COPASI specifications

Information


Unique identifier OMICS_06012
Name COPASI
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 4.15
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/COPASI

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Maintainer


  • person_outline Pedro Mendes <>

Publications for COPASI

COPASI in publications

 (225)
PMCID: 5938413
PMID: 29765315
DOI: 10.3389/fninf.2018.00020

[…] al., ; bower and beeman, ; bhalla and iyengar, ; bhalla, , ), gepasi (mendes, , ; mendes and kell, ), jarnac/jdesigner (sauro, , ), xppaut (ermentrout, ), simtool (aho, ), dizzy (ramsey et al., ), copasi (hoops et al., ), neuron (carnevale and hines, ), systems biology toolbox (schmidt and jirstrand, ), and narrator (mandel et al., ) (see table ). here, we do not provide any detailed overview […]

PMCID: 5933457
PMID: 29439915
DOI: 10.1016/j.bmc.2018.02.002

[…] interactions between the lbd and fluorescein-labeled co activator, the binding assay data were interpreted by simulating these coupled chemical reactions using the biochemical simulator copasi version 4.3., , molecular structures of all compounds (atra, gz18, gz22, gz23, gz24 and gz25) were generated using spartan ‘14 (wavefunction inc., irvine, ca). these were minimized using […]

PMCID: 5855834
PMID: 29462984
DOI: 10.3390/ijms19020612

[…] s−1. a constant adenylate cyclase (ac) activity was assumed. the fitting was also restricted by pde2 activity being less than 10% of the pde5 activity at 1 µm cgmp []., the model was implemented in copasi 4.11 (build 65, www.copasi.org), which uses an lsoda ode-solver for stiff and non-stiff systems [,]. the absolute tolerance was set to 1.0 × 10−12. the models will be deposited […]

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

[…] true if diffusion constants were reduced by half. thus, this simple model resembles a well-mixed system and an ode model will provide a good test standard., we coded a deterministic ode system in copasi [] and compared results with our stochastic model using the same kinetics. we found that the stochastic model and the ode copasi model exhibited similar time courses for all cam binding state […]

PMCID: 5775275
PMID: 29379512
DOI: 10.3389/fpls.2017.02237

[…] generate differential equations to describe the reaction stages, based on mass action kinetics. experimental data from the reactions catalyzed by taasn1 and taasn2 were entered into the model using copasi, enabling values to be determined for kinetic parameters. both the reaction data and the modeling showed that the enzymes continued to produce glutamate even when the synthesis of asparagine […]


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COPASI institution(s)
Manchester Centre for Integrative Systems Biology, University of Manchester, UK

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