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Galaxy logo
an open web-based platform for data intensive biomedical research

Galaxy is an open, web-based platform for data intensive biomedical research. Whether on this free public server or your own instance, you can perform, reproduce, and share complete analyses. Galaxy, is a platform that has thousands of data-analysis tools for biomedical research. Most are geared for genomics, though more tools specific for proteomics and imaging analysis. A community of Galaxyusers helps vet the software tools for specific applications. In addition to using the public Galaxy ser

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CellDesigner logo

CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. CellDesigner is implemented in Java and thus supports various operating systems.

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visANT logo

VisANT is a lightweight network visualization tool able to run as a browser-based applet or as a standalone Java program.

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geWorkbench logo

geWorkbench (for genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications

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NAViGaTOR logo

NAViGaTOR - Network Analysis, Visualization, & Graphing TORonto is a software package for visualizing and analyzing protein-protein interaction networks

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Cytoscape logo

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration and visualization.

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MAGNet logo

The Center for the Multiscale Analysis of Genomic and Cellular Networks (MAGNet) develops novel Structural and Systems Biology methods and tools for the dissection of molecular interactions in the cell and for the interaction-based elucidation of cellular phenotypes. These tools are made freely available to the the members of the research community.

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Protégé logo

Protégé is a free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies. It is a tool that acts like the “word processor” of an ontology and uses a language like OWL as a convenient standard. At its core, Protégé implements a rich set of knowledge-modeling structures and actions that support the creation, visualization, and manipulation of ontologies in various representation formats.

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a tool for fast network motif detection

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