This page lists software platforms that allow a broad range of scientific computing tasks.
The specific computations will depend on which modules or packages are loaded into the
environment by the user. All the platforms listed here have extensive user and developer
communities, providing additional support for the products. Click on the name to view details, or
to request access to the product.
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1296 software packages, and an active user community.
Cytoscape is an open source 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, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. They may be developed by anyone using the Cytoscape open API based on Java™ technology and App community development is encouraged. Most of the Apps are freely available from Cytoscape App Store.
RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.