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| R2011b Documentation → SimBiology | |
Learn more about SimBiology |
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| Contents | Index |
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SimBiology provides a graphical environment and programmatic tools to model, simulate, and analyze dynamic systems, focusing on pharmacokinetic/pharmacodynamic (PK/PD) and systems biology applications. It provides a block diagram editor for building models, or you can create models programmatically using the MATLAB® language. SimBiology includes a library of common PK models, which you can customize and integrate with mechanistic systems biology models.
A variety of model exploration techniques let you identify optimal dosing schedules and putative drug targets in cellular pathways. SimBiology uses ordinary differential equations (ODEs) and stochastic solvers to simulate the time course profile of drug exposure, drug efficacy, and enzyme and metabolite levels. You can investigate system dynamics and guide experimentation using parameter sweeps and sensitivity analysis. You can also use single subject or population data to estimate model parameters.
SimBiology software provides an integrated environment for modeling biological processes, simulating the dynamic behavior of these processes, and analyzing the model with simulation and experimental data. Biological processes include metabolic, genetic, and signaling pathways with transform, binding, and transport reactions.
You can also create and analyze pharmacokinetic models. For more information see Pharmacokinetic Modeling in the SimBiology documentation.
Model — Design and build models by entering reactions, species, parameters, kinetic laws, rules, and events
Import SBML models created with the SimBiology software or other modeling software that is compliant with the Systems Biology Markup Language (SBML) standard.
Export models you create with the SimBiology desktop to MATLAB and continue your simulations and analysis with command-line functions.
For more information, see Modeling.
Analyze Structure — Verify that the model can be simulated, and use the verification results to fix any incompatibilities in the model. Investigate the structure of your models, including determining conserved moieties, adjacency matrices, and stoichiometry matrices.
For more information, see Structural Analysis.
Simulate and Analyze — Observe changes in species amounts and parameter values over time. Convert your model to a system of differential equations and simulate the model numerically with various differential equation solvers. The deterministic solvers include stiff and nonstiff ordinary differential equation (ODE) solvers. The stochastic solvers include a stochastic simulation algorithm with implicit and explicit tau variations. Perform multiple stochastic ensemble runs, save data from a simulation, compare simulation and experimental data, perform sensitivity analysis, species or parameter scans, and parameter estimation.
For more information, see Simulation and Analysis.
The people who use SimBiology software come from a wide range of areas including biology, systems biology, pharmacology, computer science, and engineering. This product is intended for research scientists, computational biologists, and students who need to develop and study biological pathways at the molecular and systems level, develop custom analysis applications, or implement published pathways, and visualize results.
Industry and Professional — SimBiology software allows you to model, simulate, and analyze biochemical and system pathways for applications in drug discovery and design, target identification, and pharmacokinetic modeling.
Modeling, simulating, and analyzing a biological system can test hypotheses for a pathway, identify side effects caused by drug interactions with a target compound, and identify biochemical pathways that lead to disease.
Academia — Build rigorous, dynamic, quantitative models that allow you to understand and predict system behavior at the molecular level. Build models to explore enzyme kinetics. Leverage the MATLAB foundation to easily manipulate large data sets.
Simulating the dynamic behavior of a model can confirm the validity of the models and identify behaviors and control mechanisms not apparent from studying static models. Validate models experimentally and use the model to predict in vitro and in vivo behavior.
To use SimBiology software, you must first install the following MathWorks® product:
| MATLAB | Provides a command-line interface and an integrated software environment. For instructions, see the MATLAB installation documentation for your platform. If you have installed MATLAB and want to check which other MathWorks products are installed, enter ver in the MATLAB Command Window. |
Statistics Toolbox™ (Version 7.0 (R2008b) or later) | Provides fitting tools including functions required to analyze nonlinear mixed effects (NLME).
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| Global Optimization Toolbox | Solve optimization problems using genetic and direct search algorithms. If this toolbox is installed, you can use various genetic and direct search algorithms for parameter estimation. If this toolbox is not installed, the software uses the optimization algorithms available in MATLAB. | |
| Optimization Toolbox™ | Optimization Toolbox extends the MATLAB technical computing environment with tools and widely used algorithms for standard and large-scale optimization. These algorithms solve constrained and unconstrained continuous and discrete problems. If the Optimization Toolbox product is installed, you can use some algorithms included this product for parameter estimation in SimBiology software. If the Optimization Toolbox product is not installed, the software uses the optimization algorithms available in MATLAB. | |
| C Compiler | Required to prepare the model for accelerating simulations. For a list of supported compilers, see Supported and Compatible Compilers. |
| Bioinformatics Toolbox™ | Read, analyze, and visualize genomic, proteomic, and microarray data. |
 | Introduction | Integrating SimBiology Models into Your Existing Workflow |  |
See how to analyze, visualize, and model biological data and systems using MathWorks products.
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