Neurobiology Laboratory Exercises
in Software

Research-quality Software
for Neuroscience Education



This project addresses the basic need in neuroscience education for a means to illustrate and explore the processes that underlie neuronal function. To meet this need, we are creating a series of laboratory simulation exercises designed to advance neuroscience education by


Goals and Background
Starting Point
Integrating these exercises into the curriculum
Simulations and "wet lab" experiments


NEURON's home page at Yale


The Development Team

Ted Carnevale, Department of Psychology, Yale University
Michael Hines, Department of Computer Science, Yale University
David Jaffe, Division of Life Sciences, University of Texas, San Antonio



Project goals

The primary aim of this project is to create a set of laboratory simulation exercises, with an accompanying manual, that will advance neuroscience education. The emphasis is on education at the undergraduate level, but these exercises should also be suitable for introductory graduate level courses.

An important secondary aim of this project is to make a powerful simulation tool available to neuroscience students early in the course of their education. NEURON is used widely in research, so students who go on to advanced studies will experience a double benefit from these exercises.


Simulations for neuroscience education

Neuronal function involves the interaction of chemical and electrical signals that are distributed in space and time. These signals are generated by mechanisms that typically have complex dynamics and nonlinearities. Therefore a student's introduction to neuronal function should not be limited to static figures on a printed page.

What is needed is a means to illustrate and explore the processes that underlie the function of nerve cells and brain circuits. Integrating properly selected and designed simulation exercises into the neuroscience curriculum can increase motivation, enhance correct intuition, and help students visualize concepts. The simulations we are developing are designed to meet this need.


Empowering the next generation of Neuroscientists

For the first time in the history of neuroscience education, a simulation tool that is used widely in neuroscience research will be introduced to undergraduate students. The potential importance of this becomes clear when one considers that SPICE and other simulation tools appropriate for the physical sciences have long been available on microcomputers to engineering undergraduates, whereas until recently no research-grade neural simulator has been accessible to undergraduates. This disparity is even more striking when one reflects on the fact that the dynamics and nonlinearities of neuronal mechanisms are more complex than those encountered by electrical engineering undergraduates (Weiss et al. 1992).

Reference Weiss, T.F., Trevisan, G., Doering, E.B., Shah, D.M., Huang, D. and Berkenblit, S.I.. Software for teaching physiology and biophysics. J. Science Education and Technology 1:259-274, 1992.


Strengths of this project

These exercises

Limitations of present "educational simulators"

Unlike engineering or physics students, who acquire both knowledge and skills while they do their homework with SPICE (Nagel 1975), Mathematica (Wolfram Research, Inc.), or MatLab (The MathWorks, Inc.), a student who uses one of the present "educational simulators for neuroscience" is not simultaneously learning about a tool that will be helpful in his or her future career.

All assume a single compartment.
Most are limited to Hodgkin-Huxley currents and simple synaptic conductances.

Most are linked to only one text.
All are limited to one or two platforms.

The exercises we are developing have none of these limitations.



Nagel, L.W.. SPICE2: a computer program to simulate semiconductor circuits. ERL Memo No. ERL-M520, Electronics Research Laboratory, Berkeley, CA, University of California, May, 1975.



Our starting point

In the fall of 1994, David Jaffe first used NEURON in his laboratory course in neurobiology for undergraduates at the University of Texas, San Antonio. The exercises he created covered a wide variety of topics including electrotonus, synaptic plasticity, and intracellular calcium dynamics. The simulations were implemented using NEURON under UNIX and had a simple text-based user interface with oscilloscope-like graphic output.

In one laboratory session, students examined the properties of conductance-increase synapses. One of the tasks was to examine the effects of synaptic location on synaptic potency (ability to trigger action potentials) and measurements made at the soma. Since the simulations were constructed with NEURON, the students were able to control synaptic placement. This helped them to immediately visualize the effects of synaptic location on voltage attenuation and the ability of synaptic inputs to fire the cell. This would not have been possible with existing educational simulators.

Students then explored non-linear summation and the effect of driving force on the amplitude of synaptic potentials. They also compared measurements of synaptic potentials and synaptic currents to learn how to use quantitative methods to study the biophysics of synapses.

Experiments such as these are simply not feasible in a typical "wet" neurobiology laboratory. However, in conjunction with classical experiments, such as measuring end-plate potentials from frog muscle, these simulations can be used to extend and enhance the wet lab experience.


