BioNB330 - home - logistics - lab

Introduction to Computational Neuroscience
BioNB 330

Lecture Schedule

The syllabus includes the lecture schedule as well as readings, assignments and dates for quizes. Readings are mandatory and I will assume that you have read them. The appendices contain background material useful for those not experts on certain topics. Notes contain some or most of what I will say in class and are meant to reduce your note taking. For some classes, I will use slides and also post those on the web. Homework and lab modules are due at 6pm on Sunday. Homework will be posted here and on blackboard. Some homework wil be accompanied by a short blackboard multiple choice quiz. There will be five in class quizzes, for each student the quiz with the worst grade will be dropped. There will be a mid-term and final, both are take home. All quizes, homeworks, lab modules, projects and exams are open book, you can use your notes and any information sources you choose. Be aware that this does not mean you should not study!

Class notes Part I

Class notes Part II

Class notes Part III

Class notes Part IV

ANNOUNCEMENT: Meeting times for 4-credit students:

Wednesday, September 19th 10 am (W245 Mudd), Friday, September 21st 3pm (W245 Mudd) - COLOR Vision assignment

Wednesday, September 26th 10 am (W245 Mudd) and Friday, September 28th 3 pm (W245 Mudd) - Contrast assignment

NO MEETING ABOUT Phase precession assigment during week of October 8th. Hand in a draft or finished product or make an appointment.

Friday 11/17 at 3pm meeting about STDP project

Midterm posted HERE - it is a take home exam due on FRIDAY, October 26nd at 6pm to Professor Linster (not blackboard) by email (
Students who submitted for the original deadline can resubmit if they so wish.

Take home final posted HERE. Final is due December 14th at 6pm. Email to, DO NOT submit to Blackboard!

Homework will be submitted via Blackboard.

For those new to Blackboard:

Check the website:

To find the course, click the “All Blackboard sites” tab after setting up an account and logging in, and search for “Computational neuroscience”. Homework assignments can be found in the “Homework assignments” folder  after clicking the “Assignments” button.When you are ready to submit your homework, click on the "Homework Dropbox" button from the menu and then click the "Send File" button on the next page. This will bring you to the page that allows you to upload your homework. Please title your homework with your name and the Assignment number."

A. Basic concepts : Class Notes Part I

1 Lecture (Wed, 8/23)

Introduction, course logistics, historical overview.
What is Computational Neuroscience


2 Lecture (Mon, 8/27 )

Computing with Neurons: Simplified models of Neurons

Appendix 1: Cells
Appendix 2: Neurons

Lab module: Types of model neurons – due Sunday, 9-9 at 6pm

Slides used in class

3 Lecture (Wed, 8/29 )

Neural Coding: Can it be defined?

Appendix 4: Coding
Homework: Coding – due Sunday, 9-9 at 6pm - Key

Lab module: Neural Codes – due Sunday, 9-9 at 6pm

Slides used in class

(Mon, 9/3) Labor Day - No Class

4 Lecture (Wed, 9/5)

Receptive fields and tuning curves

Reading: Chapin. J., Moxon, KA., Markowitz, RS. And Nicolelis, M (1999). Real-time control of a robot arm using simultaneously recorded neurons in the motor cortex. Nature Neuroscience, 2(7): 664.

Homework: Tuning curves – due Sunday, 9-9 at 6pm

Slides used in class

5 Lecture (Mon, 9/10)

Quiz 1 – Lectures 2-4 - KEY
Population vectors

Appendix 4: Mathematical aside
Reading: Lewis JE. Sensory processing and the network mechanisms for reading neuronal population codes. J Comp Physiol [A] 185: 373-378, 1999.

