(Q36951227)

17 August 2017

Algorithms and software for stochastic simulation of biochemical reacting systems (English)

1 reference

17 August 2017

0 references

0 references

3

Linda R Petzold

1 reference

17 August 2017

Hong Li

1

1 reference

17 August 2017

Yang Cao

series ordinal

2

1 reference

17 August 2017

Daniel T Gillespie

series ordinal

4

1 reference

17 August 2017

26 September 2007

1 reference

17 August 2017

Biotechnology Progress

1 reference

17 August 2017

24

1 reference

17 August 2017

1

1 reference

17 August 2017

56-61

1 reference

Spectral methods for parametric sensitivity in stochastic dynamical systems

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

Efficient step size selection for the tau-leaping simulation method

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

Avoiding negative populations in explicit Poisson tau-leaping

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

Regulation of the eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

Stochastic mechanisms in gene expression

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

Sensitivity analysis of discrete stochastic systems

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

Adaptive explicit-implicit tau-leaping method with automatic tau selection

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

Comment on "nested stochastic simulation algorithm for chemical kinetic systems with disparate rates" [J. Chem. Phys. 123, 194107 (2005)].

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

The finite state projection algorithm for the solution of the chemical master equation

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

On the origins of approximations for stochastic chemical kinetics

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

Accelerated stochastic simulation of the stiff enzyme-substrate reaction

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

Overcoming stiffness in stochastic simulation stemming from partial equilibrium: a multiscale Monte Carlo algorithm.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

The slow-scale stochastic simulation algorithm.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

The numerical stability of leaping methods for stochastic simulation of chemically reacting systems

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

Efficient formulation of the stochastic simulation algorithm for chemically reacting systems

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

the JigCell model builder and run manager.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

Kinetic Monte Carlo simulations with minimal searching.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

Faster Monte Carlo simulations.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2664303

Comment on "Stiffness in stochastic chemically reacting systems: the implicit tau-leaping method" [J. Chem. Phys. 119, 12784 (2003)]

4 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17894470

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/BP070255H

1 reference

17 August 2017

1 reference

17 August 2017

PubMed publication ID

17894470

1 reference