Signal Transduction & Dynamic Modeling (ODE/PDE) — Hands-on

Learn how to translate signal transduction pathways into quantitative dynamic models using ordinary and partial differential equations. This module covers receptor level events, cascades and feedback, time course simulations, dose response analysis, and basic spatial considerations, implemented using COPASI, CellDesigner, SBML and Python/R based workflows.

Signal Transduction and Dynamic Modeling (ODE/PDE)

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Session Index

Session 1 — Signal Transduction Pathways & Motifs Session 2 — ODE Based Dynamic Modeling Session 3 — Advanced Dynamics, Feedback & PDE Preview Session 4 — Mini Capstone: Build & Simulate a Signaling Model

Session 1

Fee: Rs 8800

Signal Transduction Pathways & Motifs

Biological foundations of signal transduction

receptors and ligands second messengers phosphorylation cascades

Canonical pathways and network motifs

MAPK style cascades feedforward and feedback loops switches and bistability concepts

From pathway diagrams to reaction schemes

mass action and Michaelis Menten style reactions state variables and observables SBML and diagram tools overview

Session 2

Fee: Rs 11800

ODE Based Dynamic Modeling

Writing ODEs for signaling reactions

state variables and rate laws parameter sets and units initial conditions and inputs

Time course simulation workflows

dose response and time response curves transient vs steady state behaviour oscillations and adaptation patterns

Implementation toolkit for ODE models

COPASI and CellDesigner basics Python / SciPy ODE solvers R deSolve style workflows

Session 3

Fee: Rs 14800

Advanced Dynamics, Feedback & PDE Preview

Feedback loops and dynamic behaviours

negative vs positive feedback sensitivity and gain concepts hysteresis and bistability examples

Parameter estimation and sensitivity analysis

fitting to time course data local sensitivity scans global sensitivity overview

PDE and spatial effects preview

diffusion like terms compartment vs spatial gradients tools that support PDE style models

Session 4

Fee: Rs 18800

Mini Capstone: Build & Simulate a Signaling Model

Construct an ODE model for a chosen signaling pathway

Theory + Practical

Run time course, dose response and perturbation scenarios

ligand titration experiments inhibitor or knockout like perturbations key plots and response metrics

Deliverables: model files, simulation notebook & report

SBML and COPASI/CellDesigner model Python/R simulation notebook PDF/HTML dynamic behaviour summary

PDF

Signal Transduction & Dynamic Modeling (ODE/PDE) Training | Pathways, ODEs, Time Courses

Signal Transduction & Dynamic Modeling (ODE/PDE) — Hands-on