Table 1 Comparing Galaxy to other genomic workbenches
Galaxy functionality | Description | GenePattern comparison | Mobyle comparison |
|---|---|---|---|
Making computation accessible | Â | Â | Â |
   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 | Â | Â | Â |
   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 | Â | Â | Â |
   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 |