Build Models
Build mechanistic systems biology models or PK/PD models
Build QSP, PBPK, PK/PD, and systems biology models graphically using a block diagram editor or programmatically using MATLAB® functions. Use doses to model various dosing regimens and use variants to represent biological variability and what-if scenarios.
Apps
SimBiology Model Builder | Build QSP, PK/PD, and mechanistic systems biology models interactively (Since R2020b) |
SimBiology Model Analyzer | Analyze QSP, PK/PD, and mechanistic systems biology models |
Functions
sbiomodel | Construct model object |
sbioroot | Return SimBiology root object |
sbioreset | Delete all model objects |
sbioselect | Search for objects with specified constraints |
sbiodiff | Compare SimBiology models and diagram information (Since R2022a) |
getComponents | Get model components associated with SimBiology model comparison results (Since R2022a) |
visdiff | Visualize SimBiology model comparison results (Since R2022a) |
addcompartment | Create compartment object and add to model or compartment |
addCompartment | Add compartment to PKModelDesign object |
addobservable | Add observable object to SimBiology model (Since R2020a) |
addspecies | Create species object and add to model or compartment |
addparameter | Create parameter object and add to model or kinetic law object |
addreaction | Create reaction object and add to model |
addrule | Add rule object to model |
addevent | Add event object to model object |
construct | Construct SimBiology model from PKModelDesign object |
generateCode | Generate MATLAB function to recreate SimBiology model (Since R2024a) |
Objects
Topics
Model Building
- Create Model of Receptor-Ligand Kinetics
Create and simulate a simple receptor-ligand kinetics model using SimBiology apps. - Incorporate SGLT2 Inhibition into Physiologically Based Glucose-Insulin Model Using SimBiology Model Builder
Update a glucose-insulin model to integrate sodium-glucose co-transporter 2 (SGLT2) receptor inhibition by a hypothetical compound. - Construct a Simple Model
This example shows how to construct a simple model programmatically. - Compare SimBiology Models
Compare any two SimBiology models to find out the differences between them. - Merge SimBiology Models
Merge differences between two SimBiology Models. - Model a Gene-Regulation Pathway
This example shows how to construct a simple gene-regulation model and simulate it. - Create and Simulate a Model with a Custom Function
This example shows how to create a custom function and incorporate it in model simulation. - Define Reaction Rates with Mass Action Kinetics
Use mass action kinetics to define zero-order, first-order, second-order, and reversible reactions. - Define Reaction Rates with Enzyme Kinetics
Use differential equations, mass action kinetics, or Michaelis-Menten kinetics to define enzyme reactions. - Events in SimBiology Models
In SimBiology, an event is a discrete transition in value of a quantity or expression in a model. - Create Pharmacokinetic Models
SimBiology lets you create one-, two-, or multi-compartment pharmacokinetic models for model simulation and parameter estimation.
Model Definitions
- What is a SimBiology Model?
A SimBiology model is a dynamic system described by a set of quantities and mathematical expressions. - Species Object
Aspecies object
represents a species, which is the amount of a chemical or entity that participates in reactions. - Doses in SimBiology Models
Use doses to model different dosing regimens. - Variants in SimBiology Models
Use variants to store alternate parameter values and initial conditions of a model. - Definitions and Evaluations of Rules in SimBiology Models
Rules are mathematical expressions that allow you to define or modify model quantities, namely compartment capacity, species amount, or parameter value. - Definitions and Evaluations of Reactions in SimBiology Models
A reaction is a mathematical expression that describe a transformation, transport, or binding process that changes one or more species. - SimBiology Model Matching Policy
SimBiology uses certain criteria and rules to compare models.