Containers

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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Containers for HPCBy Krishna Kumar, Institute's fellow, University of Cambridge

The University of Cambridge with the support of the Software Sustainability Institute is organising a workshop on Containers for HPC: A Workshop on Singularity and Containers in HPC and Cloud on 29th and 30th June 2017. The aim of the workshop is to give an overview of container technologies in the context of Research Computing, with a specific focus on enabling HPC and GPU workloads.

The main focus will be around Singularity which is available in the current HPC system at Cambridge and is also the chosen technology that will be implemented in the new Cambridge Service for Data Driven Discovery at Cambridge (CSD3). Alongside a few special keynote talks, an afternoon session will cover practical examples from running a container on HPC to building your own Singularity container images.

Further information and registration is available at Containers for HPC workshop website. Places are limited, please make sure you have a real interest and need of this container technology and you are also familiar with Linux environments.

Containers for High Performance Computing

Reproducible…

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Ship and containersBy Raniere Silva, Community Officer, Software Sustainability Institute.

The Docker Containers for Reproducible Research Workshop (C4RR) is one of the Institute’s 2017 events. It will bring together members of the research software community—researchers and developers—to present, discuss, network and explore the landscape of containers when applied to research and reproducibility of results. C4RR will take place at Department of Engineering, University of Cambridge, from 27th to 28th June 2017.

If you wish to attend C4RR, register here.

C4RR is focused on the hot topics of reproducible research and containers such as Docker. Containers promise deep changes to the way that we run some software on our local machines or on the cloud, which could have a big impact on research and how to reproduce it.

Our call for papers closed on 31st March. We are now contacting successful authors and will add more details to the…

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For all enquiries about sponsorship, please contact Graeme Smith.

Sponsorship Packages for Docker Containers for Reproducible Research Workshop

 

Scholarship Bronze Silver Gold Platinum

Free tickets

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Thanks (on website)

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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.

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.

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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