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Table 1 Comparing Galaxy to other genomic workbenches

From: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

Galaxy functionality Description GenePattern comparison Mobyle comparison
Making computation accessible    
   Unified, web-based tool interface All tool interface share same style and use web components; tool interfaces are generated from tool configuration file Same functions as Galaxy Same functions as Galaxy
   Simple tool integration Tool developers can integrate tools by writing a tool configuration file and including tool file in Galaxy configuration file Similar but not as flexible tool configuration file; easy installation of selected tools via a web-based interface Remote services can be added using a server configuration file
   Integrated datasources Transparent access to established data warehouses No similar functions No similar functions
Ensuring reproducibility    
   Automatic metadata Provenance, inputs, parameters, and outputs for each tool used; analysis steps grouped into histories Same functions as Galaxy Same functions as Galaxy
   User tags Can apply short tags to histories, datasets, workflows, and pages; tags are searchable and facilitate reuse No similar functions No similar functions
   User annotations Can add descriptions or notes to histories, datasets, workflows, workflow steps, and pages to aid in understanding analyses Cannot annotate a history but can annotate a workflow (pipeline) with an external document No similar functions
   Creating and running workflows Can create, either by example or from scratch, a workflow that can be repeatedly used to perform a multi-step analysis Same functions as Galaxy, although editor is form-based rather than graphical In development
   Workflow metadata Automatic documentation is generated when a workflow is run; users can also tag and annotate workflows and workflow steps Same functions as Galaxy for generating automatic metadata; cannot annotate workflow steps In development
Promoting transparency    
   Sharing model Datasets, histories, workflows, and Pages can be shared at progressive levels and published to Galaxy's public repositories; datasets have more advanced sharing options, including groups Can share analyses and workflows with individuals or groups No similar functions
   Item reuse, display framework and public repositories Shared or published items displayed as webpages and can be imported and used immediately; public repositories can be searched; archives of analyses and workflows for sharing between servers are under development Can create an archive of an analysis or workflow and share that with others; author information is included in archive Can create an archive of an analysis and share that with others
   Pages with embedded items Can create custom webpages with embedded Galaxy items; each page can document a complete experiment, providing all details and supporting reuse of experiment's outputs Microsoft Word plugin enables users to embed analyses and workflows in Word documents No similar functions
   Coupling between analysis workspace and publication workspace Can import and immediately start using any shared, published, or embedded item without leaving web browser or Galaxy Can run embedded analyses and save results in Microsoft Word documents No similar functions
  1. A summary of Galaxy's functionality and how Galaxy's functionality compares to the functionality of two other genomic workbenches, GenePattern and Mobyle. Galaxy's novel functionality includes (but is not limited to) integrated datasources, user annotations, a graphical workflow editor, Pages with embedded items, and coupling the workspaces for analysis and publication using an open, web-based model.