Skip Navigation



Bioinformatics Advance Access published online on August 22, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl443
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
22/21/2704    most recent
btl443v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Zi, Z.
Right arrow Articles by Klipp, E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Zi, Z.
Right arrow Articles by Klipp, E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received June 15, 2006
Revised August 2, 2006
Accepted August 14, 2006

Applications note

SBML-PET: a systems biology markup language based parameter estimation tool

Zhike Zi 1 and Edda Klipp 1 *

1 Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany

* To whom correspondence should be addressed.
Edda Klipp, E-mail: klipp{at}molgen.mpg.de


  Abstract

Summary: The estimation of model parameters from experimental data remains a bottleneck for a major breakthrough in systems biology. We present a Systems Biology Markup Language (SBML) based Parameter Estimation Tool (SBML-PET). The tool is designed to enable parameter estimation for biological models including signaling pathways, gene regulation networks, and metabolic pathways. SBML-PET supports import and export of the models in the SBML format. It can estimate the parameters by fitting a variety of experimental data from different experimental conditions. SBML-PET has a unique feature of supporting event definition in the SMBL model. SBML models can also be simulated in SBML-PET. Stochastic Ranking Evolution Strategy (SRES) is incorporated in SBML-PET for parameter estimation jobs. A classic ODE Solver called ODEPACK is used to solve the Ordinary Differential Equation (ODE) system.

Availability: http://sysbio.molgen.mpg.de/SBML-PET/. The website also contains detailed documentation for SBML-PET.

Associate Editor: Satoru Miyano
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J R Soc InterfaceHome page
L. Endler, N. Rodriguez, N. Juty, V. Chelliah, C. Laibe, C. Li, and N. Le Novere
Designing and encoding models for synthetic biology
J R Soc Interface, August 6, 2009; 6(Suppl_4): S405 - S417.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
A. Csikasz-Nagy
Computational systems biology of the cell cycle
Brief Bioinform, July 1, 2009; 10(4): 424 - 434.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Kumar, B. C. Han, Z. Shi, J. Jia, Y. P. Wang, Y. T. Zhang, L. Liang, Q. F. Liu, Z. L. Ji, and Y. Z. Chen
Update of KDBI: Kinetic Data of Bio-molecular Interaction database
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D636 - D641.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
N. Erjavec, M. Cvijovic, E. Klipp, and T. Nystrom
Selective benefits of damage partitioning in unicellular systems and its effects on aging
PNAS, December 2, 2008; 105(48): 18764 - 18769.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. Quach, N. Brunel, and F. d'Alche-Buc
Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference
Bioinformatics, December 1, 2007; 23(23): 3209 - 3216.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.