Comparing Simulation Results of SBML Capable Simulators

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2008 Jun 27

PMID 18579569

Citations 15

Authors

Frank T Bergmann

Herbert M Sauro

Affiliations

Soon will be listed here.

Abstract

Motivation: Simulations are an essential tool when analyzing biochemical networks. Researchers and developers seeking to refine simulation tools or develop new ones would benefit greatly from being able to compare their simulation results.

Summary: We present an approach to compare simulation results between several SBML capable simulators and provide a website for the community to share simulation results.

Availability: The website with simulation results and additional material can be found under: http://sys-bio.org/sbwWiki/compare. The software used to generate the simulation results is available on the website for download.

Citing Articles

From FAIR to CURE: Guidelines for Computational Models of Biological Systems.

Sauro H, Agmon E, Blinov M, Gennari J, Hellerstein J, Heydarabadipour A ArXiv. 2025; .

PMID: 40034129 PMC: 11875277.

SBML Level 3: an extensible format for the exchange and reuse of biological models.

Keating S, Waltemath D, Konig M, Zhang F, Drager A, Chaouiya C Mol Syst Biol. 2020; 16(8):e9110.

PMID: 32845085 PMC: 8411907. DOI: 10.15252/msb.20199110.

Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures.

Manninen T, Acimovic J, Havela R, Teppola H, Linne M Front Neuroinform. 2018; 12:20.

PMID: 29765315 PMC: 5938413. DOI: 10.3389/fninf.2018.00020.

Network modelling of gene regulation.

Ho J, Charleston M Biophys Rev. 2017; 3(1):1-13.

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How to test bioinformatics software?.

Kamali A, Giannoulatou E, Chen T, Charleston M, McEwan A, Ho J Biophys Rev. 2017; 7(3):343-352.

PMID: 28510230 PMC: 5425734. DOI: 10.1007/s12551-015-0177-3.

References

Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N . COPASI--a COmplex PAthway SImulator. Bioinformatics. 2006; 22(24):3067-74. DOI: 10.1093/bioinformatics/btl485. View

Le Novere N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H . BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 2005; 34(Database issue):D689-91. PMC: 1347454. DOI: 10.1093/nar/gkj092. View

Machne R, Finney A, Muller S, Lu J, Widder S, Flamm C . The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. Bioinformatics. 2006; 22(11):1406-7. DOI: 10.1093/bioinformatics/btl086. View

Evans T, Gillespie C, Wilkinson D . The SBML discrete stochastic models test suite. Bioinformatics. 2007; 24(2):285-6. DOI: 10.1093/bioinformatics/btm566. View

Shapiro B, Hucka M, Finney A, Doyle J . MathSBML: a package for manipulating SBML-based biological models. Bioinformatics. 2004; 20(16):2829-31. PMC: 1409765. DOI: 10.1093/bioinformatics/bth271. View