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Jenkins and Bioinformatics, catch us at BOSC 2012

R. Tyler Croy
R. Tyler Croy
June 19, 2012

[ Editor’s Note: The following is a post from Jenkins CIA member Bruno P. Kinoshita ]

Jenkins will be represented at this years Bioinformatics Open Source Conference (BOSC 2012) on July 13-14th in Long Beach, California. I will be talking about Jenkins during my talk about BioUno.

BOSC 2012 will be held just before ISMB 2012, while registration is through ISMB you don’t have to register for ISMB in order to register for BOSC.

I will be at the event with some Jenkins stickers and available to answer questions you might have about BioUno and Jenkins!

About BioUno

BioUno is a project that uses Jenkins as basis for building biology workflows. BioUno provides an alternative update center with custom plug-ins for bioinformatics tools like MrBayes, Structure, Figtree, Beast, among others.

While the actual task of analysing or displaying data is handled by specific tools, that are wrapped by plug-ins, Jenkins is responsible for user control, web interface, notifications, distributed execution, job schedule and management, as well as other important low level tasks.

BioUno is similar to BioHPC, Galaxy and Taverna, in that all these tools enable creating and managing pipelines using different bioinformatics tools.

However, as it is using Jenkins, BioUno has the advantage of having an Open Source community of hackers that can answer questions and provide assistance for creating new plug-ins. There is plenty documentation for extending Jenkins and troubleshooting issues, as well as plenty existing plug-ins (that can be used as reference while writing new plug-ins).

There are projects and plug-ins that enable Jenkins to use resources in clouds or turn Jenkins into a Hadoop node, for big data processing. The next steps of the project include the deployment of BioUno to a computer facility, basic infrastructure for BioUno, definition of the process for releasing plug-ins, the creation of more plug-ins and a study on how to handle large data structures, used by many bioinformatics tools.

The project is being developed by TupiLabs under MIT License, and contributions and new plug-ins are welcome.

About the author

R. Tyler Croy

R. Tyler Croy

R. Tyler Croy has been part of the Jenkins project for the past seven years. While avoiding contributing any Java code, Tyler is involved in many of the other aspects of the project which keep it running, such as this website, infrastructure, governance, etc.