Genetic programming: on the programming of computers by means of natural selection
Genetic programming: on the programming of computers by means of natural selection
Journal of Computer and System Sciences
A New Class of Symbolic Abstract Neural Nets: Tissue P Systems
COCOON '02 Proceedings of the 8th Annual International Conference on Computing and Combinatorics
System Modeling in Cellular Biology: From Concepts to Nuts and Bolts
System Modeling in Cellular Biology: From Concepts to Nuts and Bolts
Efficient stochastic sensitivity analysis of discrete event systems
Journal of Computational Physics
EvoBIO '09 Proceedings of the 7th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
Stochastic Simulations on a Grid Framework for Parameter Sweep Applications in Biological Models
HIBI '09 Proceedings of the 2009 International Workshop on High Performance Computational Systems Biology
The Oxford Handbook of Membrane Computing
The Oxford Handbook of Membrane Computing
Simulation methods in systems biology
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Computing with energy and chemical reactions
Natural Computing: an international journal
Tau leaping stochastic simulation method in p systems
WMC'06 Proceedings of the 7th international conference on Membrane Computing
A novel variant of p systems for the modelling and simulation of biochemical systems
WMC'09 Proceedings of the 10th international conference on Membrane Computing
Review: Stochastic approaches for modelling in vivo reactions
Computational Biology and Chemistry
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BioSim Ware is a novel software that provides a user-friendly framework for the modeling and stochastic simulation of complex biological systems, ranging from cellular processes to population phenomena. BioSim Ware implements several stochastic algorithms to simulate the dynamics of single or multivolume models, as well as automatic tools to analyze the effect of variation of the system parameters. BioSim Ware supports SBML format, and can automatically convert stochastic models into the corresponding deterministic formulation. The main features of BioSim Ware are presented in this paper, together with some applications which highlight the most relevant aspects of the computational tools that it provides.