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Introduction to Rule-based modeling

Introduction to Rule-based modeling. … using BioNetGen. When/why should we use RBM. Many interacting components Multiple components interact with each other and create large ensembles of complexes . Multiple states for each component

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Introduction to Rule-based modeling

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  1. Introduction to Rule-based modeling … using BioNetGen

  2. When/why should we use RBM • Many interacting components Multiple components interact with each other and create large ensembles of complexes. • Multiple states for each component Post-translational modifications alter the behavior of the proteins in the system. • RB makes modeling actually “possible” Use only a set of biologically sensible rules in order to generate the full system.

  3. In biochemical modeling, what do we • usually know? Information about protein-interactions Information about kinetic laws • need to have? Consistent system of interactions of the required components Set of ODE’s to describe the behavior of this system Flexibility to define observables from our system • want to avoid? Missing any important interactions Making unjustified assumptions

  4. For example… RULE-BASED FORMULATION FOR LARGE ODE SYSTEMS (A) Localization &Contact Map (B) State transition Reaction Network Define the differential equation for each specie manually Define mechanistic rules, and generate the system of equations automatically

  5. Rule-based modeling concepts

  6. Structure of a RB model • Parameters: Define the parameters that govern the dynamics of the system (rate constants, the values for initial concentrations of species in the biological system) • Molecule types: Define molecules, including components and allowed component states • Seed species: Define the initial state of system (initial species and their concentrations) • Observables: Define model outputs, which are functions of concentrations of species having particular attributes • Reaction rules: Define rules that describe how molecules interact • Actions: Methods to generate and simulate network

  7. Summary of possible rules Five basic transformations • Add a bond “A(a)+B(b) –> A(a!1).B(b!1) k_bind” • Delete a bond “A(a!1).B(b!1) –> A(a) + B(b)k_unbind” • Change a component state label “EGFR(Y1068 ~ P) –>EGFR(Y1068 ~ U) k_dephos” • Add a molecule “I() –>I() + A(a,Y~U) k_synth” • Delete a molecule “A() –>Trash() k_deg”

  8. Example

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