Abstract
Recent technological advances have lead to the ability to generate large amounts of data for model and non-model organisms. Whereas, in the past, there have been a relatively small number of central repositories that serve genomic data, an increasing number of distinct specialized data repositories and resources have been established. Here, we describe a generic approach that provides for the integration of a diverse spectrum of data resources into a unified analysis framework, Galaxy (http://usegalaxy.org). This approach allows the simplified coupling of external data resources with the data analysis tools available to Galaxy users, while leveraging the native data mining facilities of the external data resources.Database URL: http://usegalaxy.org
Highlights
The rate of generation of genomic data is increasing at a rapid pace for both model and non-model organisms
We describe an implementation of such a solution using Galaxy. Available both as (i) a publicly available web service providing tools for the analysis of genomic, comparative genomic and functional genomic data and (ii) a freely downloadable package that can be deployed in individual labs or on Cloud resources (9), Galaxy attempts to serve both sides of the user distribution: experimental biologists and bioinformaticians
Using Galaxy, researchers are able to directly query data providers using the native data mining facilities provided by the external resource
Summary
The rate of generation of genomic data is increasing at a rapid pace for both model and non-model organisms. We describe an implementation of such a solution using Galaxy (http://usegalaxy.org; 5–8) Available both as (i) a publicly available web service (http://usegalaxy.org) providing tools for the analysis of genomic, comparative genomic and functional genomic data and (ii) a freely downloadable package (http://getga laxy.org) that can be deployed in individual labs or on Cloud resources (9), Galaxy attempts to serve both sides of the user distribution: experimental biologists and bioinformaticians. Galaxy provides a software framework that allows the simplified coupling of external data resources with the data analysis tools available to Galaxy users, while leveraging the native data mining facilities of the external data resources This solution is agnostic to the type of data that is returned from a particular data resource, which may itself be the result of previous analysis. When the data provider is hosting their resource using code which is not-yet Galaxy capable, the amount of time is dependent upon the steps required on the data provider’s part to modify and configure their own code-base; the time required to configure the Galaxy instance remains similar
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