Limited tickets still available for 'Bio in Docker' Symposium (November 2015)

This free symposium — organised by Kings College London and the Biomedical Research Centre (BRC) — will bring together people interested in using Docker images in the field of bioinformatics, and will include a 'mini-hackday' session.

Event description

Docker is now establishing itself as the de facto solution for containerization across a wide range of domains. The advantages are attractive, from reproducible research to simplifying deployment of complex code.

This event will bring together some notable cases to discuss how advantage of this new technology can best be achieved within the Bioinformatics space.

Event details

  • November 9–10, 2015
  • London, UK at the Wellcome Collection
  • Register through Eventbrite

Talk details

  • Peter Belmann (Bioboxes): i) Evaluating and ranking bioinformatics software using docker containers. ii) Overview of the BioBoxes project
  • Nebojsa Tijanic (SB Genomics): Portable workflow and tool descriptions with Common Workflow Language and Rabix
  • Paolo Di Tommaso (Nextflow / Notredame Lab, CRG): Manage reproducibility in genomics pipelines with Nextflow and Docker containers
  • Amos Folarin & Stephen Newhouse (NGSeasy/KCL): Next generation sequencing pipelines in Docker
  • Tim Hubbard (Genomics England / KCL): Pipelines to analysis data from the 100,000 genomes project as part of the Genomics England Clinical Interpretation Partnership (GeCIP)
  • Fabien Campagne (Campagne lab): MetaR and the Nextflow Workbench: application of Docker and language workbench technology to simplify bioinformatics training and data analysis.
  • Elijah Charles (Intel): Bioinformatics and the packaging melee
  • Brad Chapman (Blue Collar Bioinformatics): Improving support and distribution of validated analysis tools using Docker
  • Michael Ferranti / Kai Davenport (ClusterHQ): Data, Volumes and portability with Flocker
  • Ilya Dmitrichenko (Weave): Application-oriented networking with Weave
  • Aanand Prasad (Docker): Orchestrating Containers with Docker Compose

BioDocker and BioBoxes: the containerization of bioinformatics

Thanks to a post on the BioCode's Notes blog I have discovered that there is a project called BioDocker which aims to generate lots of Docker containers to help make bioinformatics more reproducible by standardizing how bioinformatics software is packaged. From the BioDocker website:

The main purpose of this project is to spread the use of Docker on the Bioinformatics and Computational Biology areas. By using pre-configured containers with different bioinformatic softwares some critical aspects of Bioinformatics like reproducibility are minimized. Here you will find a list of containers with different bioinformatics software and how to use it.

BioDocker was created by Felipe da Veiga Leprevost in 2014, and the associated GitHub repository currently has a dozen or so containers.

When I was first read about BioDocker I was confused because I know that there is also the Bioboxes project which aims to er…make bioinformatics more reproducible by standardizing how bioinformatics software is packaged. From the Bioboxes manifesto:

Software has proliferated in bioinformatics and so have the problems associated with it: missing or unobtainable code, difficult to install dependencies, unreproducible workflows, all with terrible user experiences. We believe a community standard, using software containers, has the opportunity to solve these problems and increase the standard of scientific software as a whole.

I think the aims of these two projects are similar, but not identical and Bioboxes probably has a broader remit. Both projects are aware of each other and it looks like they have had some productive exchanges.

All of this makes me feel that the bioinformatics community seems to be slowly, but steadily, embracing Docker. Any approaches to standardize how we do bioinformatics should be welcomed, but some of us with long memories will recall that we have been in this situation before. Anyone remember the promises of how CORBA and then SOAP were going to increase interoperability in bioinformatics?

Too many genome assemblers to keep track of? to the rescue!

Yesterday, I presented an updated version of my 'Genome Assembly: Then and Now' talk. I'll try to post the full set of slides (with notes) later today on Slideshare. But I thought I'd share just one of the new slides from the talk; here are six papers that describe new genome assembly tools…

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