BU MA665 + MA666 (Fall 2025)

MA665

Introduction

• Read the syllabus
• Read: Wilson et al, Good enough practices in scientific computing, 2017
• Read: Riquelme and Gjorgjieva, Towards readable code in neuroscience, 2021
• Code: Set up ChatGPT
• Please confirm you can complete the items in Introduction to Python
• Advanced: 100 numpy exercises
• Advanced: Beautiful, Idiomatic Python

Integrate & Fire Neuron

• Read: Abbott, Brain Res Bull, 1999.
• Read: Chapter 1, pages 5-12 @ C. Koch, Biophysics of computation, 1998.
• Lecture Slides
• Code: Integrate & Fire Neuron in Python

Hodgkin-Huxley Neuron

• Read: Chapter 2, pages 25-42 @ E. Izhikevich, Dynamical Systems in Neuroscience, 2007.
• Read: Hodgkin-Huxley 1-page cheat sheet
• Advanced: Hodgkin and Huxley, J Physiol, 1952.
• Lecture Slides
• Code: Hodgkin-Huxley Neuron in Python

Perceptron

• Read: Electronic Brain Teaches Itself, New York Times, 13 July 1958
• Read: Perceptron Tested for Photo Analysis, Aviation Weekly, 1961
• Read: Undercover Algorithm, O’Connor, 2022
• Lecture Slides
• Code: Training a Perceptron in Python

Backpropagation

• Read: Lee or Delusions of Artificial Intelligence, 2023
• Watch: Inside an artificial brain
• Lecture Slides
• Code: Backpropagation in a Simple Neural Network in Python

Regression

• Read: Chapter 3 of An Introduction to Statistical Learning (Free via BU Library)
• Lecture Slides
• Code: Regression Example in Python

MA666

Introduction to Rhythms

• Read: Jell-O Test Finds Lifelike Signals, New York Times, 6 March 1976
• Read: Neuronal Oscillations in Cortical Networks
• Lecture Slides
• Code: Rhythms Introduction

Analyzing Rhythms

• Read: Kramer, SFN Short Course Document.
• Advanced Read: Chapter 3 @ Kramer & Eden, Case studies in neural data analysis, 2016.
• Advanced Read: Chapter 4 @ Kramer & Eden, Case studies in neural data analysis, 2016.
• Very Advanced Read: Chapter 4 @ Percival & Walden, Spectral Analysis for Physical Applications.
• Lecture 1 Slides
• Lecture Code 1: Analyze Rhythms Lab 1 - Practicals
• Lecture 2 Slides
• Lecture Code 2a: Analyze Rhythms Lab 2a - Autocovariance of noise
• Lecture Code 2b: Analyze Rhythms Lab 2b - Autocovariance of data
• Lecture 3 Slides
• Lecture Code 3: Analyze Rhythms Lab 3 - Spikes

Coherence

• Read: Chapter 5 @ Kramer & Eden, Case studies in neural data analysis, 2016.
• Read: Fries, A mechanism for cognitive dynamics: neuronal communication through neuronal coherence, TINS, 2005
• Extra Read: Chapter 25 @ M. X. Cohen, Analyzing neural time series data, 2014.
• Extra Read: Chapter 26 @ M. X. Cohen, Analyzing neural time series data, 2014.
• Advanced Read: Lepage et al, The Dependence of Spike Field Coherence on Expected Intensity, 2011.
• Lecture 1 Slides
• Lecture Code 1: Coherence Lab 1
• Lecture Code 2: Coherence Lab 2
• Lecture 2 Slides
• Lecture Code 3: Coherence Lab 3

Cross-frequency coupling

• Read: Chapter 7 @ Kramer & Eden, Case studies in neural data analysis, 2016.
• Read: Canolty et al., High Gamma Power Is Phase-Locked to Theta Oscillations in Human Neocortex, 2006
• Extra Read: Tort et al, J Neurophysiol, 2010.
• Extra Read: Hyafil et al, Trends Neurosci, 2015.
• Lecture Slides
• Lecture Code: Cross-frequency Coupling Lab

Gamma rhythms

• Read: Chapter 30 (PING) @ Borgers, An Introduction to Modeling Neuronal Dynamics, 2017
• Read: Chapter 31 (ING) @ Borgers, An Introduction to Modeling Neuronal Dynamics, 2017
• Extra Read: Whittington et al, Inhibition-based rhythms, Int J Psychophys, 2000
• Lecture Slides
• Lecture Code: Gamma Lab

Bursting rhythms

• Extra Read: Traub et al, Fast Rhythmic Bursting Can Be Induced…, 2003
• Extra Read: Roopun et al, A beta2-frequency (20–30 Hz) oscillation…, 2006
• Lecture Slides
• Lecture Code: Bursting Lab

A simple model

• Extra Read: Kramer et al, Golden rhythms as a theoretical framework…, 2022
• Extra Read: Roopun et al, Temporal interactions between cortical rhythms…, 2008
• Extra Read: Spyropoulos et al, Spontaneous variability in gamma dynamics…, 2022
• Lecture Slides
• Lecture Code: SHO Lab

Aperiodic exponent

• Read: Donoghue et al., Parameterizing neural power spectra…, 2020
• Extra Read: Gao et al., Inferring synaptic excitation/inhibition balance…, 2017
• Extra Read: Kramer & Chu, A General, Noise-Driven Mechanism…, 2024
• Lecture Slides
• Lecture Code: Aperiodic Exponent Lab