Forge Capsule

Systems Biology: Metabolic Networks, Flux Balance Analysis, and Omics

Systems biology: organisms as integrated networks, not isolated parts. Metabolic network: nodes=metabolites, edges=reactions. Flux balance analysis (FBA): steady-state, max objective (biomass). Stoichiometric matrix S: S·v=0 (steady state). Linear programming: max c^T v subject to S·v=0, lb≤v≤ub. COBRA toolbox. Gene regulatory networks: Boolean models (Kauffman), ODE models. Protein interaction networks: PPI, hub proteins. Omics layers: genomics, transcriptomics, proteomics, metabolomics, multi-omics integration. KEGG, BiGG databases. Synthetic biology: BioBricks, standardized parts. CRISPR circuits. Cell-free systems. Forge: biology domain 890+ capsules, provenance chains from PubMed, KEGG.