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The systems biology simulation core algorithm.

Roland Keller1, Alexander Dörr, Akito Tabira

  • 1Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.

BMC Systems Biology
|July 6, 2013
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Summary
This summary is machine-generated.

An efficient algorithm solves Systems Biology Markup Language (SBML) models described by ordinary differential equations. This algorithm, implemented in the Systems Biology Simulation Core Library, facilitates complex systems biology research.

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Area of Science:

  • Systems Biology
  • Computational Biology
  • Mathematical Modeling

Background:

  • High-dimensional time course data in systems biology necessitates robust mathematical descriptions of dynamical systems.
  • Systems Biology Markup Language (SBML) is a common format for encoding these models, but its complexity poses evaluation challenges.

Purpose of the Study:

  • To develop and describe an efficient algorithm for solving Systems Biology Markup Language (SBML) models.
  • To provide a flexible reference implementation of the algorithm within the Systems Biology Simulation Core Library.

Main Methods:

  • Formal mathematical representation of SBML models interpreted as ordinary differential equations.
  • Detailed explanation of the algorithm, including preprocessing steps.
  • Implementation within the Systems Biology Simulation Core Library, featuring numerical solvers and custom differential equation system interfaces.

Main Results:

  • An efficient algorithm for solving SBML models represented by ordinary differential equations has been developed.
  • The algorithm was tested against the entire SBML Test Suite and all models in the BioModels Database, demonstrating its capabilities.
  • A flexible reference implementation is available as part of the Systems Biology Simulation Core Library.

Conclusions:

  • The formal mathematical description aids in implementing the algorithm in specialized programs.
  • The reference implementation serves as a simulation backend for Java™-based applications.
  • Source code and documentation are available under LGPL v3; community contributions are welcomed via mailing list.