Reproducible research

Docker Containers & Reproducible ResearchBy Raniere Silva, Community Officer.

Docker Containers for Reproducible Research Workshop (C4RR) is only a month away, 27-28th of June 2017 at the University of Cambridge. This workshop offers many talks on the use of containers applied to improve reproducibility on desktop, cloud and HPC environments and some practical sessions.

For those interested in HPC, some talks will surely make the workshop worth for all our attendees, Michael Bauer's one about Singularity, Matthew Hartley's one about ways to make the transition from the desktop to the HPC smother and Jeroen Schot's one describing how the Dutch National e-Infrastructure is empowering containers.

Meanwhile, the talks from Nick James, David Mawdsley and Matthew Upson are aimed at attendees who are more interested in reproducibility. Nick will talk about an open source data analysis pipeline from the European Bioinformatics Institute that employs containers. If you are an R user and are looking for ways to use Knitr with Docker to make easy for your colleagues to reproduce your R Markdown documents, David's talk is for you. And Matthew will take the attendees through a journey…

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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.

Sponsorship Packages for Docker Containers for Reproducible Research Workshop

 

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Free tickets

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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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Update on 1st April 2017: Submissions are now closed and notifications will be made on 28th April 2017.

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

Submissions are now closed. Accepted talks, lightning talks and demos are listed on the agenda.

Register

If you would like to attend, register here.

Who is attending

See who is attending C4RR.

Venue

Baker Building, Department of Engineering
Trumpington Street
University of Cambridge

Maps and more information are available here.

Accommodation

Please see the C4RR Accommodation page for suggestions of where to stay.

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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.

From the grand problems that push the boundaries of human knowledge, to day-to-day research tasks, software has made an invaluable contribution to advancing research. 

We believe that the full benefits of software in research will only be realised when software is accepted as a valid research output.

We call for all researchers to have access to basic software training to help them harness the power of software for their research.

We say that there must be reward and recognition for Research Software Engineers: the people who contribute to research by developing software.

Finally, we argue that good software practices create better software, and that better software improves the reproducibility and reusability of research.

The Software Sustainability Institute represents the needs of software users and developers in the research community. We lobby for the recognition of the role of software in research, better software education for the research community, recognition of the role of people who develop research software and better engineering of software to provide confidence in the results that software generates.

Recognition of software as a research output

Many researchers invest a considerable amount of time into the development of software for their research, but this time is not rewarded in the same way as time that is invested into writing papers. The metrics used for determining the quality of research must be updated to reflect the role of software in research, and to reward the time invested…

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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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