GEPASI statistics

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Citations per year

Number of citations per year for the bioinformatics software tool GEPASI
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Protocols

GEPASI specifications

Information


Unique identifier OMICS_20020
Name GEPASI
Alternative name GEneral PAthway Simulator
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Windows
Programming languages C
License GNU General Public License version 3.0
Computer skills Medium
Version 3.30
Stability Stable
Maintained No

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Publication for GEneral PAthway Simulator

GEPASI citations

 (12)
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

[…] berg et al., ; Bartocci and Lió, ; Olivier et al., ). In this study, we used the following simulation tools: GENESIS/Kinetikit (Wilson et 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 […]

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Inhibition of Non flux Controlling Enzymes Deters Cancer Glycolysis by Accumulation of Regulatory Metabolites of Controlling Steps

2016
Front Physiol
PMCID: 5033973
PMID: 27721794
DOI: 10.3389/fphys.2016.00412
call_split See protocol

[…] The previous kinetic models of glycolysis built for HeLa and AS-30D cells (Marín-Hernández et al., ; Moreno-Sánchez et al., ) using the metabolic simulator GEPASI version 3.3 (Mendes, ) were modified for the HK, HPI, TPI, and GAPDH rate equations as described below. The other rate equations remained unaltered, however, they are here fully described (Supp […]

library_books

In Silico Models for Dynamic Connected Cell Cultures Mimicking Hepatocyte Endothelial Cell Adipocyte Interaction Circle

2014
PLoS One
PMCID: 4266517
PMID: 25502576
DOI: 10.1371/journal.pone.0111946

[…] ield).Literature offers many attempts to model and simulate molecular processes, ranging from genetic regulatory networks to metabolic pathways, and presents several software packages, such as MIST , GEPASI , SCAMP , JARNAC , METAMODEL , E-CELL SE , BIOSPICE . Most of these packages have been developed for the quantitative simulation of biochemical metabolic pathways and are based on the numerical […]

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Genome Scale Modeling in Systems Biology: Algorithms and Resources

2014
Curr Genomics
PMCID: 4009841
PMID: 24822031
DOI: 10.2174/1389202915666140319002221

[…] of current software platforms and projects that face up this as well as an overview about computational requirements for this purpose hav been given. Common systems among others for this purpose are Gepasi, COPASI, E-Cell, ProMoT/Diva, Virtual Cell or the Systems Biology Workbench (SBW) and its add-ons. Some of these tools are shown in (Table ).A comprehensive list of modeling and simulation tool […]

library_books

Software LS MIDA for efficient mass isotopomer distribution analysis in metabolic modelling

2013
BMC Bioinformatics
PMCID: 3720290
PMID: 23837681
DOI: 10.1186/1471-2105-14-218

[…] topomer analyses.In comparison with other existing approaches [-], the combined features in LS-MIDA are not available in standard packages for metabolite modelling such as Metatool [], Yanasquare [], Gepasi [] or FiatFlux [] (here fluxes are predicted after the isotopologue data have been processed). There are two software solutions available for isotopomer data processing, Envelop [] and Isotope […]

library_books

Improved Inhibitor Screening Experiments by Comparative Analysis of Simulated Enzyme Progress Curves

2012
PLoS One
PMCID: 3468632
PMID: 23071631
DOI: 10.1371/journal.pone.0046764

[…] c knowledge in enzyme kinetics. This is in contrast to other more advanced simulation software for more general usage, which are also considerably more complex, e.g. Dynafit , , Fitsim/Kinsim , , and Gepasi , with its successor Copasi .A general observation that emerges when using the simulation tool is that Δmax[P] occurs at the end of the linear phase of the uninhibited reference reaction (cf. […]


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GEPASI institution(s)
Department of Biological Sciences, University of Wales, Aberystwyth, Dyfed, UK
GEPASI funding source(s)
Supported by the JNICT, Portugal (grant BD-197/90-IF).

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