Notes: Bio in Docker Symposium 2015 day 2: Docker infrastructure and hackathon

I’m at day 2 of the Bio in Docker Symposium at the Wellcome Collection in London. This is a great 2 day set of talks and coding sessions around the use of Docker containerization in biology workflows. The idea is to coordinate around using these tools to be able to improve our ability to do science. There is hackathon for half of today but the morning talks focus on tools within the Docker ecosystem and learning how to use these to design better applications for biology. There is a ton of cool engineering ongoing, but untangling all of the different components is a challenge hopefully these talks will help with.

  • Notes for day 1: NGS pipelines, workflow tools and data volume management


F1000Research – a publishing platform for the Docker community

Thomas Ingraham & Michael Markie

F1000 Research is an open publisher that both handles traditional articles but also outputs like posters and presentations. The do open post-publication peer review and are generally a great way to publish research. Articles are only indexed and officially published when passing peer review. Articles have versions so you can see changes over time. Collections organize related content for easier discoverability. One example is the Bioinformatics Open Source Conference (BOSC) channel. Today they’re announcing a channel for Container virtualization in informatics. A great way to make Docker-enabled posts publicly available.

New Docker functionality

Weaving Containers in Amazon’s ECS

Alfonso Acosta

Microservice oriented architecture model work around small components that each do a single job. This helps avoid complexity, but introduces challenges in coordinating and putting things together. WeaveWorks has tools to connect, observe and control containers. It connects containers, managed IP issues, sorts out DNS, and does load balancing between identically named containers. It handles node failures with recovery. Weave does not require a distributed key/value store – uses gossip in a peer-to-peer fashion so resistant to failures. On each machine you start up a new weave client. It only needs to know the name of one other host on the network, then they’re all connected. Then you start and register containers in the network. Weave sits on top of Amazon ECS, providing all of the container registry and discovery

Orchestrating containers with docker compose

Aanand Prasad

Docker compose allows defining and running multi-container Docker applications. Motivation is that multi-container apps are a hassle to setup, configure and coordinate. Coordinates with Docker machine, which creates Docker hosts on a machine, and Docker swarm, which provides clustering of Docker containers. From our previous talk, it looks like Weave can work with Swarm directly. For a demo, Aanand shows docker compose talking directly to a swarm cluster. The swarm integration with Docker is nice – all of the standard docker commands work when you’re running a coordinated cluster. It does a great job of distributing containers across multiple hosts. Docker machine does work on running inside VMs in an easy way, but you also lose all the native goodness of docker by going this route.

Manage your infrastructure like Google

Matt Barker & Matt Banes

JetStack helps with management and orchestration of containers. At Google everything runs in a container with 2 billion containers a week. Kubernetes is the open source version of their internal cluster management tool. Pods look really cool and are a way to group together multiple applications with shared volumes. The replication controller does the work of maintaining a consistent state of pods, restarting when things fail. Kubernete’s shared-state scheduler does the job of scheduling containers to machines based on resource requests. Services provides a way to label pods and then do discovery based on the naming, instead of introducing this complexity into your code. As of the new version, Kubernetes now has a Job object which explicity managed jobs. Nice live example wrapping Mykrobe predictor inside a Docker container and then running with Kubernetes – mykrobe predictor spits out JSON which gets sucked into MongoDB from a watcher in another container. Kubernetes is impressive and the discoverability of coordinating between services is nice.

Docker and real world problems

Clive Stringer and Adam Hatherly

King’s College London is a NHS hospital with big hospital problem. Many of the components don’t fit well together so things don’t interoperate. Major need is components that slot together easily. CIAO (Care Integration and Orchestration) is an open source middleware to make it easier to use standards and share information. The NHS is a complex set of organizations so not set up to work as a whole system. Encapsulates the complex XML integration code inside of components composed in Docker containers. Each components is a microservice and self-contained. Each component in a reference standard for libraries. A second focus is on trying to characterize genes based on genetic components. Challenge is to make medical records available.

OSwitch: One-line access to other operating systems.

Yannick Wurm

Yannick works with ants, and starts with a plugs for ant being cool. Shows example of leaf cutter ants using symbiotic fungus to digest leaves. Sold. Then he motivates about the difficulties of working with computational tools to answer biological questions. Also sold. oSwitch is an awesome tool that provides a small wrapper around Docker. It creates an interactive instance around a tool, run things on the files in the current directory, then exiting. It removes all of the abstraction around Docker. We should have docs on debugging bcbio runs with oSwitch when running more with Docker.


The afternoon of the workshop is for working on problems and getting coding done. The organizers have nicely setup up tutorials ranging from learning Docker, to learning advanced Docker concepts to working with tools like Nextflow and Nextflow workbench that build on top of Docker. I’m working on continuing to improve CWL support in bcbio, moving towards the vision of bcbio running on alternative infrastructure presented in my talk at the conference.


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