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!!