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ChemCell specifications

Information


Unique identifier OMICS_28294
Name ChemCell
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data The geometry of the cell and a list of chemical species and reactions with their associated diffusion coefficients and reaction rates.
Output data The species concentrations in time and space.
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainers


  • person_outline Steven Plimpton
  • person_outline Alex Slepoy

Additional information


http://chemcell.sandia.gov/doc/Manual.html

Publication for ChemCell

ChemCell citations

 (7)
library_books

Simulation tools for particle based reaction diffusion dynamics in continuous space

2014
BMC Biophys
PMCID: 4347613
PMID: 25737778
DOI: 10.1186/s13628-014-0011-5

[…] ticle positions explicitly in continuous physical space (as opposed to lattice based approaches) and allow reactions between them. These approaches include the following ten tools: CDS [], Cell++ [], ChemCell [], eGFRD [] (derived from GFRD [],[] and E-Cell []), Klann et al. [],[], MCell [],[], ReaDDy [], Rigdway et al. [], Smoldyn [],[] and SRSim [].The tools discussed here allow the modeling of […]

library_books

Using cellzilla for plant growth simulations at the cellular level

2013
Front Plant Sci
PMCID: 3797531
PMID: 24137172
DOI: 10.3389/fpls.2013.00408

[…] vide general purpose platforms; examples include MCell (Stiles and Bartol, ), designed originally to simulate the synaptic junction; Smoldyn (Andrews, ), primarily emphasizing nano-scale specificity; ChemCell (Plimpton and Slepoy, ), which models protein networks within cells; and CompuCell3D (Cickovski et al., ) which focuses on cellular function.Of particular interest is the use of rule-based mo […]

library_books

A Machine Learning Method for the Prediction of Receptor Activation in the Simulation of Synapses

2013
PLoS One
PMCID: 3720878
PMID: 23894367
DOI: 10.1371/journal.pone.0068888

[…] extracellular and membrane interactions or ion channel permeation , while some biochemical processes, such as molecular reaction-diffusion, require Monte Carlo particle-based simulators like MCell , ChemCell or Smoldyn . For the modeling of longitudinal ionic diffusion up to the level of neuronal circuits, some simulators such as NEURON , GENESIS or similar software (reviewed in ) use various a […]

library_books

Rule based spatial modeling with diffusing, geometrically constrained molecules

2010
BMC Bioinformatics
PMCID: 2911456
PMID: 20529264
DOI: 10.1186/1471-2105-11-307

[…] kages is available for the spatial simulation of explicitly defined reaction networks. Examples are MCell [], Cell++ [], Virtual Cell [,], SmartCell [], mesoRD [], Smoldyn [], Project Cybercell [] or ChemCell []. While our notion of "space" in this paper focuses on the particle and macromolecule geometry, also the geometric aspects of the reactor might be of interest [,].But the combination of spa […]

library_books

Detailed Simulations of Cell Biology with Smoldyn 2.1

2010
PLoS Comput Biol
PMCID: 2837389
PMID: 20300644
DOI: 10.1371/journal.pcbi.1000705

[…] akes these methods ideal for systems that can have long delays between individual reactions, but very computationally intensive for most cellular processes .The dominant particle based simulators are ChemCell , MCell ,, and Smoldyn , (see also ). These programs have many common features, but differ in other features and in the quantitative accuracy of their simulations. Of the three, ChemCell has […]

library_books

Probability distributed time delays: integrating spatial effects into temporal models

2010
BMC Syst Biol
PMCID: 2847994
PMID: 20202198
DOI: 10.1186/1752-0509-4-19

[…] d to a variety of scenarios of molecular translocation and association processes, reaching a good compromise between accuracy and computational costs. Our simulations, as compared to those yielded by ChemCell (a single-particle tracking algorithm developed in Sandia National Laboratories [], see Methods), show high accuracy while being computed several orders of magnitude faster. Additionally, we […]

Citations

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ChemCell institution(s)
Sandia National Laboratories, Albuquerque, NM, USA
ChemCell funding source(s)
Supported by the US Department of Energy’s Genomics: GTL program under project, “Carbon Sequestration in Synechococcus Sp. From Molecular Machines to Hierarchical Modeling”.

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