FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis
Computational Biology and Chemistry
Metabolica: A statistical research tool for analyzing metabolic networks
Computer Methods and Programs in Biomedicine
International Journal of Systems Science - Dynamics Analysis of Gene Regulatory Networks
Design of a framework for modeling, integration and simulation of physiological models
Computer Methods and Programs in Biomedicine
Spatial modeling in cell biology at multiple levels
Proceedings of the Winter Simulation Conference
Probabilistic model checking of the PDGF signaling pathway
Transactions on Computational Systems Biology XIV
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Summary: We present a Systems Biology Toolbox for the widely used general purpose mathematical software MATLAB. The toolbox offers systems biologists an open and extensible environment, in which to explore ideas, prototype and share new algorithms, and build applications for the analysis and simulation of biological and biochemical systems. Additionally it is well suited for educational purposes. The toolbox supports the Systems Biology Markup Language (SBML) by providing an interface for import and export of SBML models. In this way the toolbox connects nicely to other SBML-enabled modelling packages. Models are represented in an internal model format and can be described either by entering ordinary differential equations or, more intuitively, by entering biochemical reaction equations. The toolbox contains a large number of analysis methods, such as deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis and bifurcation analysis. Availability: The Systems Biology Toolbox for MATLAB is open source and freely available from http://www.sbtoolbox.org. The website also contains a tutorial, extensive documentation and examples. Contact: henning@fcc.chalmers.se