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GEPASI specifications


Unique identifier OMICS_20020
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




No version available

Publication for GEneral PAthway Simulator

GEPASI citations


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

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 […]


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

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 […]


Activity Regulation by Fibrinogen and Fibrin of Streptokinase from Streptococcus Pyogenes

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 […]


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

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 […]


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

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 […]


A Futile Redox Cycle Involving Neuroglobin Observed at Physiological Temperature

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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