Rdesigneur Examples

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``.

Building Chemical-Electrical Signalling Models

Building a compartment

testRdesigneur.main()

This illustrates the use of rdesigneur to build a simple dendrite with spines, and to confirm that the chemical contents of the spines align with the electrical. Just a single molecule Ca is involved. It diffuses and we plot the distribution. It causes 'inject' of the relevant compartment to rise.

Inserting Spines and viewing

insertSpines.main()

This example illustrates loading a model from an SWC file, inserting spines, and viewing it.

Proceeding with Spines

testWigglySpines.main()

This illustrates the use of rdesigneur to build a simple dendrite with spines, and then to resize them using spine fields. These are the fields that would be changed dynamically in a simulation with reactions that affect spine geometry.

testWigglySpines.p2(x)

Print to 2 sig fig