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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


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.