Abstract
We provide the description for the nondeterministic waiting time (NWT) algorithm, a biochemical modeling approach based on the membrane systems paradigm of computation. The technique provides a unique (different to Gillespie’s algorithm or ODE modeling) perspective on the biochemical evolution of the cell. That is, depending on the reactions and molecular multiplicities of a given model, our simulator is capable of producing results comparable to the alternative techniques—continuous and deterministic or discrete and stochastic. Some results for sample models are given, illustrating the differences between the NWT algorithm, the Gillespie algorithm, and the solutions to systems of ordinary differential equations. We have previously used this simulation technique to address issues surrounding Fas-induced apoptosis in cancerous cells and so-called latent HIV-infected cells.
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For the remainder of the paper, we will interchangeably use reaction/rule and species/protein.
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Acknowledgements
Research was partially supported by the National Science Foundation Grant CCF-0523572, INBRE Program of the NCRR (a division of NIH), support from CNCSIS grant RP-13, support from CNMP grant 11-56 /2007, support from the Ministerio de Ciencia e Innovación (MICINN), Spain, under project TIN2009-14421 and the program I3, by the Comunidad de Madrid (grant No. CCG09-UPM to the LIA research group), and by the European Commission funding through the Seventh Framework Programme grant BACTOCOM (project reference: 248919).
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Jack, J., Păun, A. & Rodríguez-Patón, A. A review of the nondeterministic waiting time algorithm. Nat Comput 10, 139–149 (2011). https://doi.org/10.1007/s11047-010-9195-z
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DOI: https://doi.org/10.1007/s11047-010-9195-z