Project Outline

Development of the exercises will be a pragmatic, iterative process guided by an assessment of needs derived from our own in-classroom experience, a formal evaluation mechanism, and the recommendations of an Advisory Panel. The Advisory Panel includes educators who have considerable experience teaching neuroscience to undergraduates. Some of our advisors have themselves developed software for neuroscience education. Their input will be indispensable in topic selection and in "fine-tuning" the exercises.

Achieving the objectives of this project entails five related tasks:

1. Selecting topics. Topic selection will be motivated only by pedagogical considerations and will not be restricted by mere technical factors, since far more sophisticated simulations than these are feasible using NEURON on microcomputers that currently cost $1000 or less.

2. Designing and implementing the exercises. Each exercise will have both a text component and a software component.

The text component will contain a statement of the purpose of the exercise, pointers to background material in several neuroscience textbooks, and a brief description of internals of the model. We do not intend to produce a stand-alone neuroscience textbook, but a short statement of the key scientific principles that are involved will be included, with citations of the primary literature as appropriate. This will be followed by a set of questions and suggested computer activities to motivate and convey the didactic content of the exercise.
The software component will implement a model that embodies the principles that are under consideration, and will have a student-friendly, graphical user interface. We will try to facilitate incorporation of the exercises in undergraduate neurobiology "wet lab" courses by designing the models to emulate aspects of common experimental preparations.

3. Keying the exercises to widely-used neuroscience texts. The final selection of texts will depend on the best current educational practice. This list will be strongly influenced by needs assessment conducted with our Advisory Panel.

4. Evaluating and revising the exercises is discussed here.

5. Communicating project results and distributing the exercises is covered here.


Project evaluation

The educational utility of these exercises will be assessed by their impact on student performance and attitudes regarding neuroscience. We want the exercises to focus on learning rather than the computer, and are particularly interested in optimizing the ratio of effort to insight. Therefore we must know the results of "hands-on" use in many classrooms other than ours. For overall guidance in project evaluation, we have enlisted the assistance of a consultant who is an expert in the evaluation of the use of computers in education. We are also getting feedback from a panel of advisors who have considerable experience teaching neuroscience to undergraduate and graduate students at several colleges and universities

Project dissemination

5. Communicating project results and distributing the exercises. Communications between the development team and the Advisory Panel will be facilitated through the Internet. Research users of NEURON are already supported through an extensive set of Web pages and an electronic "mailing list." New revisions of the educational software and text will be distributed to the advisors via a new family of WWW "project pages," and we will establish a project newsgroup to enable communication among the development team and advisors.

We will also bring the results of this project to the broader community of neuroscience educators, in part through the Internet and in part through poster presentations and special interest gatherings at the annual meetings of the Society for Neuroscience.

One direct outcome of this project will be a manual that documents the completed exercises. To help educators tailor these simulations to their own needs, the manual will also contain a short tutorial on how to modify and create models with NEURON. We will arrange for the manual and software to be distributed by a major scientific publisher. Initial discussions have already begun with several publishers, and all are quite enthusiastic about this project.

Integrating these exercises into the curriculum

Measures that we are taking to help integrate these exercises into the curriculum include:

These measures will increase the utility and availability of these exercises to all students who are exposed to neuroscience.

Simulations and "wet lab" experiments

One item that will receive special attention is how to coordinate these exercises with "wet lab" experiments. The educational process ideally should include both simulations and wet lab. The value of wet lab experiments can be reinforced and amplified by simulations that include thought-provoking "what if" scenarios. It will be highly desirable for future neuroscientists to be able to combine these investigational strategies in their research activities, whether independently or in collaboration with others. Regardless of whether one is primarily an experimentalist or a modeler, it is useful to have some experience with both.

Therefore some or all of the simulation exercises will be designed to be complementary to actual experiments on preparations that are appropriate for undergraduates, e.g. frog sciatic nerve, crayfish neuromuscular junction. The strategy we ultimately use will depend on our own in-class experience and the recommendations of our Advisory Panel.

To accommodate differences in emphasis, selection of topics, and teaching style, it is important to give teachers the ability to tailor simulations to their own classroom and laboratory needs. Therefore we will offer assistance to those members of our Advisory Panel who are interested in modifying or creating their own simulations. Furthermore, a section of the manual will include examples that illustrate how to modify the model source code. In this manner we hope to draw students from using "canned simulations" into creating their own models.

The outcome of this project will be a set of exercises that can be used in conjunction with almost any undergraduate lecture or lab course in order to stimulate student interest and participation, illustrate concepts that are otherwise difficult to grasp, and foster correct intuitions about important mechanisms in neurobiology.