Load - Run - Save models

How to run these examples

Each of the following examples can be run by clicking on the green source button
on the right side of each example, and running from within a ``.py`` python file
on a computer where moose is installed.

Alternatively, all the files mentioned on this page can be found in the main
moose directory. They can be found under

    (...)/moose/moose-examples/snippets

They can be run by typing

    $ python filename.py

in your command line, where filename.py is the python file you want to run.

All of the following examples show one or more methods within each python file.
For example, in the ``cubeMeshSigNeur`` section, there are two blue tabs
describing the ``cubeMeshSigNeur.createSquid()`` and ``cubeMeshSigNeur.main()``
methods.

The filename is the bit that comes before the ``.`` in the blue boxes, with
``.py`` added at the end of it. In this case, the file name would be
``cubeMeshSigNeur.py``.

Load a Kinetic Model

loadKineticModel.main()

This example illustrates loading, running, and saving a kinetic model defined in kkit format. It uses a default kkit model but you can specify another using the command line python loadKineticModel.py filepath runtime solver. We use default solver as gsl. The model already defines a couple of plots and sets the runtime 20 secs.

Load an SBML Model

loadSbmlmodel.main()

This example illustrates loading, running of an SBML model defined in XML format. Default this file load's 00001-sbml-l3v1.xml which is taken from l3v1 SBML testcase. Plots are setup. Model is run for 20sec. As a general rule we created model under '/path/model' and plots under '/path/graphs'. If someone wants to load anyother file then

python loadSbmlmodel filepath runtime

Load a CSpace Model

loadCspaceModel.main()

This example illustrates loading and running, a kinetic model defined in cspace format. We use the gsl solver here. The model already defines a couple of plots and sets the runtime to 3000 seconds.

Save a model into SBML format

convert_Genesis2Sbml.main()

This example illustrates loading a kinetic model defined in Genesis format into Moose using loadModel function and using writeSBML function one can save the model into SBML format.

libsbml should be installed.

Save a model

savemodel.main()

The script demonstates to convert Chemical (Genesis) file back to Genesis file using moose