BU MA665 + MA666 (Fall 2024)
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 Google Colab
- Code: Install Python via Anaconda
- Code: Set up ChatGPT
- Please complete items in the Introduction to Python
- Advanced: 100 numpy exercises
- Advanced: Beautiful, Idiomatic Python
- Advanced: Make a pull request to the Introduction notebook to add a new exercise. Be sure to use follow syntax in quarto with quarto-pyodide
Integrate & Fire Neuron
Hodgkin-Huxley Neuron
Perceptron
Backpropagation
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 1 Slides
- Lecture 2 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
- Homework (Due 11/14/2024) Spectra Homework
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
- Homework (Due 11/21/2024) Coherence Homework
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
- Homework (Due 12/03/2024) CFC Homework
Gamma rhythms
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
- Homework (Due 12/10/2024) Rhythm Model Homework
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