Reproducible research

Video and Reproducibility in the Behavioural SciencesBy Joy Lorenzo Kennedy (Scientific Support Specialist), Karen Adolph (Principal Investigator), & Rick O. Gilmore (Principal Investigator)

Behavioural researchers are under fire due to low levels of reproducibility; more than half of the findings from psychological studies cannot be replicated. On the reasonable assumption that both the original researchers and the replication team are competent, why are they getting different results? Inability to replicate findings might be a side effect of the inability to reproduce methods and procedures with sufficient fidelity. In fact, as behavioural research expands beyond its traditional white, middle-class participant base, one of the most notable findings is the extent to which small differences in context create differences in behaviour and development. As such, slight variations in instructions, stimuli, procedures, experimenters, testing room, and so on can lead to different outcomes. No matter how detailed the method section in published works, full explication of a methodology is impossible due to the limitations of text and static images to convey the full richness of the testing situation. This makes it difficult to ensure that researchers can truly…

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Docker Containers & Reproducible ResearchBy Raniere Silva, Community Officer, Software Sustainability Institute.

Last year, during the First Conference of Research Software Engineers, Iain Emsley, Robert Haines and Caroline Jay hit on the idea to organise a meeting about Docker and how researchers are using it. Ten months later, 60 researchers, developers and librarians met in Cambridge for the Docker Containers for Reproducible Research Workshop (C4RR).

The workshop consisted of one sponsored keynote by Microsoft, 20 talks and four lightning talks and participate in one of two demo sessions. There were many success stories involving containers and, when high performance computing (HPC) was involved, the use of  Singularity as a good alternative to Docker.

Introduction

If I had to select one talk from C4RR to summarise the workshop, my choice would be Building moving castles: Scaling our analyses from laptops to supercomputers by Matthew Hartley, et al. With some images from Hayao Miyazaki’s…

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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 brought 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) toke place from 27th to 28th June 2017 at Cambridge.

Who attended

See who attended C4RR.

Venue

Baker Building, Department of Engineering
Trumpington Street
University of Cambridge

Maps and more information are available here.

Sponsors

Find out who has sponsored C4RR.

Agenda

Take a look at what happened at C4RR.

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 research software community to explore and discuss these and other questions at C4RR.

Containers refers to a server virtualisation…

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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.

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