Computational Neuroscience

  1. Tools and Techniques
    1. Simulation Environments
      1. NEURON
        1. Single neuron modeling
          1. Morphology specification
            1. Biophysical mechanisms
            2. Network simulations
              1. Connectivity patterns
                1. Synaptic mechanisms
                2. Programming interfaces
                  1. HOC language
                    1. Python interface
                  2. GENESIS
                    1. Biophysical modeling
                      1. Compartmental models
                        1. Channel kinetics
                        2. Simulation protocols
                          1. Scripting language
                          2. Brian
                            1. Spiking neural networks
                              1. Equation-oriented modeling
                                1. Code generation
                                2. Plasticity mechanisms
                                  1. Event-driven simulation
                                  2. NEST
                                    1. Large-scale simulations
                                      1. Parallel computing
                                        1. Distributed simulation
                                        2. Network models
                                          1. Spike-based communication
                                          2. ANNarchy
                                            1. Rate-based and spiking models
                                              1. GPU acceleration
                                                1. Plasticity rules
                                              2. Neural Data Analysis
                                                1. Spike Sorting
                                                  1. Detection algorithms
                                                    1. Threshold detection
                                                      1. Template matching
                                                      2. Classification methods
                                                        1. Principal component analysis
                                                          1. Clustering algorithms
                                                          2. Validation techniques
                                                            1. Cross-correlation
                                                              1. Isolation quality
                                                            2. Local Field Potential Analysis
                                                              1. Frequency bands
                                                                1. Delta, theta, alpha, beta, gamma
                                                                  1. Band-specific functions
                                                                  2. Source localization
                                                                    1. Current source density
                                                                      1. Independent component analysis
                                                                      2. Connectivity analysis
                                                                        1. Coherence
                                                                          1. Phase-locking value
                                                                        2. Time-Frequency Analysis
                                                                          1. Fourier transform
                                                                            1. Short-time Fourier transform
                                                                              1. Spectrograms
                                                                              2. Wavelet analysis
                                                                                1. Continuous wavelets
                                                                                  1. Discrete wavelets
                                                                                    1. Time-frequency resolution
                                                                                    2. Hilbert transform
                                                                                      1. Instantaneous phase
                                                                                        1. Amplitude modulation
                                                                                      2. Dimensionality Reduction
                                                                                        1. Principal component analysis
                                                                                          1. Independent component analysis
                                                                                            1. Factor analysis
                                                                                              1. Manifold learning
                                                                                            2. Model Fitting and Validation
                                                                                              1. Parameter Estimation
                                                                                                1. Optimization techniques
                                                                                                  1. Gradient descent
                                                                                                    1. Genetic algorithms
                                                                                                      1. Simulated annealing
                                                                                                      2. Bayesian estimation
                                                                                                        1. Markov chain Monte Carlo
                                                                                                          1. Variational inference
                                                                                                          2. Maximum likelihood
                                                                                                            1. Likelihood functions
                                                                                                              1. Fisher information
                                                                                                            2. Model Comparison
                                                                                                              1. Information criteria
                                                                                                                1. Akaike information criterion
                                                                                                                  1. Bayesian information criterion
                                                                                                                  2. Cross-validation
                                                                                                                    1. K-fold validation
                                                                                                                      1. Leave-one-out
                                                                                                                      2. Bayes factors
                                                                                                                        1. Model evidence
                                                                                                                          1. Posterior odds
                                                                                                                        2. Goodness-of-fit measures
                                                                                                                          1. R-squared
                                                                                                                            1. Mean squared error
                                                                                                                              1. Likelihood ratios
                                                                                                                              2. Generalization and Prediction
                                                                                                                                1. Out-of-sample testing
                                                                                                                                  1. Predictive accuracy
                                                                                                                                    1. Overfitting detection
                                                                                                                                    2. Sensitivity Analysis
                                                                                                                                      1. Parameter sensitivity
                                                                                                                                        1. Robustness testing
                                                                                                                                          1. Uncertainty quantification

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                                                                                                                                      10. Models of Higher Cognitive Functions

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                                                                                                                                      1. Introduction to Computational Neuroscience