Choosing a Simulator

Warning

Compatibility with simulators other than NEURON is currently under development.

DendroTweaks acts as a layer on top of a simulator to provide a high-level interface, additional functionality, and enable connection with the GUI. The following simulatord are currently supported:

Planned support for the following simulators:

Tip

While support for Jaxley is an ongoing effort, you can already automatically create Jaxley-compatible ion channel classes from MOD files using DendroTweaks. Learn more about creating ion channels in this tutorial.

Creating and Referencing Sections in a Simulator

Once we have created an instance of a Model and a SectionTree, we can reference the sections in the simulator. The following code snippet demonstrates how to reference the sections in NEURON.

>>> model.reference_sections(simulator='NEURON')
Created 52 sections in NEURON. Use section._ref to access the NEURON section.

Now each DendroTweaks Section is associated with a simulator-specific section. The user can access the simulator-specific section using the _ref attribute.

>>> soma = model.get_sections(lambda sec: sec.domain == 'soma')[0]
>>> soma._ref
<nrn.Section at 0x7f8b3b3b3b50>
../_images/ref.png