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GEPASI specifications

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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

 (20)
library_books

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

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

[…] 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 […]

library_books

Surface Expression, Function, and Pharmacology of Disease Associated Mutations in the Membrane Domain of the Human GluN2B Subunit

2018
PMCID: 5897658
PMID: 29681796
DOI: 10.3389/fnmol.2018.00110

[…] of 1 mm glutamate., the channel open probability (po) was assessed from the kinetics of the mk-801 (1 μm) inhibition of responses to 1 mm glutamate that was fitted to the kinetic model using gepasi software (version 3.21; mendes, , ; mendes and kell, ). the glutamate binding steps were not considered because, in the presence of 1 mm glutamate, nmdar exists with high probability […]

library_books

Activity Regulation by Fibrinogen and Fibrin of Streptokinase from Streptococcus Pyogenes

2017
PMCID: 5268773
PMID: 28125743
DOI: 10.1371/journal.pone.0170936

[…] proposed by bock and co-workers (e.g.[]), as described in results. parameters for rate constants and reactant concentrations for this model were entered into the simulation software package gepasi [, ] and time courses simulated to generate data for pna absorbance generation over time. to match model simulation and data collection methods as closely as possible, rates of pm generation […]

library_books

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

2016
PMCID: 5033973
PMID: 27721794
DOI: 10.3389/fphys.2016.00412

[…] by using human aldh2 and saturating nad+., 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 […]

library_books

Information theoretic approaches for inference of biological networks from continuous valued data

2016
PMCID: 5013667
PMID: 27599566
DOI: 10.1186/s12918-016-0331-y

[…] l for confident assertions regarding their true underlying topology []. instead, the ‘gold standard’ mendes models apply a simplified, bottom-up model (multiplicative hill kinetics [, ], simulated in gepasi []) to approximate transcriptional activity, as illustrated in fig. : 5\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepacka […]

library_books

A Futile Redox Cycle Involving Neuroglobin Observed at Physiological Temperature

2015
PMCID: 4581342
PMID: 26305249
DOI: 10.3390/ijms160820082

[…] form of the protein, ngb2+-o2 the oxygenated form of the protein and ngb3+ the oxidised form of the protein. a set of equations representing was developed andsimulated in the computer package gepasi []., the full futile redox cycle shown in was likewise simulated employing gepasi., in autoxidation rate calculations the instantaneous oxygen concentration was determined […]


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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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