Next Article in Journal
Acknowledgement to Reviewers of Computation in 2014
Previous Article in Journal
Computational and Statistical Analyses of Insertional Polymorphic Endogenous Retroviruses in a Non-Model Organism
Article Menu

Export Article

Open AccessArticle
Computation 2014, 2(4), 246-257; doi:10.3390/computation2040246

SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology

1
Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Sand 1, 72076 Tübingen, Germany
2
Systems Biology Research Group, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Received: 26 September 2014 / Revised: 19 November 2014 / Accepted: 19 November 2014 / Published: 18 December 2014
(This article belongs to the Section Computational Biology)
View Full-Text   |   Download PDF [302 KB, uploaded 18 December 2014]   |  

Abstract

The identification of suitable model parameters for biochemical reactions has been recognized as a quite difficult endeavor. Parameter values from literature or experiments can often not directly be combined in complex reaction systems. Nature-inspired optimization techniques can find appropriate sets of parameters that calibrate a model to experimentally obtained time series data. We present SBMLsimulator, a tool that combines the Systems Biology Simulation Core Library for dynamic simulation of biochemical models with the heuristic optimization framework EvA2. SBMLsimulator provides an intuitive graphical user interface with various options as well as a fully-featured command-line interface for large-scale and script-based model simulation and calibration. In a parameter estimation study based on a published model and artificial data we demonstrate the capability of SBMLsimulator to identify parameters. SBMLsimulator is useful for both, the interactive simulation and exploration of the parameter space and for the large-scale model calibration and estimation of uncertain parameter values. View Full-Text
Keywords: Systems Biology Markup Language (SBML); ordinary differential equation (ODE) modeling; simulation; parameter estimation Systems Biology Markup Language (SBML); ordinary differential equation (ODE) modeling; simulation; parameter estimation
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Dörr, A.; Keller, R.; Zell, A.; Dräger, A. SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology. Computation 2014, 2, 246-257.

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Computation EISSN 2079-3197 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top