ArticleBMC systems biology2013
The systems biology simulation core algorithm.
Article in BMC systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- A physics informed neural network approach to quantify antigen presentation activities at single cell level using omics data.Research square · 2025Article
- Publishing reproducible dynamic kinetic models.Briefings in bioinformatics · 2021Article
- Modeling of the jasmonate signaling pathway in Arabidopsis thaliana with respect to pathophysiology of Alternaria blight in Brassica.Scientific reports · 2017Article
- phraSED-ML: A paraphrased, human-readable adaptation of SED-ML.Journal of bioinformatics and computational biology · 2016Article
- libRoadRunner: a high performance SBML simulation and analysis library.Bioinformatics (Oxford, England) · 2015Article
- SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.BMC systems biology · 2015Article
- Quantitative and logic modelling of molecular and gene networks.Nature reviews. Genetics · 2015Review
- BioModels: Content, Features, Functionality, and Use.CPT: pharmacometrics & systems pharmacology · 2015Article
- SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology.Computation (Basel, Switzerland) · 2014Article
- Improving collaboration by standardization efforts in systems biology.Frontiers in bioengineering and biotechnology · 2014Review
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
backgroundWith the increasing availability of high dimensional time course data for metabolites, genes, and fluxes, the mathematical description of dynamical systems has become an essential aspect of research in systems biology. Models are often encoded in formats such as SBML, whose structure is very complex and difficult to evaluate due to many special cases.
resultsThis article describes an efficient algorithm to solve SBML models that are interpreted in terms of ordinary differential equations. We begin our consideration with a formal representation of the mathematical form of the models and explain all parts of the algorithm in detail, including several preprocessing steps. We provide a flexible reference implementation as part of the Systems Biology Simulation Core Library, a community-driven project providing a large collection of numerical solvers and a sophisticated interface hierarchy for the definition of custom differential equation systems. To demonstrate the capabilities of the new algorithm, it has been tested with the entire SBML Test Suite and all models of BioModels Database.
conclusionsThe formal description of the mathematics behind the SBML format facilitates the implementation of the algorithm within specifically tailored programs. The reference implementation can be used as a simulation backend for Java™-based programs. Source code, binaries, and documentation can be freely obtained under the terms of the LGPL version 3 from http://simulation-core.sourceforge.net. Feature requests, bug reports, contributions, or any further discussion can be directed to the mailing list simulation-core-development@lists.sourceforge.net.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.