COPASI statistics

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Citations per year

Number of citations per year for the bioinformatics software tool COPASI
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Tool usage distribution map

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Protocols

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

Versioning


No version available

Maintainer


  • person_outline Pedro Mendes

Publications for COPASI

COPASI citations

 (295)
library_books

Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures

2018
Front Neuroinform
PMCID: 5938413
PMID: 29765315
DOI: 10.3389/fninf.2018.00020

[…] lts needed several requirements to be fulfilled. First, the usability of the simulation tools and existence of proper manuals were crucial. For example, even beginners were able to use Dizzy, Gepasi, Copasi, and Jarnac/JDesigner, but former experience in MATLABⓇ was required for Systems Biology Toolbox and SimTool. Second, the lack of standards and interfaces between tools also made the comparabil […]

library_books

Probing biological activity through structural modelling of ligand receptor interactions of 2,4 disubstituted thiazole retinoids

2018
PMCID: 5933457
PMID: 29439915
DOI: 10.1016/j.bmc.2018.02.002

[…] and-dependent 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., […]

library_books

PhysiCell: An open source physics based cell simulator for 3 D multicellular systems

2018
PLoS Comput Biol
PMCID: 5841829
PMID: 29474446
DOI: 10.1371/journal.pcbi.1005991

[…] We will develop SBML (systems biology markup language) importers for molecular-scale biology, most likely by the C code generation features in COPASI [] or libRoadrunner []. This will make it straightforward to integrate systems of ODEs to individual cells. We will add new cycle models for flow cytometry-driven problems (G1, S, and G2/M phas […]

library_books

Mathematical Modelling of Nitric Oxide/Cyclic GMP/Cyclic AMP Signalling in Platelets

2018
Int J Mol Sci
PMCID: 5855834
PMID: 29462984
DOI: 10.3390/ijms19020612

[…] 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 in the biomodels […]

library_books

Biophysical attributes that affect CaMKII activation deduced with a novel spatial stochastic simulation approach

2018
PLoS Comput Biol
PMCID: 5814094
PMID: 29401454
DOI: 10.1371/journal.pcbi.1005946

[…] also 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 s […]

library_books

Genomic, Biochemical, and Modeling Analyses of Asparagine Synthetases from Wheat

2018
Front Plant Sci
PMCID: 5775275
PMID: 29379512
DOI: 10.3389/fpls.2017.02237

[…] l for the reactions catalyzed by asparagine synthetases TaASN1 and TaASN2 was constructed using the SNOOPY® tool () for designing, animating, and simulating Petri Nets. The model was then exported to Copasi 4.16 (Build 104; ). Data for the reaction parameters were taken from the Brenda enzyme database. […]


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

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