How to use the gillespy2.Model function in gillespy2

To help you get started, we’ve selected a few gillespy2 examples, based on popular ways it is used in public projects.

Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.

github StochSS / stochss / stochss-pkg / Tests / test_convert_sbml.py View on Github external
def test_sbml_to_gillespy_success_with_stochss_model(self):
        sbml_file = "stochss-pkg/tests/mock_file_sys/sbml_files/test1.sbml"
        gillespy2_model, errors = convert_to_gillespy_model(sbml_file)
        self.assertIsInstance(gillespy2_model, Model)
        self.assertIsInstance(errors, list)
github StochSS / stochss / stochss / handlers / util / run_model.py View on Github external
stddev_plot["config"] = {"responsive": True,}
            plots['stddev'] = stddev_plot

            avg_plot = results.average_ensemble().plotplotly(return_plotly_figure=True)
            avg_plot["config"] = {"responsive": True,}
            plots['avg'] = avg_plot

        plot = results.plotplotly(return_plotly_figure=True)
        plot["config"] = {"responsive": True,}
        plots['trajectories'] = plot

        with open(os.path.join(self.res_path, 'plots.json'), 'w') as plots_file:
            json.dump(plots, plots_file, cls=plotly.utils.PlotlyJSONEncoder)


class _Model(Model):
    '''
    ##############################################################################
    Build a GillesPy2 model.
    ##############################################################################
    '''
    def __init__(self, name, species, parameters, reactions, events, rate_rules, 
                    assignment_rules, function_definitions, endSim, timeStep, volume):
        '''
        Initialize and empty model and add its components.

        Attributes
        ----------
        name : str
            Name of the model.
        species : list
            List of GillesPy2 species to be added to the model.