Introduction to Computational Neuroscience

Psychology 4/503c - Fall 2010.

- General Information.

• Syllabus
• Intructor: Jean-Marc Fellous.
  Office Hour: Wed 3:00 pm - 4:00 pm, LSN 384. ( How to get to LSN )
• Notes:
  The University has incorrectly listed our room number to Life Science SOUTH 340. It is actually life Science NORTH 352. The building is secure, so you will need to be setup to access it. We will do this the first day of class (Aug 25th, 1pm). On August 25th, please wait downstairs and someone will come pick you up at 1pm.

- Do I have the necessary computational and biological background to take this class? Self Test.

- Data and Code (secure, need password)

- Other classes in computational neuroscience

- Readings

Week 1: Introduction to Modeling

(Sejnowski, Koch, Churchland, 1988) and (Abbott, 2008)

Other optional readings:
(Olsen et al, 2007): Examples of models, neuromorphic engineering emphasis.
(Lytton 2008): Multilevel modeling in the context of epilepsy. How to understand a phenomenon at multiple levels of investigation (from channels to large networks) using computational models.
(Gerstner and Naud, 2009): How good are neural models, detailed Vs abstract models.
23 problems in systems neuroscience. Oxford University Press, 2005. van Hemmen and Sejnowski (Eds): As the title suggests...! wide-field view of computational issues from insects to monkeys. Good examples of how basic principles cut across preparation and modeling levels. requires some background in neuroscience.

Week 2: Introduction to NEURON

(Hines, Carnevale 2001) (Hines, Carnevale 2000)

Week 3: Sodium, Potassium and the Action Potential

(Hodgkin and Huxley, 1952) (Naundorf et al. 2006):
Clayton's Slides

Week 4: The Current Flora

(Khorkova et al. 2007) (Traub et al. 1991):
Jessica' Slides, Brian's Slides

Week 5: Calcium Dynamics

... no assigned readings ...

Week 6: Morphology and Dendritic Integration (passive dendrites)

(Rall 2003) (Stuart and Spruston 1998):
Derek's Slides Greg Slides

Week 7: Midterm (Oct 6th) and Dendritic Processing (active dendrites)

Note: Papers covered are those from week 4-6 included. The take home portion can be found in the assignment area of the website.

Week 8: Synaptic transmission. The receptor flora

(Wilson Laurent 2005) (Kuhn et. al. 2004)
Adam and Kat slides

Week 9: Realistic synaptic transmission - Short term synaptic dynamics

(Abbott and Regehr, 2004) (Pfister et. al. 2010)
Eliot slides

Week 10: Small networks and central pattern generators

(Lieb and Frost, 1997) (Purvis et al, 2007)
Rafael and Sarah slides

Week 11: Q and A session: Update on projects and debugging

... no assigned readings ...

Week 12: Simplified models of neurons and networks

(Koch 1997)
Laurel's slides
Links for today's Emergent demos: The AX tutorial

Project presentations:

Jessica and Derek: The learning network
Rafael and Ryan: Identifying good figures
Greg and Sarah: Model of glia-neuron interaction
Clayton and Alie: A single compartment model of intrinsic hair cell tuning to low-frequency stimuli
Adam and Kat: Modeling the local field potential
Brian: Phase Precession in a Modified Dual Oscillator Model
Eliot and Laurel: Biophysical models of working memory

Week 14: Final
Wednesday, Dec 15th, 1pm in the usual room: Comprehensive (lecture and simulation materials), final project presentations (as posted above) and papers covered in weeks 4-12 (graduate students) and 4-8 (undergraduate students).