Systems Biology

  1. Mathematical Modeling
    1. Modeling Frameworks
      1. Deterministic Models
        1. Ordinary Differential Equations
          1. Partial Differential Equations
            1. Delay Differential Equations
            2. Stochastic Models
              1. Stochastic Differential Equations
                1. Master Equations
                  1. Jump Processes
                  2. Discrete Models
                    1. Boolean Networks
                      1. Petri Nets
                        1. Cellular Automata
                      2. Kinetic Modeling
                        1. Enzyme Kinetics
                          1. Michaelis-Menten Kinetics
                            1. Allosteric Regulation
                              1. Competitive and Non-Competitive Inhibition
                              2. Gene Regulation Models
                                1. Hill Functions
                                  1. Transcriptional Regulation
                                    1. Post-Transcriptional Regulation
                                    2. Signal Transduction Models
                                      1. Receptor-Ligand Binding
                                        1. Phosphorylation Cascades
                                          1. Second Messenger Systems
                                        2. Constraint-Based Modeling
                                          1. Stoichiometric Networks
                                            1. Stoichiometric Matrix
                                              1. Null Space Analysis
                                                1. Conservation Laws
                                                2. Flux Balance Analysis
                                                  1. Linear Programming
                                                    1. Objective Functions
                                                      1. Flux Variability Analysis
                                                      2. Elementary Flux Modes
                                                        1. Pathway Enumeration
                                                          1. Minimal Cut Sets
                                                            1. Robustness Analysis
                                                          2. Model Analysis Techniques
                                                            1. Steady-State Analysis
                                                              1. Fixed Point Analysis
                                                                1. Stability Analysis
                                                                  1. Bifurcation Analysis
                                                                  2. Dynamic Analysis
                                                                    1. Phase Plane Analysis
                                                                      1. Limit Cycles
                                                                        1. Chaos Theory
                                                                        2. Sensitivity Analysis
                                                                          1. Local Sensitivity
                                                                            1. Global Sensitivity
                                                                              1. Parameter Identifiability
                                                                              2. Model Selection and Validation
                                                                                1. Information Criteria
                                                                                  1. Cross-Validation
                                                                                    1. Experimental Design

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                                                                                7. Dynamic Systems Analysis