BIOS 418/518 Methods in Computational Neuroscience
Lecture, discussion, and computer lab. Introduction to mathematical and computational techniques for modeling single neurons and networks of neurons. Cable theory; Rall's model; compartmental models; introduction to available software for simulating neurons and networks; voltage-dependent conductances; Hebbian synapses; synaptic modification rules; quantal analysis; neural networks. Students are expected to complete simulation project using one of the available software packages. 3 lec, 2 computer lab.
In recent years NEURON has been taught. Available from http://www.neuron.yale.edu
Grading Basis: In a typical year, grading basis is 40% homework and problem sets, 20% midterm during week 6, 30% term project, and 10% group oral exam the last day of classes.
Sample syllabus: Suggested readings are from BOG (Bower and Beeman,
Book of Genesis http://www.genesis-sim.org/GENESIS/iBoG/index.html),
K (Koch, Biophysics of Computation) and NB
(Carnevale and Hines, The NEURON Book). Extensive lectures notes will be available
on-line. Lecture overheads will be
distributed in class. Topics covered up
to the mid-term are fairly static.
Topics after the mid-term may vary depending on interests.
Week 1 INTRODUCTION (BOG 1,2,11; K 1,2 pp. 25-32)
Jan. 3: Introduction, Review of basic concepts
Jan. 5: Cable theory, derivation of cable equation
Computer lab—NEURON Cell Builder (NB 1)
Week 2 DENDRITES (BOG 5.1-5.4; K 2,3 pp. 32-58)
Jan. 8: Steady-state solutions to the cable equation
Jan. 10: Solutions for dendritic trees with branching
Jan. 12: Transient solution, Rall's equivalent cylinder model
Computer lab—NEURON commands, hoc files (NB 5)
Week 3 COMPARTMENTAL MODELS (BOG 2, 5.5-end; K 3 pp. 58-66)
Jan. 15:
Jan. 17: Compartmental models
Jan. 19: General cable equation, Parameters needed to do models
Computer lab—NEURON program management, setting up GUIs,
Cable
tutorial (NB 6)
Week 4 HODGKIN-HUXLEY EQUATIONS AND THE ACTION POTENTIAL
(BOG 4,7; K 6,8)
Jan. 22: Hodgkin-Huxley equations
Jan. 24: Action potential
Jan. 26: Voltage-dependent and other conductances
Computer lab—Action Potential simulations, HH equations
Week 5 VOLTAGE-DEPENDENT CONDUCTANCES, SYNAPTIC CONDUCTANCES
(BOG 7,6; K 9,4; NB 9)
Jan. 29: Voltage and calcium-dependent conductances
Jan. 31: Synaptic Conductances
Feb. 2: Synaptic conductances (2)
Computer lab—Voltage dependent and calcium dependent conductances
(NB 9)
Week 6 SYNAPTIC CONDUCTANCES, NETWORKS (BOG 6; K 5; NB 10, 11, 4)
Feb. 5: Synaptic interactions--spatial and temporal summation
Feb. 7: Network Builder and coding Networks
Feb. 9: catch-up or Numerical method considerations
Computer lab—Networks and Network Builder (NB
11)
(Discuss Term project plans with instructor by Feb. 9. Term project plans due Feb. 14)
Week 7 NEURON CONSIDERATIONS (K Appendix C; Handout; NB 4)
Feb. 12: Getting morphological data into NEURON
Feb. 14: EXAM
Feb. 16: Implementing calcium-dependent conductances in NEURON
Computer lab—Getting data into NEURON (NB 12, end)
Week 8 CALCIUM DIFFUSION, DENDRITIC SPINES
(K 11,12)
Feb. 19: Gap junctions, calcium diffusion, buffering and pumps
Feb. 21: Gap junctions, calcium diffusion, buffering and pumps (2)
Feb. 23: Function of dendritic spines
Computer lab— Gap junctions, Ca diffusion, buffering and pumps
Week 9 SYNAPTIC MODIFICATION, LTP, DIFFUSION (K 13; BOG 10.1-2)
Feb. 26: Dendritic Spines –calcium diffusion
Feb. 28: MCell; Stochastic Models–Ion Channels and Reaction/Diffusion
Mar. 2: Synaptic modification, long-term potentiation
Computer lab—Multiple Run Fitter—fitting data with models
(Abstract of term project due Mar. 9)
Week 10 CENTRAL PATTERN GENERATORS, NETWORKS (BOG 8; K 16)
Mar. 5: Coupled oscillators, CPGs
Mar. 7: Neural Networks
Mar. 9: Oral EXAM and discussion
Computer lab—Synapses with facilitation and depression, extracellular
potassium accumulation, Traub’s CA3 model
Exam Week,
Project presentations and Papers due at scheduled exam time,
Thursday
Mar. 15,