Software and research: the Institute's Blog

Practice of Reproducible ResearchBy Justin Kitzes, University of California, Berkeley

We are very happy to announce the launch of our open, online book The Practice of Reproducible Research, to be published in print by the University of California Press later this year. In short, this book is designed to demonstrate and teach how research in the data-intensive sciences can be made more reproducible. The book centres on a collection of 31 contributed case studies, in which experienced researchers provide examples of how they combined specific tools, ideas, and practices in order to improve the reproducibility of a real-world research project. These case studies are accompanied by a set of synthesis chapters that introduce and summarise best practices for data-intensive reproducible research.

Within the overall context of reproducibility, our book focuses specifically on the goal of achieving computational reproducibility in individual research projects. We defined a research project as computationally reproducible if a second investigator can recreate the final reported results of the project, including key quantitative findings, tables, and figures, given only a set of files and written instructions. This focus reflects our belief that computational reproducibility forms a first and most foundational goal for individual investigators interested in the broad goals of reproducible…

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Participation in distributed open source projectsBy Mario Antonioletti, Software Sustainability Institute, Nikoleta Evdokia Glynatsi, Cardiff University, Lawrence Hudson, Natural History Museum, Cyril Pernet, University of Edinburgh, Thomas Robitaille, Freelance.

Running an open-source project with geographically distributed participants is a substantial undertaking. Attracting and retaining participants can be hard. Communicating project progress via social media, websites and mailing lists can take a lot of time, as does organising and running regular meetings since contributors are typically separated both by geography and time zones. It is important to identify mechanisms for (i) attracting participants (social aspect), (ii)  communications and development processes (which can encompass workflows, standards, conventions, project administration) and (iii) remote collaboration. In this blog post, we summarise some social and technical challenges and…

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Software Sustainability PracticeBy Blair Archibald, University of Glasgow, Gary Leeming, University of Manchester, Andy South, Freelancer, Software Sustainability Institute Fellows

Software plays a key role in a modern research environment with over 92% of academics reporting the use of research software. With such a large impact there is huge variation in the potential audience for the work of the Software Sustainability Institute across different disciplines. In some areas there already exists best practice, but many may find it difficult to understand the value or justification for making the effort to engage with software sustainability. Our mission, as fellows, is to help them.

As fellows, we need to interact with different stakeholders: the individual researchers who use and write software as part of their general practice, groups and disciplines who use software to enable new results to push their field forward, and policy makers who have global influence over the software conditions of funding and practice. We can target each of these stakeholders differently and provide a justification of improved software practice.

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Collaborations Workshop 2017, IoT, Open Data, research softwareBy Shoaib Sufi, Community Lead

If you are a PhD candidate, Jisc are offering a bursary for you to attend CW17— apply now!

Collaborations Workshop 2017 (CW17) is nearly upon us. It takes place from the 27-29th of March 2017 at the Leeds University Business school.

Day one will have you enthralled with knock out keynotes on The Internet of Things (IoT) and Open Data from real experts who have been there and done it. If you want to know more about this area and can only spare a day, you can choose to come along just for the day. Day one also includes a panel on IoT and Open Data with leading experts from industry, academia and publishing. We then have our signature speed blogging session, where you can write a blog collaboratively about a hot discussion topic. We wrap up day one with a mini-workshop session where you get to explore some of the topics raised in more depth. Evening of day one then moves onto a historical tour of the campus, a time to get cultured and connect with other attendees, and then a…

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Open sourceBy Alice Harpole, University of Southampton, Danny Wong, Royal College of Anaesthetists, and Eilis Hannon, University of Exeter, Software Sustainability fellows

There has been a collective push in recent years to make all empirical data open access, and this is often a requirement where it has been funded by taxpayers. One reason for this is to improve the overall quality of research and remove any barriers from replicating, reproducing or building on existing findings with the by-product of promoting a more collaborative style of working. In addition to making the data available, it is important to make it user-friendly by providing clear documentation of what exactly it is and how the data was generated, processed and analysed. There are a number of situations, where the key contribution from the research is not simply the underlying data but the software used to produce the findings or conclusions, for example, where a new methodology is proposed, or where the research is not based on any experimental data but instead on simulations. Openly sharing software is as critical here as sharing the raw data for experimental studies. What’s more, there are likely many projects where both the data and software are equally as important, and while there is an expectation to provide the data, this currently…

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