Smoldyn statistics

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Smoldyn specifications

Information


Unique identifier OMICS_14947
Name Smoldyn
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 2.54
Stability Stable
Maintained Yes

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  • person_outline Steven Andrews <>

Publication for Smoldyn

Smoldyn in publications

 (45)
PMCID: 5938413
PMID: 29765315
DOI: 10.3389/fninf.2018.00020

[…] ), or track each molecule individually in a certain volume with brownian dynamics combined with a monte carlo procedure for reaction events, such as mcell (stiles and bartol, ; kerr et al., ) and smoldyn (andrews et al., ). few studies to compare different reaction-diffusion tools exist (dobrzyński et al., ; oliveira et al., ; schöneberg et al., ). in this study, however, […]

PMCID: 5864077
PMID: 29529021
DOI: 10.1371/journal.pcbi.1006016

[…] approaches, such as the spatial gillespie algorithm [–]; exact brownian dynamics, such as green’s function reaction dynamics [,]; and direct particle-based simulations, as implemented in smoldyn and mcell [,]. we cannot adequately cover the full spectrum of approaches and computational tools here, but refer the reader to excellent reviews that describe the theoretical underpinnings […]

PMCID: 5799302
PMID: 29402931
DOI: 10.1038/s41467-018-02864-2

[…] side. we thus investigated the accuracy of the analysis methods by simulating the various experiments and comparing input with “observed” diffusion coefficients. all simulations were performed in smoldyn, which simulates particles undergoing random walks on specified geometries. further analysis of simulated trajectories was performed in mathematica. for the frap simulations we used a sphere […]

PMCID: 5814094
PMID: 29401454
DOI: 10.1371/journal.pcbi.1005946

[…] be modeled. to study the ca2+-calmodulin-camkii reaction network with detailed kinetics while including the effect of diffusion, we have customized an existing stochastic particle-based simulator, smoldyn, to manage the problem of combinatorial explosion. with this new method, spatial and temporal aspects of the signaling network can be studied without compromising biochemical details. we used […]

PMCID: 5714874
PMID: 29250071
DOI: 10.3389/fimmu.2017.01692

[…] immunological synapse involving b cells (–) or t cells (, ). besides this work on immune cell receptor–ligand interaction, there exist software packages for the simulation of various type, such as smoldyn () and mcell (, ). even though these simulators represent molecular diffusion in lattice-free continuous space, they lack features that are essential in the present study. for example, […]


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Smoldyn institution(s)
Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Isaac Newton Institute for Mathematical Sciences, Cambridge, UK
Smoldyn funding source(s)
This work was supported by a Simons Foundation grant awarded and by EPSRC grant EP/K032208/1 awarded to the Isaac Newton Institute.

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