director of Open Source Chris DiBona cited the move of projects away from Google Code to other services such as GitHub and BitBucket - indeed Google itself has moved thousands of its projects to GitHub.

The first thing to stress is: don't panic. Google has provided a long time for you to migrate your project, along with tooling to make the process easier.

What the Flip? Getting girls to code through games

By Kate Howland and Judith Good, Department of Informatics, University of Sussex

This article is part of our series Women in Software, in which we hear perspectives on a range of issues related to women who study and work with computers and software.

With calls for all UK children to learn computer science from a young age, we need teaching methods and tools which can help novice programmers to learn in a way which both motivates and is more accessible for them, and which builds on their existing skills and interests.

The Flip programming language teaches coding by setting a task for users to creae a narrative-based 3D role playing game. An evaluation study suggests that girls match and in some cases exceed boys’ performance with the language, which is encouraging given concerns about the underrepresentation of women in the technology industry.

Collaborations Workshop lives up to its name

By Robin Wilson, Researcher, University of Southampton.

As a Fellow of the Software Sustainability Institute in 2013, I attended the Collaborations Workshop 2013. To be honest, I did so rather reluctantly: I was in a very busy stage of my PhD at the time, and although it was seemed like a reasonable way to spend a few days, I felt that it was unlikely to produce anything of direct benefit to me. I couldn't have been more wrong.

In the first session at that year's workshop I met someone from the IT as a Utility Network+ and showed off a proof of concept instrument that I'd been developing during my PhD (in all honesty, I'd brought it with me so that if the conference was boring I could slip back to my room and test the instrument!). He was fascinated by it, and strongly suggested that we apply for a IT as a Utility Network+ pilot project to get some funding to continue development. We did so, and won £50,000 of funding – which was enough to employ a post-doc for six months and develop a full prototype instrument. The Collaborations Workshop was living up to its name: within an hour of the start of the conference I'd developed a collaboration which led to significant funding!

Making biology compute with CGAT

By Alexander Hay, the Institute’s Policy & Communications Consultant, talking with Andreas Hegar, CGAT.

This article is part of our series: Breaking Software Barriers, in which Alexander Hay investigates how our Research Software Group has helped projects improve their research software. If you would like help with your software, let us know.

Life Sciences often suffer from a lack of programming skills. This isn’t always a problem – you don’t need to know how to code in order to gauge the diurnal eating habits of squirrels, for example – but it does become an issue when you need to work with large datasets.

This is a growing problem. Next Generation sequencing techniques produce vastly more data than ever before, and more people are needed to properly handle this and analyse it. Many life scientists do not need these skills, or at least, have not needed them until recently. The most sensible solution to this, then, is to train biologists these skills.

Array of Python coders aim high at Diamond Hackathon

By Steve Crouch, Research Software Group Leader, and Mark Basham, SSI Fellow and Senior Software Scientist at Diamond Light Source.

January 30th 2015 saw the latest Institute-sponsored Hackathon at Diamond Light Source, bringing together top coding talent from across the STFC Rutherford Appleton Laboratory and beyond.

Participants were able to propose interesting scientific and software development projects related to Python, and work on them in groups. One constraint, however, was that these groups be formed of individuals that don't normally work together, and this led to some surprising results.

Fellows 2015 inaugural meeting

By Shoaib Sufi, Community manager.

Thursday 29 January 2015, on the day a mini blizzard struck Manchester and closed its airport something much more important to software in research was happening in sunny London. The Fellows 2015 Inaugural meeting took place in rooms annexed to the library at Imperial College London. The Fellows were introduced to the Institute, discussed thorny problems related to software and data and helped each other create plans for their Fellowship year.

We kicked off with a brief overview of the Institute with a focus on insights into our strategically important research into understanding the research software community;  understanding how best to engage their communities, and how to benefit from our web and social media presence. There was a lot of interest in running Software Carpentry events and taking part in our Open Call for projects.

Next stop was discussion time. There was a highly informing discussion about the challenges that the Fellows faced in using software in their research domains. A number of themes stood out, such as the difficulty of recruiting and maintaining software engineering effort (highly relevant to our with with Research Software Engineers), getting credit for software outputs; support for sharing data - especially big data, standards for reviewing code and data for journals, and clarifying intellectual property rights in software and data.

How open is your software?

OSS Watch app

By Mike Jackson, Software Architect.

The UK open source service, OSS Watch, have recently published their Openness Rating tool. This tool allows projects to assess their openness and can be applied to both open and closed source software. In this blog post, I'll provide a summary of the Openness Rating tool and how it complements our own online Sustainability Evaluation Service.