Multi Scale & Agent Based Modeling — Hands-on

Learn how to build multi scale and agent based models that bridge molecular, cellular and tissue level dynamics. This module focuses on ABM concepts, spatial modelling, coupling with ODE/PDE systems and practical simulation workflows so that you can capture heterogeneity and emergent behaviour in realistic systems biology and network medicine applications.

Multi Scale & Agent Based Modeling

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Session Index

Session 1 — Multi Scale Modeling Concepts & Paradigms Session 2 — Agent Based Modeling Foundations & Toolchains Session 3 — Coupling ODE / PDE with ABM & Calibration Session 4 — Mini Capstone: Spatial Tissue / Microbiome ABM

Session 1

Fee: Rs 8800

Multi Scale Modeling Concepts & Paradigms

Why multi scale models in systems biology

molecular–cellular–tissue couplings heterogeneity and spatial structure emergent behaviours

Model classes and representation choices

lumped ODEs vs PDEs vs ABM lattice vs off lattice agents hybrid continuum–discrete schemes

Linking scales conceptually and practically

bottom up vs top down coupling time step and scale separation trade offs in complexity vs runtime

Session 2

Fee: Rs 11800

Agent Based Modeling Foundations & Toolchains

Agents, rules and environments in ABMs

states and behaviours neighbourhoods and interactions scheduling and update schemes

Common ABM platforms and ecosystems

NetLogo and Repast overview PhysiCell / CompuCell3D glimpse Python ABM libraries

Designing ABMs for biological questions

tumour growth and invasion immune cell or microbiome dynamics model scope and simplifications

Session 3

Fee: Rs 14800

Coupling ODE / PDE with ABM & Calibration

Hybrid continuum–discrete coupling patterns

diffusing fields with PDEs agents sensing and secreting fields time integration schemes

Parameterisation and calibration strategies

link to imaging and histology data summary statistics and ABC intuition exploring parameter sensitivities

Running, visualising and analysing simulations

spatial plots and movies population level readouts replicates and variability summaries

Session 4

Fee: Rs 18800

Mini Capstone: Spatial Tissue / Microbiome ABM

Design and implement a small multi scale ABM

Theory + Practical

Explore scenarios and intervention strategies

dose / schedule changes environmental or nutrient shifts cell or species level perturbations

Deliverables: code, visualisations and brief report

simulation notebook or project files time lapse figures or videos methods, assumptions and insights

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Multi Scale & Agent Based Modeling Training | Hybrid Spatial & Multiscale Systems Biology

Multi Scale & Agent Based Modeling — Hands-on