simbiology | Open SimBiology Model Builder |
sbiomodel | Construct model object |
sbioroot | Return SimBiology root object |
sbioreset | Delete all model objects |
sbioselect | Search for objects with specified constraints |
sbiolastwarning | SimBiology last warning message |
sbiolasterror | SimBiology last error message |
verify | Validate and verify SimBiology model |
addcompartment | Create compartment object |
addobservable | Add observable object to SimBiology model |
addspecies | Create species object and add to compartment object within model object |
addparameter | Create parameter object and add to model or kinetic law object |
addreaction | Create reaction object and add to model object |
addrule | Create rule object and add to model object |
addevent | Add event object to model object |
findUnusedComponents | Find unused species, parameters, and compartments in a model |
findUsages(species,parameter,compartment) | Find out how a species, parameter, or compartment is used in a model |
findUsages | Find out how observable object is used in SimBiology model |
findUsages(unit,unitprefix) | Find out how a unit or unit prefix is used |
findUsages(AbstractKineticLaw) | Find out how an AbstractKineticLaw object is used |
updateInitialAssignments | Update initial assignment rules to remove order dependencies |
Model | Model and component information |
Observable | Object containing expression for post-simulation calculations |
Compartment | Object containing compartment information |
Species | Object containing species information |
Parameter | Parameter and scope information |
Reaction | Object containing model reaction information |
KineticLaw | Kinetic law information for reaction |
Rule | Hold rule for species and parameters |
Event | Store event information |
Root | Hold models, unit libraries, and abstract kinetic law libraries |
PKModelDesign object | Helper object to construct pharmacokinetic model |
PKCompartment object | Used by PKModelDesign to create SimBiology model |
PKModelMap object | Define SimBiology model components’ roles |
construct | Construct SimBiology model from PKModelDesign object |
addCompartment | Add compartment to PKModelDesign object |
SimBiology Model Builder | Build QSP, PK/PD, and mechanistic systems biology models interactively |
SimBiology Model Analyzer | Analyze QSP, PK/PD, and mechanistic systems biology models |
Create Model of Receptor-Ligand Kinetics
This example shows how to create and simulate a simple model of receptor-ligand kinetics using the SimBiology Model Builder and SimBiology Model Analyzer apps.
Incorporate sodium-glucose co-transporter 2 (SGLT2) receptor inhibition by a hypothetical compound into an existing glucose-insulin model.
This example shows how to construct a simple model programmatically.
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.
A SimBiology® model is a dynamic system described by a set of quantities and mathematical expressions.
You can view the system of equations that SimBiology creates when you build a model using reactions, rules, events, variants, and doses.
A species object
represents a species, which is the amount of a chemical or entity that participates in reactions.
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.
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.
In SimBiology, an event is a discrete transition in value of a quantity or expression in a model.
Use doses to model different dosing regimens.
SimBiology lets you create one-, two-, or multi-compartment pharmacokinetic models for model simulation and parameter estimation.
SimBiology lets you find species, parameters, compartments, and observables that are not used in a model and find out how they are used.
Evaluation of Model Component Names in Expressions
SimBiology follows some precedence rules when evaluating names in expressions.