NSC 4368.
501—Computational Neuroscience—Spring 2007
Green Hall GR4.708 (neuroscience teaching lab) Thursday evenings, 7:00PM – 9:45PM
Instructor Contact Information
Larry Cauller Ph.D.
JO4.214 972-883-2436
lcauller@utdallas.edu
Office hours: Tuesdays and Thursdays 1:00PM
Teaching Assistants
______________________________________________________________________________________________________
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Prerequisites: NSC 4356, Neurophysiology
(may be waived with instructor permission)
Course Description:
In this course, you will learn how to use state-of-the-art
computer software to construct realistic neural models and
simulate the dynamic behavior of realistic neurons and
networks of neurons connected with realistic synapses.
Computer simulation provides an unprecedented method to
study the complex interplay of the biophysical mechanisms that
govern the biologically realistic behavior of neurons and
synaptic neural networks. The tremendous growth of
computational neuroscience over the past three decades has
paralleled the development of powerful neuron-simulation
software. Two sophisticated neuron-simulation environments
have been developed with major funding from the NSF and
ONR, and have now been released for public distribution. By
providing a standardized forum for controlled experimentation
and critical scientific analysis, this state-of-the-art software has
unified the computational neuroscience community and spurred
the further growth of active research employing these advanced
methods for neuro-simulation.
These new tools have been developed specifically to make
these powerful neuro-simulation methods available to many
more students, educators and researchers who lack the
specialized training and advanced computer programming
skills previously needed to perform the sophisticated neuro-
simulaiton operations embodied in these new tools. These new
tools provide a friendly graphical user interface (GUI)
environment that enables all neuroscientists, novice and expert
alike, to quickly build 3-D computer models of neurons and load
them with neural mechanisms from an extensive built-in library
by means of simple point-drag-and-click operations. Unlike the
simulators of the past, when users had to wade through the
obscure codes of text-based programs, with the advent of
friendly new GUI environments neuro-simulation research today
is more like drawing objects with popular applications such as
Illustrator or mathCAD, and playing video games (especially if
you’re a neuro-nerd).
Students will gain the essential skills to use these new tools by
working hands-on with the software in the classroom to
complete a series of increasingly sophisticated Exercises.
Students will learn how to use the software in class where they
can directly observe the instructor step through each Exercise
on a large-screen computer monitor. The instructor will
introduce each new Exercise by openly demonstrating new
operations to the class, and will follow-up after students have
completed the Exercise, by personally completing the Exercise
in class to discuss the significance of the results and personally
address any specific problems students may have encountered.
This incremental training method, with personal supervision in
the classroom, is specifically intended to maximize the
opportunity for every student to acquire the essential skills to
take full advantage of these sophisticated neuro-simulation
tools.
Students will receive advanced instruction on topics spanning
neuroscience, from cellular to systems, specifically related to
the preparation and interpretation of the computational models
presented as part of the course. The course will work on
models specifically chosen to demonstrate how students may
employ these new tools to gain a deeper understanding of
specific neural mechanisms (e.g. voltage-sensitive channels or
synaptic plasticity) with respect to the roles such mechanisms
may play in neural behavior and the functions it serves.
Computational neuroscience research recognizes the essential
complexity of biological systems and embraces the intractable
complexity generated by simulations constructed with realistic
mechanisms. Students will become familiar with many of these
realistic mechanisms including the non-linear kinetics and
multi-factor dependence of ionic channels, spatial and temporal
summation of synaptic and neuromodulatory inputs, synaptic
plasticity and neural interactivity, oscillations, pattern generation
and dynamical network behavior. Neuro-simulation makes it
possible to access every variable at every moment and control
every parameter to examine in detail the role of each
mechanism in the overall behavior of the system. Students will
discover they may use their simulations to realize their
understanding and express their explanation of how specific
mechanisms influence neural behavior.
It is important for students to recognize that the methods of
computational neuroscience are fundamentally different from
the methods of ‘artificial intelligence’ or artificial ‘neural
networks’. Such artificial systems are founded upon extreme
mathematical simplification and are based upon top-down
designs that implement theoretical models. While the
simplification of artificial systems has facilitated progress
through the era of relatively slow computer power, the limitations
of such simplified systems are now widely acknowledged. In
contrast, ‘biological realism’ is the foremost concern of
contemporary research in computational neuroscience which
emphasizes reconstruction of realistic neural structures
assembled from the bottom-up out of realistic neural elements.
