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SimBiology Product Overview

Integrated Environment

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 Functionality.

  • 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 What is a Model?.

  • 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 Overview of 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.

Expected Users

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.

Required Software

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.

Optional Software

Statistics Toolbox™ (Version 7.0 (R2008b) or later)

Provides fitting tools including functions required to analyze nonlinear mixed effects (NLME).

    Note:   Statistics Toolbox is required to use SimBiology to perform population fitting using sbionlmefit or sbionlmefitsa, or to perform individual fitting using sbionlinfit.

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 CompilerRequired to prepare the model for accelerating simulations. For a list of supported compilers, see Supported and Compatible Compilers.

Related Software

Bioinformatics Toolbox™

Read, analyze, and visualize genomic, proteomic, and microarray data.

Compiler Setup

To prepare your models for accelerated simulations, install and set up a compiler:

  1. Install a C compiler (if one is not already installed on your system). For a current list of supported compilers, see Supported and Compatible Compilers atwww.mathworks.com.

  2. Ensure that any user-defined functions in your model can be used for code generation from MATLAB, so they can convert to compiled C. For more information, see Code Generation from MATLAB Code.

    Tip   On 32-bit Windows® platforms, the LCC compiler is automatically installed. However, for better performance of the acceleration functionality, you may want to install a supported compiler other than LCC, and it will be selected automatically.

    On 64-bit Windows platforms, if you have not installed another compiler, SimBiology uses the LCC64 compiler for model accelerations. If you have installed another supported compiler, it will be selected automatically.

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