pathway

pathway provides integrated computational systems-biology capabilities for genome informatics, pathway and regulatory informatics, metabolic reconstruction and modeling, and analysis of gene-expression and metabolomics data within the BioCyc database collection.

Key Features:

• Comprehensive Integration: Integrates genome informatics, pathway informatics, regulatory informatics, and omics data analysis to construct and manage knowledge linking genes, gene products, regulatory circuits, and metabolic networks.
• Metabolic Modeling: Supports execution of metabolic models, a gap-filling mechanism, and construction of models for organism communities distributed across spatial grids.
• Visualization and Query Tools: Provides graphical representations of model results and query tools for exploration of pathway and genome data.
• Omics Data Analysis Tools: Includes the Omics Dashboard, pathway collages (multi-pathway diagrams), a pathway-covering algorithm for metabolomics data analysis, and an algorithm to generate mechanistic explanations of multi-omics data.
• Database Management: Offers multi-organism search tools, enhanced graphics rendering, and database features for pathway/genome database management.

Scientific Applications:

• Metabolic flux model construction: Derives metabolic flux models from pathway and pathway/genome databases.
• High-throughput data interpretation: Uses pathway and regulatory information to interpret gene-expression, metabolomics, and other high-throughput datasets.
• Systems biology and bioinformatics analyses: Supports metabolic reconstruction, modeling, and multi-omics integration for systems biology and bioinformatics research.

Methodology:

Computational methods explicitly include metabolic model execution, gap-filling, community modeling across spatial grids, pathway-covering algorithms, mechanistic-explanation algorithms for multi-omics, the Omics Dashboard and pathway collage generation, multi-organism query indexing, and graphics rendering.