The new neuro-simulation software is poised to leap ahead
with the accelerating pace of computational power which is
rapidly approaching the point where the full potential of
computational neuroscience methods will produce significant
breakthroughs, both with the realistic simulation of increasingly
large-scale models of complex neural behavior, and with the
identification of the neural mechanisms whose importance for
higher functions is otherwise lost in the process of artificial
simplification.
This course will culminate in Final Student Projects that will give
students the opportunity to demonstrate their ability to
successfully employ these new tools. Students will construct
neural models and run simulations related to specific neural
functions chosen from suggestions offered in class (e.g. listed
below) or developed by students with the help of the instructor to
address particular student interests. This final exercise is
primarily intended to strengthen student confidence in the use of
these new tools and kindle their enthusiasm to employ neuro-
simulation methods as part of their independent exploration into
the neural basis of the higher functions (e.g. perception or
learning) or dysfunctions (e.g. Alzheimers or Parkinsons
Disease) that engage their personal interests and motivate their
long-term effort to become professional neuroscientists,
researchers and physicians.
Specifically, this course will train students how to use the
NEURON simulation environment developed at Duke and Yale
Universities (east coast), one of the two popular neural
simulation applications (versus GENESIS from Caltech, west
coast), both of which are freely available over the internet (see
NEURON link below). The authors of NEURON have played a
central role in the growth of neural simulation methods for
research. The National Science Foundation has funded the
development of NEURON specifically as a teaching tool for
medical and neuroscience educators, and we will take
advantage of the NEURON lessons available from their website.
NEURON provides a great range of tools that are
simultaneously simple enough for users to quickly learn and
make significant progress, and yet powerful enough to meet the
demands of even the most advanced researchers (i.e.
customized mechanisms and simulation objects may be written
in MODL and compiled into the NEURON environment).
NEURON is rather fun to play with, but it is no toy... it is a
sophisticated, state-of-the-art neuro-simulation environment
used worldwide.
While some familiarity with computers is required for this
course, it is not necessary for students to be computer
programmers or to have technical knowledge of programming
languages or computer hardware. Students that have taken the
Neurophysiology core course will be better prepared to grasp
the significance of the Exercises and tackle more sophisticated
Projects. However, a basic understanding of action potentials
(i.e. membrane potential and voltage-dependent sodium and
potassium channels) is sufficient to complete the Exercises,
learn how to use NEURON and successfully complete the
course. While students may receive special permission to take
this course without the Neurophysiology prerequisite, this
course is not recommended for students that have absolutely
no background in neuroscience.
Student Learning Objectives:
After completing the course, students should be able to:
1. Describe the fundamental principles of Computational
Neuroscience
2. Explain the importance of Computational Neuroscience
methods for neuroscience research.
3. Interpret and criticize published applications of neuron-
simulation methods.
4. Skillfully employ state-of-the-art neuro-simulation software to
construct and simulate realistic computer models of
neurons.
5. Construct and successfully simulate neuro-simulations of
complex neural functions.
6. Employ neuro-simulation to study and explain fundamental
neural mechanisms.
7. Orally present a neuro-simulation project.
8. Write a formal paper to report the rationale, methods, results
and conclusions of a neuro-simulation project.
9. Be qualified to apply for positions in neuroscience research
laboratories.
Textbooks and materials:
No textbooks are required for this course.
Students interested in a general survey of Computational
Neuroscience Methods may find the following recommended
text useful:
Lytton WW (2002) From Computer to Brain (paperback),
Springer-Verlag, NY, NY.
This course will employ the latest version of the NEURON
simulation software which may be downloaded for free from…
http://www.neuron.yale.edu/neuron/install/install.html
Students are encouraged to install NEURON on their personal
computers.
Additional materials useful for the course may be accessed
from that Yale NEURON website…
http://www.neuron.yale.edu
The neurophysiology worksheets available from my website
provide a basic primer that may be useful for this course…
NeuroPhysiologyWorksheets
Exercises and Student Projects
All students will be given sufficient opportunity to complete all
course requirements during class time and/or by appointment
using the computer systems available in the Neuroscience
Teaching Lab classroom (GR4.708).
Exercises: Students must complete 7 Exercises involving the
use of NEURON on computers in the lab during class time
under the direct supervision of the instructor.
Student Projects: Students will be required to complete
simulation Projects that successfully demonstrate their ability to
use the NEURON simulator.
