Making the Most of Galaxy

June 15, 2011

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Videos of presentations from the 2011 Galaxy Community Conference are now up on Vimeo. The conference is organized by the Netherlands Bioinformatics Centre (NBIC) and was held at the Conference Centre De Werelt in Lunteren in the Netherlands.

Galaxy is an open-source, scalable framework for software tool and data integration. The Galaxy project currently contains a slew of bioinformatics software applications including next-generation sequencing tools and workflows for metagenomics, ChIP-seq, RNA-seq, and much more.

The meeting covered a range of topics, such as the development of new tools, visualization, programming with the Galaxy API, and Galaxy CloudMan. The conference was aimed at software engineers, IT professionals, and analysis tool developers. Application areas touched upon in the talks included biomedical informatics, Taverna workflows in Galaxy, moving data onto Galaxy, next-generation sequencing for pathogen genomes in the clinic, and proteomics data analysis, just to name a few.

Illumina software engineer Kirt Haden presented a talk on how Illumina implemented Galaxy for high-throughput sequencing data analysis. Haden says that he and his team analyze up to 100TB of data per month, and needed a scalable tool that was customizable, allowed for easily automated workflows that were reproducible. They have already developed some customized graphical user interface tools, which they are submitting into the Galaxy code base, including theConsensus Assessment of Sequence and Variation (CASAVA) software, which they've demonstrated on very large data sets.

Freddy de Bree, a researcher at the Central Veterinary Institute at Wageningen UR, gave a talk on integrating tools into Galaxy to facilitate pathogenomics analysis and visualization. Bree and his colleagues are using Galaxy to elucidate zoonoses, including diseases such as Q-fever, Rift Valley virus, Swine fever, and PRRSV. He is also using a Galaxy platform for the development of diagnosis and intervention tools. In his talk, he described how they have Galaxy platforms up and running on a six-core development server and a 32-core production server where they use the pathogen detection program eDetectiV (R package).

About 15 videos of Galaxy presentations from the conference are now available, so head on over to Vimeo and check them out if you're currently using, or considering using, Galaxy for your omics projects.

Crazy timing! I wasn't aware

Submitted by james.ireland on Thu, 06/16/2011 - 16:31.

Crazy timing! I wasn't aware of this meeting, but we just blogged about our own Galaxy experience this morning:

http://blog.5amsolutions.com/2011/06/diy-bioinformatics-whole-new-galaxy...

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