4-credit student Project 1: Color Blindness - indicate when you are available for discussion section here

Slides used in class

6 Lecture (Wed, 9/12)

Tuning tuning curves – contrast enhancement – cortical circuits

Reading: Barlow, RB (1969) Inhibitory fields in the Limulus lateral eye. J. Gen. Physiol. 54(3):383.
Homework: Contrast enhancement – to be written

Lab module: Receptive fields – due Sunday, 9-16 at 6pm

Appendix: The structure of neocortical circuits

Homework Population vector and contrast enhancement - due Sunday, 9-16 at 6pm - KEY

Slides used in class

7 Discussion (Mon, 9/17)

Applications, discussion, review

4-credit students Project 2: Contrast

B. Beyong the basics: Temporal codes, oscillations, synchrony: Class Notes Part II

8 Discussion (Wed, 9/19)

Beyond firing rates – oscillations, synchrony and cell assemblies
Readings: Singer W. Time as coding space? Curr Opin Neurobiol 9: 189- 194, 1999.
Gray CM. The temporal correlation hypothesis of visual feature integration: still alive and well. Neuron, 24 (1), 1999, Pages 31-47.
Homework: Oscillations - due Sunday, September 23rd at 6pm KEY
Lab module: Oscillations - due Sunday, September 23rd at 6pm
Appendix: Synchrony

9 Lecture (Mon, 9/24)

Quiz 2 - Lecture 2 - 7 - in class

Representations in rate and synchrony
Readings: Stopfer M, Bhagavan S, Smith BH, and Laurent G. Impaired odour discrimination on desynchronization of odour-encoding neural assemblies. Nature 390: 70-74, 1997
Laurent, G. Dynamical representation of odors by oscillating and evolving neural assemblies. Trends Neurosci. 1996 Nov;19(11):489-96. Review.

Slides show in class

10 Lecture (Wed, 9/26)

Rate and temporal code – hippocampal place cells
Appendix: Hippocampus
Readings: Buzsaki G.  Theta rythm of navigation: link between path integration and landmark navigation, episodic and semantic memory.
Hippocampus 15: 827-840, 2005.
Huxter J, Burgess N, and O'Keefe J. Independent rate and temporal coding in hippocampal pyramidal cells. Nature 425: 828-832, 2003;

4-credit students Project 3: Phase precession

Blackboard quiz due Wednesday, 9/26 at 6pm

Homework: Place cells due Tuesday, October 2nd at 6pm KEY

Slides shown in class

11 Lecture (Mon, 10/1)

More about synchrony - was canceled

Readings: Riehle A, Grun S, Diesmann M, and Aertsen A. Spike synchronization and rate modulation differentially involved in motor cortical function. Science 278: 1950-1953, 1997
Diesmann M, Gewaltig MO, and Aertsen A. Stable propagation of synchronous spiking in cortical neural networks. Nature 402: 529-533, 1999.;
Appendix: Phase_plots

Blackboard quiz due Monday, 10/1 at noon

Slides shown in class


12 lecture (Wed, 10/3)

More about synchrony

Readings: Riehle A, Grun S, Diesmann M, and Aertsen A. Spike synchronization and rate modulation differentially involved in motor cortical function. Science 278: 1950-1953, 1997
Diesmann M, Gewaltig MO, and Aertsen A. Stable propagation of synchronous spiking in cortical neural networks. Nature 402: 529-533, 1999.;
Appendix: Phase_plots

Slides shown in class

Homework due Tuesday, October 9th at 6pm - KEY

(Mon, 10/8) Fall break - no lecture

Plasticity - Class Notes Part III

13 Lecture (Wed, 10/10)

Review, catch up, discussion
Plasticity – LTP, hebbian learning, Pavlov’s dog
Appendix: LTP, Pavlov

Homework: Hebbian Learning due Tuesday, 10-16 at 6pm KEY

Lab module: Learning rules a) Hebbian learning due Tuesday, 10-16 at 6pm

14 Lecture (Mon, 10/15)

Quiz 3 Lectures 2-12

Tuning curves that change and adapt
Readings: Knudsen EI. Instructed learning in the auditory localization pathway of the barn owl. Nature 417: 322-328, 2002.

Feldman, DE and Brecht, M. Map plasticity in somatosensory cortex. Science. 2005 Nov 4;310(5749):810-5. and references therein.

