ModelingNeuralDynamics

Python and Brian2 examples for An Introduction to Modeling Neuronal Dynamics by Christoph Börgers.

Installation

pip install modelingneuraldynamics

To run notebooks from a source checkout:

uv sync --all-groups
uv run jupyter lab

See the Python guide and Brian2 setup and coverage guide for details. Brian2 notebooks cover representative examples from each chapter.

Chapters

Open the Python or Brian2 notebooks in Google Colab, or read the chapter guide. Chapters 2 and 6 have no examples in this repository; chapter 3 is Python only.

#	Chapter	Python (Colab)	Brian2 (Colab)	Guide
1	Modeling a Single Neuron			Guide
3	The Classical HH ODEs		—	Guide
4	Numerical Solution of HH ODEs			Guide
5	The Simple Model of Neurons in Rodent Brains			Guide
7	Linear Integrate-and-Fire (LIF) Neurons			Guide
8	Quadratic Integrate-and-Fire (QIF) and Theta Neurons			Guide
9	Spike Frequency Adaptation			Guide
10	The Slow-Fast Phase Plane			Guide
11	The Saddle-Node Bifurcation			Guide
12	Two-Dimensional Bifurcation Analysis			Guide
13	Hopf Bifurcations			Guide
14	Model Neurons of Bifurcation Type 2			Guide
15	Canard Explosions			Guide
16	Model Neurons of Bifurcation Type 3			Guide
17	Frequency-Current Curves			Guide
18	Bistability Resulting from Rebound Firing			Guide
19	Bursting			Guide
20	Chemical Synapses			Guide
21	Gap Junctions			Guide
22	A Wilson-Cowan Model of an Oscillatory E-I Network			Guide
23	Entrainment by Excitatory Input Pulses			Guide
24	Synchronization by Fast Recurrent Excitation			Guide
25	Phase Response Curves (PRCs)			Guide
26	Phase Locking of Two Oscillators			Guide
27	Phase Locking with Delays			Guide
28	Weakly Coupled Oscillators			Guide
29	Stability of the Synchronous State			Guide
30	The PING Model of Gamma Rhythms		More examples	Guide
31	ING Rhythms			Guide
32	M-Current PING and Poisson PING			Guide
33	M-Current PING and PINB			Guide
34	Nested Gamma-Theta Rhythms			Guide
35	Periodic Inhibition			Guide
36	F-I Curves: Pulsed Excitation			Guide
37	Thresholding in PING			Guide
38	Gamma Coherence			Guide
39	Short-Term Depression and Facilitation			Guide
40	Spike-Timing-Dependent Plasticity (STDP)			Guide

Book and original MATLAB code · License