MOOSE-Notebooks

These notebooks present hands-on tutorials for topics in modeling in Neuroscience and Systems Biology. The contents are

1. Using MOOSE on Colab
2. MOOSE overview
3. Resting membrane potential Discussion of Nernst-Planck and Nernst equation and Goldman-Hodgkin-Katz equation
4. Getting started with compartmental modelling in MOOSE Shows how to create a passive neuronal compartment in MOOSE
5. More complex current injection protocol Shows how to generate various patterns of (current) pulses for injecting into a compartment
6. Multi-compartmental neuron model Describes how you can connect several compartments to create a neuronal cable
7. Cable theory Derives the cable equation and then shows its approximation using a voltage clamped multicompartmental cable
8. Hodgkin and Huxley's model of K+ current Implements Hodgkin and Huxley's model of K+ current. This is the first step towards modeling action potentials in the squid giant axon.
9. Hodgkin and Huxley's model of Na+ current Implements Hodgkin and Huxley's model of Na+ current. The Na+ current is responsible for depolarizing the neuron for an action potential, whereas the K+ current repolarizes it.
10. Action potentials Puts together the Na+ and K+ currents to demonstrate Hodgkin and Huxley's model of action potential generation in the squid giant axon.
11. Synapses Explains the components of the basic synapse model in MOOSE. There can be multiple ways to model a synapse at different complexities, all based on these basic ideas.
12. Leaky integrate and fire (LIF) neurons and synapse Implementation of a network of simple integrate-and-fire neurons connected via synapses.