COMPUTATIONAL NEUROSCIENCE

iten
Code
80575
ACADEMIC YEAR
2021/2022
CREDITS
6 credits during the 2nd year of 11159 BIOENGINEERING (LM-21) GENOVA
SCIENTIFIC DISCIPLINARY SECTOR
ING-INF/06
LANGUAGE
English
TEACHING LOCATION
GENOVA (BIOENGINEERING)
semester
1° Semester
Teaching materials

OVERVIEW

Computational Neuroscience is an advanced course offered to students in the last year of the master's degree in Bioengineering aimed at providing the tools and methods for modeling the nervous system at different scales, from single neurons to complex neuronal networks. In particular, transmembrane ion channels, single neurons, synapses and neuron networks will be studied and analyzed using different modeling strategies.

AIMS AND CONTENT

LEARNING OUTCOMES

Neurons: advanced biophysical modeling and computer simulation techniques. Synapses: Phenomenological models vs biophysical models; Exponential synapses at one and two time constants; Synaptic plasticity; Neuron networks: simplified models; Role of connectivity in network dynamics

AIMS AND LEARNING OUTCOMES

Goal of the teaching is to provide the theoretical contents for modeling neuronal structures at different scale, from single neuron up to large-scale complex networks. For this reason, the course will be focused on how to model and simulate the electrophysiological activity of neuronal structures. Based on the tools offered, the objectives of the course are:

- model neuronal networks with particular patterns of electrophysiological activity
- choose the correct neuron models based on experimental needs
- solve advanced theoretical problems of neuronal computation
- choose the best computational strategy based on the required problem

PREREQUISITES

Advanced knowledge of mathematics, mathematical analysis; analysis of electrophysiological signals; neurophysiology

TEACHING METHODS

Combination of traditional lectures, classroom discussion, and lab activities.

SYLLABUS/CONTENT

  • Biophysical Model of Neurons
    • Brief introduction on equivalent membrane circuit and membrane electric properties
    • Passive models and propagation equation
    • Hodgkin and Huxley (HH) model and dynamics
    • From HH to multichannel neuron models
    • Role of neuron morphology and dendritic tree in the electrophysiological patterns
    • Reduced models: from multi-compartments to 2-3 compartments neurons
    • Calcium dynamics
  • Neuronal dynamics, excitability threshold, oscillations
    • Mathematical background of non-linear systems and portrait analysis
    • Hodgkin and Huxley model
    • Morris-Lecar model
    • Fitzhug-Nagumo model
       
  • From bio-inspired to abstracted point neurons
    • The family of integrate-and-fire (IF) neurons
    • Leaky-Integrate-and-Fire (LIF)
    • Exponential-Integrate-and-Fire (EIF)
    • Quadratic-Integrate-and-Fire (QIF)
    • Advantages and limitations of IF models
    • The Izhikevich model
    • Stochastic models
    • Poissonian process
    • Renewal process
       
  • The synaptic transmission and plasticity
    • Exponential synapse
    • Alpha function synapse
    • Dynamical models
    • Desthexhe model
    • Markovian models
    • Modeling the synaptic plasticity
    • Hebbian rule
    • Depression, Facilitation, Augmentation (short-term plasticity)
    • Long Term Potentiation/Depression
    • Spike Timing Dependent Plasticity (STDP)
  • Network Models
    • Firing Rate Model
    • Spiking Model
    • Point vs. multicompartmental networks
    • Balanced networks
    • Network architecture
    • Networks dynamics
    • Interplay between dynamics and connectivity
    • Different kind of connectivities
    • Building a graph
    • Properties of a graph
    • Functional, Structural, Effective connectivity

RECOMMENDED READING/BIBLIOGRAPHY

Slides available on Aulaweb.

  • Methods in Neuronal Modeling, Koch and Segev, MIT press, 1999.
  • Spiking Neuron Models, Gerstner and Kistler, Cambridge press, 2002.
  • Dynamical systems in neuroscience,. Izhikevich, MIT press, 2007.
  • Computational Modeling Methods for Neuroscientists, De Schutter, MIT press, 2010.
  • Theoretical Neuroscience, Dayan and Abbott, MIT press, 2001.

TEACHERS AND EXAM BOARD

Office hours: Appointment by e-mail

LESSONS

TEACHING METHODS

Combination of traditional lectures, classroom discussion, and lab activities.

Class schedule

All class schedules are posted on the EasyAcademy portal.

EXAMS

EXAM DESCRIPTION

Oral exam about all the topics of the teaching.
Exams will be during the months of December, January, February, June, July, and September. No others exams will be provided during the year. After the exam, the student has 1 week to decide if the mark is fine or not. After this 1 week, the exam will be signed with the assigned mark.

ASSESSMENT METHODS

Oral exam about the advanced techniques for modeling neuronal structures from single neuron up to large-scale neuronal networks.

Exam schedule

Date Time Location Type Notes
20/12/2021 10:00 GENOVA Orale
17/01/2022 10:00 GENOVA Orale
14/02/2022 10:00 GENOVA Orale
13/06/2022 10:00 GENOVA Orale
05/07/2022 10:00 GENOVA Orale
14/09/2022 10:00 GENOVA Orale