Docker

Python codeBy Mike Jackson, Software Architect

As part of my open call consultancy for LUX-ZEPLIN (LZ), I was asked about the feasibility of developing a web service that accepted Python code from users and executed their code server-side within a Linux environment. In this blog post I give a brief overview of a number of approaches that could be taken to implement such a service, focusing on those that protect the web service, and its underlying server, from code that is, whether by accident or design, malicious.

First things first, developing a web service that accepts Python code from users and runs this server-side is, in itself, it is not technically challenging. Any developer could knock up a proof-of-concept quite rapidly. The challenges are how to ensure that the web service is able to successfully run a user’s code, and how to protect the web service from the user’s code.

The first challenge, how to ensure that the server is able to successfully run a user’s code, can be restated as how to ensure that users only submit code that can successfully run on the server. At its simplest, this can be handled by publishing information about the environment within which the server will run the user’s code (e.g. operating system version, Python interpreter and…

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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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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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Check the list of talks, lightning talks and demos. All video recording are on YouTube.

Monday 26 June 2017

If you are planning to arrive in Cambridge on 26th June and need a place to dinner, we recommend the Novi.

Tuesday 27 June 2017 - Day 1

  • 10:00-10:40: Registration and Coffee
  • 10:40-10:50: Welcome

  • 10:50-11:10: Docker Containers for Deep Learning Experiments - Paul K. Gerke, Diagnostic Image Analysis Group, Radboudumc Nijmegen (slides, video)

  • 11:10-11:30: Reproducible high energy physics analyses - Diego Rodríguez, CERN (slides, video)

  • 11:30-11:50: HPC infrastructure for high energy density physics research - Arturas Venskus, First Light Fusion Limited, Richard King, First Light Fusion Limited (video)

  • 11:50-12:10: Singularity Containers for Reproducible Research - Michael Bauer, University of Michigan / Lawrence Berkeley National Lab (video)

  • 12:10-12:30:

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Clare Bridge, CambridgeSome suggested places to book accommodation for Docker Containers for Reproducible Research Workshop in Cambridge. Note that hese are just suggestions based on distance closest to the venue of the workshop and reasonable price.

Or you may wish to look at TripAdvisor or other sites for nearby and available hotels.

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

✔ (1)

✔ (1)

✔ (1)

✔ (2)

✔ (4)

Thanks (on website)

✔ (name)

✔ (small logo)

✔ (medium logo)

✔ (large logo)

✔ (huge logo)

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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.

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