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Dynetica specifications

Information


Unique identifier OMICS_11486
Name Dynetica
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 2.0
Stability Beta
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Lingchong You

Publication for Dynetica

Dynetica citations

 (3)
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Simulation of E. coli Gene Regulation including Overlapping Cell Cycles, Growth, Division, Time Delays and Noise

2013
PLoS One
PMCID: 3637171
PMID: 23638057
DOI: 10.1371/journal.pone.0062380
call_split See protocol

[…] Currently, there are several popular simulation tools available, such as E_Cell , Dizzy , Virtual Cell , CellLine , STOCHSIM and Dynetica . These tools are user-friendly and can work well on many biochemical networks and simplified gene regulatory processes. However, these tools simplify gene regulatory processes and are not so […]

library_books

Cascading signaling pathways improve the fidelity of a stochastically and deterministically simulated molecular RS latch

2009
BMC Syst Biol
PMCID: 3225856
PMID: 19615050
DOI: 10.1186/1752-0509-3-72

[…] rate, kf, or dissociation of one molecule into others with a rate, kr. The user can then specify time points for the addition or removal of molecules.Deterministic simulations were carried out using Dynetica []. […]

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Sensing and Integration of Erk and PI3K Signals by Myc

2008
PLoS Comput Biol
PMCID: 2265471
PMID: 18463697
DOI: 10.1371/journal.pcbi.1000013

[…] Based on the reaction network outlined in , we developed a kinetic mathematical model in Dynetica, a graphics-based, integrated simulation platform . We further simplified the model by lumping the sequential destabilization processes together into the phosphorylation rate constant for Myc […]


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Dynetica institution(s)
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA; Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, USA; Department of Chemical Engineering, University of Wisconsin-Madison, Madison, WI, USA
Dynetica funding source(s)
Funding of this work was provided by the National Science Foundation.

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