A G C T A C G A A A A G T A C G A T T    T A A C G T A C C C C T A C G T A C G T A C G T  A C G T A C G T A C   A C G T A A C G T A C G T A C G
A G C T A C  A A A A G T A C G A T T    T A A C G T A C C C C T A C G T A C G T A C G T  A C G T A C G T A C   A C G T  C G T A C G T A C G
A G C T A C G A A A A G T A C G A T T    T A A C G T A C C C C T A C G T A C G T A C G T  A C G T A C G T A C   A C G T A A C G T A C G T A C G
A G C T A C  A A A A G T A C G A T T G C A G T A A C G T A C C C C G A C G T A C G T A C G T  A C G T A C G T A C   A C G T  C G T A C G T A C G
A G C T A C  A A A A G T A C G A T T    T A A C G T A C C C C G A C G T A C G T C C G T  A C G T A C G T A C   A C G T  C G T A C G T A C G
A G C T A C  A A A A G T A C G A T T    T A A C G T A C C C C G A C G T A C G T C C G T  A C G T A C G T A C   A C G T  C G T A C G T A C G
A G C T A C A A A A A  T A C G A T T    T A A C G T A C C C C T A C G T A C G T A C G T  A C G T A C G T A C   A C G T  C G T A C G T A C G
A G C T A C  A A A A G T A C G A T T    T A A C G T A  C C T A C G T A C G T A C G T  A C G T A C G T A C   A C G T A A C G T A C G T A C G
A G C T A C  A A A A G T A C G A T T    T A A C G T A  C C T A C G T T T T T C C G T  A C G T A C G T A C   A C G T A A C G T A C G T A C G
A G C T A C  A A A A G T A C G A T T G C A G T A A C G T A  C C T A C G T T T T T A C G T  A C G T A C G T A C   A C G T A A C G T A C G T A C G
A G C T A C A A A A A G  A C G A T T    T A A C G T A C C C C T A C G T T T T T A C G T  A C G  C G T A C   A C G T A A C G T A C G T A C G
A G C T A C  A A A A G T A C G A T T    T A A C G T A  C C C T A C G T T T T T A C G T  A C G  C G T A C   A C G T A A C G T A C G T A C G
A G C T A C G A A A A G T A C G A T T G C A G T A A C G T A C C C C T A C G T T T T T A C G T  A C G  C G T A C   A C G T A A C G T A C G T A C G
A G C T A C  A A A A G T A C G A T T G C A G T A A C G T A C C C C T A C G T T T T T A C G T  A C G  C G T A C   A C G T  C G T A C G T A C G
A G C T A C  A A A A G T A C G A T T    T A A C G T A C C C C T A C G T T T T T A C G T  A C G  C G T A C   A C G T  C G T A C G T A C G

C

A

M

I

Critical

Assessment

of

Metagenome

Interpretation

What is Cami?

In just over a decade, metagenomics has developed into a powerful and productive method in microbiology and microbial ecology. The ability to retrieve and organize bits and pieces of genomic DNA from any natural context has opened a window into the vast universe of uncultivated microbes. Tremendous progress has been made in computational approaches to interpret this sequence data but none can completely recover the complex information encoded in metagenomes. A number of challenges stand in the way. Simplifying assumptions are needed and lead to strong limitations and potential inaccuracies in practice. Critically, methodological improvements are difficult to gauge due to the lack of a general standard for comparison. Developers face a substantial burden to individually evaluate existing approaches, which consumes time and computational resources, and may introduce unintended biases. The Critical Assessment of Metagenome Interpretation (CAMI) is a new community-led initiative designed to help tackle these problems by aiming for an independent, comprehensive and bias-free evaluation of methods. [read more]

CAMI Challenge:
CAMI Evaluation Workshop takes place May 11-13, 2016. Agenda: goo.gl/JNZJTS Live streaming: goo.gl/ewfAIC
May 10, 2016
CAMI Challenge:
CAMI challenge evaluation of profiling tools online, check out data.cami-challenge.org/analyse
Feb 1, 2016
CAMI Challenge:
Check CAMI webpage frequently for updates and more evaluation metrics in coming weeks.
Jan 19, 2016
CAMI Challenge:
First results of @CAMI_challenge evaluations online! Check out data.cami-challenge.org/analyse Visualizations to better compare results coming soon
Jan 19, 2016
CAMI Challenge:
.@linsalrob We are on it and will post the first assembly evaluation soon. Binning and profiling will follow afterwards...
Sep 24, 2015
bioboxes:
Example of using a biobox for the first time - bioboxes.org/docs/example-b…
Sep 3, 2015

Up- and Download

Participate by downloading datasets and submitting your computed assembly, binning or profiling.

Learn More

Analyse

In this section you will be able to analyse the assembly, binning or profiling quality based on different metrics.

Learn More

Compare

The compare section will allow you to upload your own assembly and compare the quality with the assemblies of an already finished competition.

Learn More

What is Docker?

Docker is a platform that allows you to define software within a container. This container can then be executed anywhere as long as the Docker daemon is available. It is very similar to a virtual machine, with the difference that you do not have to install a full operating system. [read more]

Why Docker?

Works Everywhere
Docker containers run (almost) everywhere. You can deploy containers on desktops, physical servers, virtual machines, into data centers, and up to public and private clouds.

Portability
Since Docker runs on so many platforms, its easy to move your applications around. You can easily move an application from a testing environment into the cloud and back whenever you need.

Efficiency
As Docker speeds up your work flow, it gets easier to make lots of small changes instead of huge, big bang updates. Smaller changes mean reduced risk and more uptime.

Faster Development
Docker containers are lightweight and fast! Containers have sub-second launch times, reducing the cycle time of development, testing, and deployment.

These are just a few benefits mentioned on docker.com
[read more]



Summary

Docker Installation

Our Docker Images

Built-in Tasks
  • --list-spec Lists the environment variables for the respective Image.
  • --list-mount Lists the directories that have to be mounted.
  • --list-var Lists variables for fine-grained control of your container (i.e. DCKR_THREADS).
  • --shell Starts a shell inside the container.
  • --versionVersion of the Interface being used.

Our specifications
We are using bioboxes. Bioboxes is community driven and has the aim to develope standards for interoperable bioinformatics container interfaces. At the moment the most interfaces are at version 0.8. So if you can not build your container with the specified variables, please contact us (support@cami-challenge.org) or write an issue on GitHub.

Share Your Container
  1. Get an account on Docker Hub
  2. Upload your Image
  3. Tell us your Repository ID (i.e.:cami/binning) and the task you have created and executed on the respective dataset.