Free and Open Environment for Microarray & NGS Analysis

MeV (MultiExperiment Viewer) is a versatile microarray data analysis tool, incorporating sophisticated algorithms for clustering, visualization, classification, statistical analysis and biological theme discovery. Galaxy is an open-source framework for integrating various computational tools and databases into a cohesive workspace. The IGV (Integrative Genomics Viewer) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

    MeV   IGV  EGAN

EGAN (Exploratory Gene Association Networks) is a software tool that allows a bench biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships (protein-protein interactions, literature co-occurrence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN has been built using Cytoscape libraries for graph visualization and layout, and is comparable to DAVID, GSEA, Ingenuity IPA and Ariadne Pathway Studio.

Free Resources for Modeling & Simulation

SBW(Systems Biology Workbench), is a suite of tools for carrying out simulations of biochemical processes that include metabolic, protein and gene regulatory networks. All the tools support SBML and host a variety of analyses including time course simulations, steady state, metabolic control analysis and analysis of stoichiometry.