galaxy: an open web-based analysis platform
DESCRIPTION
Galaxy: an Open Web-Based Analysis Platform. Core4Life Retreat Bioinformatics Unit CRG (Barcelona, Spain) Ernesto Lowy 22-23 November 2012. Introduction. Developed by Nekrutenko and others at Penn State, along with James Taylor at Emory University - PowerPoint PPT PresentationTRANSCRIPT
Galaxy: an Open Web-Based Analysis Platform
Core4Life RetreatBioinformatics Unit
CRG (Barcelona, Spain)Ernesto Lowy
22-23 November 2012
Developed by Nekrutenko and others at Penn State, along with James Taylor at Emory University
Galaxy is an open web-based tool for biomedical research
Accessible: users without programming experiencecan easily specify parameters and run tools and workflows
Reproducible: Galaxy captures information so that any user can repeat and understand a complete computationalanalysis
Introduction
Introduction
Allow experimental biologists to do complex bioinformatics analyses (including BigData) without computational skills
Galaxy is completely open source and is unique
There are commercial solutions but are a waste of moneybecause technology changes every 2 weeks
Galaxy Interface
Analysis Modules
Data browser
History
Running Bowtie trough Galaxy
Choosing Bowtie Parameters
Input Fastq file
Checking Results of Bowtie
Run finished
Alignment in SAM format
Workflows Workflows can be easily created from ‘History’
Pro:Not need installationCon: Slow uploads Long queues before launching
the analysis Old versions of some tools Lack of control on your data
Local InstallationPro: Add your own tools Adapt resources used by Galaxy depending on the number of users
and the type of analyses Data is secured in your own institutionCon: Dedicated staff for setting-up the platform
Type of InstallationFree Public ServerAt: UseGalaxy.org NBIC Other listed on Galaxy Wiki
Galaxy@CRG Currently being developed by the Bioinformatics Unit (mainly Jean François Taly)Will: Include our (Bioinformatics Core) pipelines Replace commercial solutions we have in our Institute Increase the visibility of the tools developed in-house Be an interface to the High Performance Computing infrastructure at the CRGFinally: CRG will be trained on Bioinformatics data analysis using Galaxy as an interface
Implementation details
THANKS FOR YOUR ATTENTION!!