Neuronal simulations in MOOSEGUI

Aditya Gilra

October 1, 2012

Introduction

Neuronal models in various formats can be loaded and simulated in the MOOSE Graphical User Interface. The GUI displays the neurons in 3D, and allows visual selection and editing of neuronal properties. Plotting and visualization of activity proceeds concurrently with the simulation. Support for creating and editing channels, morphology and networks is planned for the future.

Neuronal models

Neurons are modelled as equivalent electrical circuits. The morphology of a neuron can be broken into isopotential compartments connected by axial resistances Ra denoting the cytoplasmic resistance. In each compartment, the neuronal membrane is represented as a capacitance Cm with a shunt leak resistance Rm. Electrochemical gradient (due to ion pumps) across the leaky membrane causes a voltage drive Em, that hyperpolarizes the inside of the cell membrane compared to the outside.

Each voltage dependent ion channel, present on the membrane, is modelled as a voltage dependent conductance Gk with gating kinetics, in series with an electrochemical voltage drive (battery) Ek, across the membrane capacitance Cm, as in the figure below.


<strong
>Equivalent circuit of neuronal compartments</strong
>

Equivalent circuit of neuronal compartments


Neurons fire action potentials / spikes (sharp rise and fall of membrane potential Vm) due to voltage dependent channels. These result in opening of excitatory / inhibitory synaptic channels (conductances with batteries, similar to voltage gated channels) on other connected neurons in the network.

MOOSE can handle large networks of detailed neurons, each with complicated channel dynamics. Further, MOOSE can integrate chemical signalling with electrical activity. Presently, creating and simulating these requires PyMOOSE scripting, but these will be incorporated into the GUI in the future.

To understand channel kinetics and neuronal action potentials, run the Squid Axon demo installed along with MOOSEGUI and consult its help/tutorial.

Read more about compartmental modelling in the first few chapters of the Book of Genesis.

Models can be defined in NeuroML, an XML format which is mostly supported across simulators. Channels, neuronal morphology (compartments), and networks can be specified using various levels of NeuroML, namely ChannelML, MorphML and NetworkML. Importing of cell models in the GENESIS .p format is supported for backwards compatibitility.

Neuronal simulations in MOOSEGUI

Quick start

User interface help is available at Help -> User Interface. Here we delve into neuronal simulations.

Modelling details

MOOSEGUI uses SI units throughout.

Some salient properties of neuronal building blocks in MOOSE are described below. Variables that are updated at every simulation time step are are listed dynamical. Rest are parameters.

Demos