Kinetic Modeling, ODE Parameter Estimation & Identifiability — Hands-on

Learn how to convert pathway diagrams and time course data into executable kinetic models. This module covers ODE based modeling, parameter estimation, identifiability and uncertainty analysis so that your dynamic systems models are calibrated, robust and ready for downstream simulation and decision support in systems biology and network medicine.

Kinetic Modeling, ODE Parameter Estimation & Identifiability

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Session Index

Session 1 — ODE Modeling & Kinetic Foundations Session 2 — Building & Simulating Kinetic Models Session 3 — Parameter Estimation & Identifiability Session 4 — Mini Capstone: Calibrated Kinetic Pathway Model

Session 1

Fee: Rs 8800

ODE Modeling & Kinetic Foundations

From biochemical reactions to ODEs

state variables and rates mass action kinetics Michaelis–Menten forms

Kinetic parameters and scaling considerations

rate constants and Km / Vmax dimension and units checking non dimensionalisation basics

Qualitative behaviour of simple ODE systems

steady states and trajectories stability intuition timescales and stiffness overview

Session 2

Fee: Rs 11800

Building & Simulating Kinetic Models

Model construction workflows and tools

SBML based models COPASI / tellurium / libRoadRunner Python / R ODE solvers

Numerical integration and solver settings

explicit vs implicit schemes stiff and non stiff solvers tolerances and step sizes

Basic simulation experiments and plots

dose response curves time courses and phase plots parameter sweeps

Session 3

Fee: Rs 14800

Parameter Estimation & Identifiability

Formulating parameter estimation problems

objective functions and residuals least squares and likelihoods noise models and weighting

Optimisation algorithms and practical fitting

gradient based methods global search heuristics overview initial guesses and bounds

Identifiability and uncertainty analysis basics

structural vs practical identifiability profile likelihood intuition confidence intervals for parameters

Session 4

Fee: Rs 18800

Mini Capstone: Calibrated Kinetic Pathway Model

From pathway diagram and data to calibrated model

Theory + Practical

Parameter estimation, validation and scenario testing

fit to time course or dose response data goodness of fit plots simulation of interventions

Deliverables: model files, fit report and README

SBML model or equivalent notebook with estimation workflow documentation of assumptions and limits

PDF

Kinetic Modeling, ODE Parameter Estimation & Identifiability Training | Dynamic Pathway Models

Kinetic Modeling, ODE Parameter Estimation & Identifiability — Hands-on