CISC 3250: Systems Neuroscience



Class times: Monday and Thursday, 10:00 – 11:15am, John Mulcahy Hall (JMH) 342
Instructor: Prof. Daniel D. Leeds (my homepage)
Office: JMH 332
E-mail:
Office hours: Monday 11:30am – 12:30pm and Thursday 4:30 – 5:30 pm, and by appointment

Full syllabus is available here.
Course announcements and assignments will be posted over the course of the semester.

Course text: "Fundamentals of Computational Neuroscience" (suggested); "Computational Cognitive Science" (suggested)

Matlab: We will be introduced to the Matlab computing environment in this course and use it selectively in homework assignments across the semester. You may use the copy available in the JMH 330 computer lab, but it also would be beneficial for you to download the Student license for $50 from Mathworks.

Sections below:

  1. Announcements
  2. Supplemental readings
  3. Slides
  4. Resources
  5. Assignments

Announcements:
Apr 21, 2:20pm: To remind everyone, Exam 2 covers homeworks 3 and 4 --- lectures 4, 5, M2, M3. Practice examples have been posted.

Apr 10, 11:50pm: HW 5 will be released after break and due May 1; the final will be May 11, 9:30-11:30am

Mar 27, 2:15pm: We'll meet in the computer lab for class Thursday, March 30. ALSO, Exam 2 will be on April 24.

Feb 25, 10:00pm: We'll meet in the computer lab for the start of class Monday, February 27.

Feb 10, 10:45am: Exam 1 will take place on Thursday, March 2, covering lecture 1, M1, 2, and probably 3.

Feb 9, 1:10am: Class cancelled due to snow day! Stay tuned, though --- homework 2 will be posted soon!

Jan 30, 10:30pm: We will meet in the JMH 330 computer lab on Thursday, February 2

Supplemental readings:
All readings are in Trappenberg, and they are optional.
TopicReadingEquations
Philosophy of neural modelingChapter 1: all (predominantly for perspective)
The neuron — biology and input/output behaviorChapter 2: 2.1, 2.2 (through 2.2.2);
Chapter 3: 3.1 (through 3.1.2), 3.3, 3.4.1, 3.4.5, 3.5		 3.1-3.4; 3.33, 3.35; 3.44; 3.45, 3.46
Learning in the neuronChapter 4: 4.1, 4.3 (through page 101), 4.4.3 4.3, 4.8, 4.10; 4.24, 4.27, 4.28, 4.29
Neural systems and neuroanatomyChapter 5: 5.1
Representations in the brainChapter 7: 7.1, 7.5.1, 7.5.4 7.25-7.28, 7.40-7.42
Perception(Chapter 10: 10.1 ... optional, we will cover a simpler model in class)
Attention-related cellular mechanisms: 3.5.1, 3.5.3
Online chapter 6		 3.45
Memory/learning7.3.2-3, 8.1, 9.4
Motor control9.5, 9.6 (particularly 9.6.4)


Slides:
Check slides after each lecture - I sometimes update the slides with additional content based on class discussion

Lecture 1, The neuron biology and behavior.
Animation: movement of action potential down the axon

Lecture M1, Intro to Matlab, we will use a MAT file available here and another MAT file available here

Lecture 2, Learning in the neuron

Lecture 3, Functional neuroanatomy

Lecture M2, Matlab multi-dimensional matrices, we will use a MAT file Brain Anatomy and MAT file fMRI data

Lecture 4, Representations in the brain. V1 neuron responses -- check out first 3 minutes

Lecture 5, Perception.

Lecture M3, Linear algebra and pattern comparisons, and here is related correlation data

Lecture 6, Motor control - example of failed error correction with cerebllar ataxia

Lecture 7, Memory

Lecture 8, The Big Picture

Resources:
Below are exam 1 practice questions! Questions are randomly color-coded. I recommend trying to answer one set of colored questions first (for example, red questions), review the answers to those questions, and then move on to another set of colored questions (for example, green).
Note: The term "template recognition" used in one of the practice questions is synonymous with the term "prototype recognition."

Below are exam 2 practice questions

Below are final exam practice questions

Assignments:
Homework 1 - due February 6; for the last part of Question 3, assume v(0ms)=-65mV.
Homework 1 answers.
76.5 - 85 "A range"
68 - 76.5 "B range"
59.5 - 68 "C range"
51 - 59.5 "D range"


Homework 2 - due THURSDAY February 23; for question 6 use the MAT file S11_LOCbehav.mat.
HW 2 answers - answers now completed!
56 - 62 "A range"
50 - 56 "B range"
44 - 50 "C range"
38 - 44 "D range"

Exam 1 answers
61 - 68 "A range"
54 - 61 "B range"
47 - 54 "C range"


Homework 3 - due Monday March 27; use S11_LOCbehav.mat and S1brain.mat
HW 3 answers
121 - 109 "A range"
109 - 96 "B range"
96 - 83 "C range"


Homework 4 - due Monday April 10; use S11_localizer.mat
HW 4 answers
HW71-79 "A range"
62-71 "B range"
52-62 "C range"
41-52 "D range"

Exam 2 answers
72 - 81 "A range"
63 - 72 "B range"
54 - 63 "C range"


Homework 5 - due Monday May 1
HW 5 answers