Slides used in class

4-credit student project 4: Knudsen’s data

15 Lecture (Wed, 10/17)

Memory models – Linear associator, auto-associator, Hopfield networks

Lab module: Linear associator - due Friday, 10-26 at 6pm
Appendix: Associative memories

Slides used in class

Homework: Associators, due Friday, 10-26 at 6pm

16 Discussion (Mon, 10/22)


Discussion, review examples - Canceled due to illness


17 Lecture (Wed, 10/24)

Hopfield networks revisited, Neuromodulation, Review

LabModule: Auto-associators due Tuesday, 10-30 at 6pm

Homework - No HW, included in Associators

Reading: Hasselmo ME.Neuromodulation and cortical function: modeling the physiological basis of behavior. Behav Brain Res. 1995 Feb;67(1):1-27. - Quiz on Blackboard due Wednesday 10-24 at noon

18 Discussion (Mon, 10/29)

Guest lecture: To be announced


19 Lecture (Wed, 10/31)

Spike-timing-dependent plasticity: constructing a learning rule from data – data papers
Song S, Miller KD, and Abbott LF. Competitive Hebbian learning through spike-timing-dependent synaptic plasticity. Nat Neurosci 3: 919-926, 2000.
Sjostrom PJ, Turrigiano GG, and Nelson SB. Rate, timing, and cooperativity jointly determine cortical synaptic plasticity. Neuron 32: 1149-1164, 2001.

Slides used in class

Homework: STDP - due Tuesday, 11/6 at 6pm
Lab module: Learning rules b) STDP - due Tuesday, 11/6 at 6pm

20 Discussion (Mon, 11/5)

Applications of STDP

Mehta MR, Quirk MC, and Wilson MA. STPD Experience-dependent asymmetric shape of hippocampal receptive fields. Neuron 25: 707-715, 2000.

Yao H, Shen Y, and Dan Y. Intracortical mechanism of stimulus-timing-dependent plasticity in visual cortical orientation tuning. Proc Natl Acad Sci U S A 101: 5081-5086, 2004.
Comments on readings:Yao et al.

Slides used in class

4-credit students project 5: STDP - Discussion Friday 11/17 at 3pm

21 lecture (Wed, 11/7)

Review – Discussion

Quiz 4 – Lectures 2-19 KEY


Memory models: Class Notes Part IV

22 Lecture (Mon, 11/12)

Models of human memory, why do we have a hippocampus

Rolls ET, and Kesner RP. A computational theory of hippocampal function, and empirical tests of the theory. Prog Neurobiol 79: 1-48, 2006 - not mandatory
Alvarez P, and Squire LR. Memory consolidation and the medial temporal lobe: a simple network model. Proc Natl Acad Sci U S A 91: 7041-7045, 1994

Slides used in class

23 Lecture (Wed, 11/14)

Associative memory model of human memory

Hasselmo ME, and Wyble BP. Free recall and recognition in a network model of the hippocampus: simulating effects of scopolamine on human memory function. Behav Brain Res 89: 1-34, 1997.

Stress and memory:

Becker, S, Macqueen, G and Wojtowicz, JM (2009) Computational modeling and empirical studies of hippocampal neurogenesis-dependent memory: Effects of interference, stress and depression. 2009 Nov 24;1299:45-54. Epub 2009 Aug 3.

Homework due Tuesday, 11/20 at 6pm

Slides used in class

24 Discussion (Mon, 11/19)

Working memory

Lisman JE, and Idiart MA. Storage of 7 +/- 2 short-term memories in oscillatory subcycles. Science 267: 1512-1515, 1995
Fransen E. Functional role of entorhinal cortex in working memory processing. Neural Netw 18: 1141-1149, 2005
Fuster JM. Cortical dynamics of memory. Int J Psychophysiol 35: 155-164, 2000.

(Wed 11/21) Thanksgiving break - No Class

25 Lecture (Mon, 11/26)

Quiz5 Lectures 2-23 - Key

Noradrenaline and signal-to-noise ratio

Hasselmo ME, Linster C, Patil M, Ma D, and Cekic M. Noradrenergic suppression of synaptic transmission may influence cortical signal-to-noise ratio. J Neurophysiol 77: 3326-3339, 1997
Usher M, Cohen JD, Servan-Schreiber D, Rajkowski J, and Aston-Jones G. The role of locus coeruleus in the regulation of cognitive performance. Science 283: 549-554, 1999.

26 Last lecture (Wed, 12/28)

Discussion - games - fun