Webinars |Björn Grüning
Dr Björn Grüning is with the Bioinformatics Group at Albert-Ludwigs-Universität Freiburg, in Freiburg Germany, where he heads the Freiburg Galaxy Project. His contributions include several that feature reproducible and accessible research prominently, including the recent article “Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter” (Grüning, et al, 2017). He is a prominent contributor to, and is a driving force in, the Galaxy community. In the past year alone, he helped organize the Bioconda Contribution Fest, Swiss-German Galaxy Days, the Galaxy Training Materials Contribution Fest, the Galaxy DevOps Workshop, and the Conda Dependencies Codefest, and presented and taught at GCC2016. His research interests include data visualisation, computational chemistry, and epigenetics.
15th June 2017 (14:00 – 14:45 GMT) : “Conda and Containers for a sustainable bioinformatic infrastructure”
During the webinar I will describe a community effort to create a flexible, scalable and sustainable system to fix the tool deployment problem. Bioconda is a platform for distribution of bioinformatics software using Conda, an open source package manager developed. Installation of Conda packages are fast and robust. No root privileges are required and multiple versions of every software can be installed and managed in parallel. Supported by an extensive documentation, writing a Conda package is very simple, easing the contribution. Thanks to its big and fast-growing community, more than 2,000 bioinformatic packages have been developed in the 18 months it has existed. These packages are long-term stored in a public repository (Cargo Port, the distribution center of the Galaxy Project), resolving the sustainability issue. Moreover, a technique called layer donning has been recently introduced to build containers automatically and very efficiently for all Conda packages. Docker, rkt and Singularity containers are automatically contributed to the BioContainers repository.
Building efficient Linux containers automatically ensures an even higher layer of abstraction and isolation of the base system. Thanks to these collaborative projects, their community and their collaborations, tools can be easily packaged, deployed and will be always available to help biomedical research.
We will close this webinar with an overview how this is used in the Galaxy project and demonstrate the possibilities and impact for FAIR research.