Dynamic Modeling of Biochemical Systems (ODE/SDE) — Hands-on

Master dynamic modeling of biochemical reactions using deterministic (ODE) and stochastic (SDE) formalisms. This module covers reaction system formulation, mass-action and Hill kinetics, numerical solvers, stability and bifurcation analysis, noise-driven systems, and simulation workflows using Python (SciPy) , R (deSolve) , COPASI, and Tellurium/RoadRunner. By the end, you will generate reproducible simulation notebooks, visualize trajectory behavior, and interpret dynamical signatures (steady states, oscillations, switching) .

Dynamic Modeling of Biochemical Systems (ODE/SDE)

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Session Index

Session 1 — Reaction Systems, Kinetics & ODE Setup Session 2 — Numerical Solvers, Stiffness & Stability Session 3 — Stochastic Modeling (SDE) & Noise Session 4 — Mini Capstone: Full Dynamical Model Build

Session 1

Fee: Rs 8800

Reaction Systems, Kinetics & ODE Setup

Reaction networks & kinetic laws

mass-action Michaelis–Menten Hill kinetics

Converting reactions to ODEs

stoichiometry matrices state variables rate laws

Toolchain overview

Python SciPy R deSolve COPASI / Tellurium

Session 2

Fee: Rs 11800

Numerical Solvers, Stiffness & Stability

Solvers & integration methods

Euler / RK4 LSODA / CVODE adaptive solvers

Stiffness & model behavior

timescale separation numerical instability solver troubleshooting

Stability & phase-plane analysis

Jacobian & eigenvalues steady states oscillations

Session 3

Fee: Rs 14800

Stochastic Modeling (SDE) & Noise

Sources & types of stochasticity

intrinsic noise extrinsic noise biological variability

SDE models & simulation

Langevin equations Euler–Maruyama noise terms & variance

Tools for stochastic simulation

Tellurium StochPy Python SDE libraries COPASI stochastic mode

Session 4

Fee: Rs 18800

Mini Capstone: Full Dynamical Model Build

Build a complete ODE/SDE model for a biological pathway

Theory + Practical

Simulation, visualization & interpretation

trajectories & phase-plots steady states & oscillations noise comparison

Deliverables

PDF/HTML report Python/R notebook environment.yml / requirements.txt

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Dynamic Modeling of Biochemical Systems (ODE/SDE) Training | Solvers, Stability & Stochasticity

Dynamic Modeling of Biochemical Systems (ODE/SDE) — Hands-on