Reproducible research

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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For all enquiries about sponsorship, please contact Graeme Smith.

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Docker Containers, Reproducible ResearchSubmit your abstract by 31st March 2017 at midnight.

Presenters are invited to submit abstracts for 15-minute talks (plus 5 minutes for questions) and lightning talks on the following subjects:

  • Examples of use—positive or otherwise and lessons learned
  • Position papers
  • Applications for Reproducible Research
  • Other use cases
  • Building other tools around container ecosystem
  • Comparing different types of containers
  • The future and challenges for adoption, or lack thereof, in specific communities

The Software Sustainability Institute’s Docker Containers for Reproducible Research Workshop (C4RR) will take place on from 27th to 28th June 2017 in Cambridge. C4RR aims to gain insight into the topics of containers technologies and how these impact and will impact on research. It is…

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The Software Sustainability Institute’s Docker Containers for Reproducible Research Workshop brings together researchers, developers and educators to explore best practices when using containers and the future of research software with containers. The Docker Containers for Reproducible Research Workshop (C4RR) will take place from 27th to 28th June 2017 at Cambridge.

We welcome abstracts for 15-minute talks (plus 5 minutes for questions) and lightning talks about containers, including but not limited to Docker and Singularity, on the following subjects:

  • Examples of use—positive or otherwise and lessons learned
  • Position papers
  • Applications for Reproducible Research
  • Other use cases
  • Building other tools around container ecosystem
  • Comparing different types of containers
  • The future and challenges for adoption, or lack thereof, in specific communities

Submit your proposal by 31st March 2017 at midnight.

Notifications will be made on 28th April 2017.

By Raniere Silva, Community Officer.Laptop on the beach.

The first phase of Google Summer of Code 2017 launched on January 19th and by participating as an open source project or mentor you could help make this edition the best one so far. This is an opportunity to have that change to your IDE that you have dreamt of for months, remove the bottleneck in your data analysis pipeline or test a new idea by the end of August.

Google Summer of Code (GSoC) allows projects to download developers! We at the Institute think that it’s a great opportunity for those working with research software to be a part of the wider open source community either by mentoring students (who are paid by Google to work on open source projects during the summer) or by suggesting project ideas. The first phase of the programme is when mentoring organisations can apply to participate in GSoC: the deadline is February 9, 2017 17:00 (GMT). In this phase, mentoring organisations start to collect project ideas and identify mentors; in this post we will list some ways you can contribute to GSoC's.

I want to lead my project / organisation’s application

If you are part of an open source software project, or an organisation…

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Container ship.Twitter: #C4RR

The Software Sustainability Institute’s Docker Containers for Reproducible Research Workshop brings together researchers, developers and educators to explore best practices when using containers, not only Docker, and the future of research software with containers. Docker Containers for Reproducible Research Workshop (C4RR) will take place from 27th to 28th June 2017 at Cambridge.

Call for Papers

We welcome abstracts for 15-minute talks (plus 5 minutes for questions) and lightning talks until 31st March 2017 at midnight. More information here.

Register your interest

Register your interest to attend.

Sponsorship opportunities

Sponsor our workshop and reach out to the research software community including researchers, developers and educators. Take a look at our fantastic sponsorship options.

Containers

Containers, specially Docker and Singularity, is the hottest topics at the moment for reproducible research. What impact does the use of containers have on research, how can researchers benefit from them and make their research more reproducible? The Software Sustainability Institute invites all members of the…

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Container ship.27th – 28th June, Cambridge (provisional date)

Containers, specially Docker, are the hottest topic at the moment for reproducible research. What impact does the use of containers have on research, how can researchers benefit from them and make their research more reproducible? The Software Sustainability Institute invites all members of the research software community to explore and discuss these and other questions at the Docker Containers for Reproducible Research Workshop from 27th to 28th June 2017 (date tbc) at Cambridge.

The Software Sustainability Institute’s Docker Containers for Reproducible Research Workshop will bring together researchers, developers, innovators and educators to explore best practices when using containers and the future of research software with containers. C4RR aims to gain insight into the topics of containers technologies and how these impact and will impact on research. It is also an ideal opportunity to form collaborations.

For further information and register interest, please visit the Docker Containers for Reproducible Research Workshop page.

By Scott Edmunds, Executive Editor at GigaScience.

With greater awareness of the difficulties in making scientific research more reproducible, numerous technical fixes are being suggested to move publishing away from static and often not reproducible papers - which have changed little since the 17th century - to more reproducible digital objects that better fit 21st century technology. New research in the Open Access journal GigaScience demonstrates a potential approach through publishing open data and code in containerised form using Docker, and also allowing scientists to tackle another scourge of the 21st century – climate change, through better understanding of the production of biofuels.

One of the most promising areas in biofuel development is biogas, which has huge potential as a renewable and clean source of energy. Biogas is the production of methane gas through the anaerobic digestion (fermentation) of organic matter such as agricultural or food waste. Detailed knowledge on the functioning of the fermentation process is key for optimising this process. However, the vast majority of the microbes involved remain unknown and cannot be cultivated in laboratories.

In new research just published in GigaScience, researchers from Bielefeld University in Germany have now characterised the complex communities of micro-organisms in a biogas plant that generates heat and power from maize silage and pig manure. The authors made their research more…

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The Center for Open Science have developed the TOP (Transparency and Openness Promotion) Guidelines to promote the transparency and reproducibility of research.

TOP includes eight modular standards, each with three levels of increasing stringency. Journals can select which of the eight transparency standards they wish to adopt for their journal, and select a level of implementation for the selected standards. These features provide flexibility for adoption depending on disciplinary variation, but simultaneously establish community standards.

These guidelines, including around availability of code and data, are very similar to what the Institute has been promoting in our guidance for researchers and software developers. We are therefore delighted to announce that we have become an organizational signatory to the guidelines, and that the Journal of Open Research Software has adopted the TOP Guidelines too.

For more details on the TOP guidelines, please see the Center for Open Science website.

The way in which academic papers are published makes much research unfindable, while scholars’ lack of transparency about their research methods renders many of their conclusions highly questionable.

This is the view of Carole Goble, one of the Institute's Co-Investigators, which she expressed at the Jisc Digital Festival 2015 and subsequently discussed with Chris Parr from Times Higher Education. This led to an excellent article in which Carole discusses her views on researchers' practices that result in the burying of data and research.

You can read the article on the THE website or listen to the interview with Carole on THE podcast.

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