1. The Student Project simulation must be related to a
specified neural function. Suggested functions for
simulation include:
a. The role of lateral inhibition for contrast
enhancement as in the ‘mach band’ illusion.
b. Central pattern generators for coordinated
movements such as locomotion or swimming.
c. The parameter space of cellular mechanisms
involved in spontaneous patterned or bursting
neuron behavior.
d. Networks that switch behavioral states under the
influence of neuro-modulators such as sleep-
wakefulness, or resting-seizure.
e. Additional suggestions and examples from
previous courses will be presented.
2. Alternatively, with the assistance of the Instructor, Students
may propose simulations of functions that relate to their
personal interests.
3. Teams of up to 3 students may work on a common Project
with a corresponding increase in the expected
sophistication of the simulation.
4. Students must orally present their Projects to the whole
class and respond to follow-up questions with
conscientious answers. (For teams – each student must
make an individual contribution to the presentation and the
follow-up answers.)
5. Every student must submit a Paper that summarizes their
 Projects. (Each member of a team must personally write a
separate paper.) Project Papers must include:
a. The rationale for the simulation including cited
references to any external sources of information
used in the design of the model.
b. Printed ‘screen shots’ with captions demonstrating
i. The structure of the model
ii. The results of simulations
c. A brief discussion of
i. The simulation results and
ii. Conclusions about the significance of the
simulation with respect to the neural
function it was designed to mimic
Attendance: Student attendance and participation in each
class will be directly noted by the instructor.
Grading Policy
10% of the overall grade will be based upon attendance and
participation.
40% of the overall grade depends upon the satisfactory
completion of all 7 NEURON Exercises. (The instructor will
address in class any problems students encountered in their
work on each Exercise.)
50% of the overall grade will be based upon the Student Project
25% will depend upon the oral presentation of the Project
25% will depend upon the Student Project paper
Course & Instructor Policies
Keep up with the Exercises: Every effort has been made to
maximize the opportunity for every student to acquire the
essential skills to use this sophisticated software. If you must
miss a class, you must work extra hard to catch up with the help
of a classmate.
Be considerate and helpful of your classmates: Students must
work closely in groups sharing the computers available in the
lab. Students are encouraged to bring their personal computers
into the lab with them to alleviate some of the congestion. You
should privately pass the codeword ‘body crystal’ to anyone that
drives everyone away from your computer. And everyone should
take the hint graciously in the spirit of collegiate camaraderie.
No competition is necessary for success in this course.
Cooperation will help everyone succeed.
 These descriptions and timelines are subject to change at the discretion of the Professor.
Date Topic Assignments and Due Dates
Jan. 11 Introduction to Neural Simulation Tools in Computation Explore NEURON links on
Neuroscience Yale Website…
www.neuron.yale.edu
18 NEURON Installation and Basic Operations
Introduction to NEURON Exercise 1: Cable Properties
25 Review of NEURON Exercise 1 NEURON Exercise 1 due
Introduction to NEURON Exercise 2: Action Potential Generation
Feb. 1 Review of NEURON Exercise 2 NEURON Exercise 2 due
Introduction to NEURON Exercise 3: Axonal Conduction
8 Review of NEURON Exercise 3 NEURON Exercise 3 due
Introduction to NEURON Exercise 4: Synaptic Integration
15 Review of NEURON Exercise 4 NEURON Exercise 4 due
Exploring Parameter Space: What Computational Neuroscientists
do
Introduction to NEURON Exercise 5: Exploring the Action Potential
Parameter Space
22 Review of NEURON Exercise 5 NEURON Exercise 5 due
Introduction to NEURON Exercise 6: Synaptic Interaction Between
Two Neurons
Mar. 1 Review of NEURON Exercise 6 NEURON Exercise 6 due
Initial Preparations for the Student Projects: Choosing teammates
and Project topics
8 SPRING BREAK Have fun
15 Futher Preparations for the Student Projects: Open class All teams must be identified by
discussion of this date
chosen Project topics
Introduction to NEURON Exercise 7: Dynamic Behavior of Small
Neural Networks
22 Review of NEURON Exercise 7 NEURON Exercise 7 due
Presentation of Example Student Project in class by Instructor All Project topics must be
finalized by this date.
29 Review of Progress on Student Projects with Instructor Guidance Initial progress on Project
Advanced Instruction in specific topics chosen for Student Projects expected
Apr. 5 Review of Progress on Student Projects with Instructor Guidance Further progress on Project
Examples of Published Simulation Studies Relevant to Student expected

Projects
12 Review of Progress on Student Projects with Instructor Guidance Near completion of Project
expected
19 First Presentations of Student Projects All Projects should be
completed
26 FINALS WEEK All Student Project Papers
Remaining Presentations of Student Projects Due
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