SimBiology 2.1.2

Category Cross-Omics>Pathway Analysis/Tools

Abstract SimBiology extends MATLAB (see Note 2) with tools for modeling, simulating, and analyzing biochemical pathways. You can create your own block diagram model using predefined blocks. You can manually enter in species, parameters, reactions, rules, kinetic laws, and units, or read in Systems Biology Mark-Up Language (SBML) models. SimBiology lets you simulate a model using stochastic or deterministic solvers and analyze your pathway with tools such as parameter estimation and sensitivity analysis. You can also graphically view the pathway in the block diagram explorer. A graphical user interface (GUI) provides access to most command-line functionality and lets you create and manage reactions, species, parameters, rules, units, and submodels.

Key features include:

Block diagram editor for constructing pathways -

The block diagram editor lets you - 1) Create a model using predefined blocks for species, parameters, and plots; 2) Lay the model out automatically; 3) View outputs from your model using the predefined plot block; 4) Create a library of user-defined blocks.

Tools for parameter estimation and sensitivity analysis -

Parameter Estimation - With SimBiology you can calibrate the response of your model to experimental data, eliminating the need to tune model parameters by trial and error or to develop your own optimization routines. You can estimate parameters with MATLAB or by using optimization algorithms in the Optimization Toolbox (available separately - see Note 3).

Sensitivity Analysis - Product lets you calculate the sensitivities of all system species relative to the specified parameters and species initial conditions. This analysis helps you better understand the functionality of the network and lets you determine experimental parameters and conditions of highest importance.

Sensitivity analysis options in SimBiology include - 1) Species normalization for computed sensitivities - full dedimensionalization, normalization relative to the species only, or no normalization; 2) Input factors - species initial conditions or parameters to which sensitivities will be calculated.

Stochastic, stiff deterministic, and nonstiff deterministic solvers -

Stochastic Solvers - SimBiology provides three types of stochastic solvers: a stochastic simulation algorithm (SSA), explicit tau-leaping, and implicit tau-leaping.

SSA - simulates one reaction at a time based on the propensity function for each reaction.

Explicit tau-leaping - automatically chooses the time interval, tau, so that the relative change in the propensity function is less than a user- defined error tolerance. Often used for solving large, numerically nonstiff systems, the explicit tau-leaping solver provides faster simulation speed than SSA, but represents an approximation.

Implicit tau-leaping - is similar to the explicit tau-leaping solver but works optimally with numerically stiff systems. When solving numerically stiff systems, this solver remains stable at larger time intervals than the explicit tau-leaping solver.

Deterministic Solvers -

Stiff solvers - include numerical differentiation formulas (NDFs), a modified Rosenbrock formula of order 2, an implementation of the trapezoidal rule using a free interpolant, and an implementation of TR- BDF2 (an implicit Runge-Kutta formula with a first stage that is a trapezoidal rule step and a second stage that is a backward differentiation formula of order 2).

Nonstiff solvers - include Dormand-Prince, Bogacki-Shampine, and Adams-Bashforth-Moulton.

Model components, including species, parameters, kinetic laws, reactions, algebraic rules, and units -

You can create a model by - 1) Entering equations and relevant parameters into the graphical user interface; 2) Dragging-and-dropping predefined species and reactions blocks in the block diagram editor; 3) Importing files that comply with SBML Level 2 version 1.

Note 1: The predefined species and reaction blocks are user- configurable and can be stored in libraries or used to create standardized blocks or elements. Product lets you work with the built-in kinetic laws and units or create your own. Both built-in and user-defined kinetic laws are stored in libraries for easy reuse and distribution.

Project files that store models with simulation settings and user- defined plot types -

Models created in SimBiology can be saved as project files. These files store all information related to the project, including models, kinetic law and units libraries, simulation settings, and simulation results. Models can also be exported to the SBML format.

Note 2: MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and FORTRAN.

Note 3: The Optimization Toolbox extends the MATLAB technical computing environment with tools and widely used algorithms for standard and large-scale optimization.

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Manufacturer Web Site The MathWorks, Inc.

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G6G Abstract Number 20026

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