Return to the GENESIS main index

GENESIS tutorials and examples

The directories beneath genesis/Scripts include a series of simulations designed to be run under GENESIS. In each case, you will need to change into the appropriate directory and follow the directions given in the README file for that directory.

These simulations fall into two categories. The "neuroscience tutorials" and their README files are:

These simulations were designed as interactive tutorials for teaching concepts in neurobiology and neural modeling. As their use requires no knowldge of GENESIS programming, they are suitable for use in a computer simulation laboratory which would accompany upper division undergraduate and graduate neuroscience courses. Each of these has on-line help and a number of suggested exercises or "experiments" which may be either assigned as homework or used for self-study. These tutorials may also be taken apart and modified to create your own simulations, as they are reasonably well commented. Several of them are derived from existing research simulations.

Further details of these tutorials and the theory behind them are given in "The Book of GENESIS" by James M. Bower and David Beeman. The file ../Doc/BoG.txt provides more information about this book.

The tutorial on single neuron behavior in "Scripts/neuron" is a good one to start with, as it has fairly extensive built-in help available. To run it, give the command "genesis Neuron" and click the left mouse button on the box labeled "help" once it appears.

"Scripts/squid" contains a simulation of voltage and current clamp experiments on the giant squid axon. The tutorial also provides the ability to block channels, to plot the Hodgkin-Huxley activation variables, and to generate state plots. The accompanying exercises help the student understand the Hodgkin-Huxley model and the procedure used to calculate rate parameters from voltage clamp experiments. Other exercises elucidate the basis of post-inhibitory rebound and refractory period. Documentation is contained in the file squid/squid.txt and the squid/README.txt file. Give the command "genesis Squid" to run the tutorial and then click on "help".

The "cable" tutorial simulates an extensible neuronal cable. Current injection or synaptic input may be provided to any one of the compartments, and all relevant parameters are adjustable from "pop-up" menus.

The "burster" tutorial examines mechanisms which lead to burst firing in molluscan neurons and the effects of the various types of ionic channels which are commonly found. The simulation is implemented within the Neurokit cell builder environment and can also serve as an introduction to Neurokit. This allows the user to modify most of the relevant parameters and assumptions used in the model and to investigate the causes of many of the features seen in molluscan pacemaker firing patterns. The cell which is modeled is a "generic burster", loosely modeled after the Aplysia R15 cell, although it contains channel models fitted to measurements on bursting neurons in several different molluscs. The README file gives instructions for running the tutorial.

The "traub91" tutorial is based upon a GENESIS recreation of the hippocampal pyramidal cell model of Traub, et. al. [R.D.Traub, R. K. S. Wong, R. Miles, and H. Michelson, Journal of Neurophysiology, Vol. 66, p. 635 (1991)] This tutorial also uses Neurokit to explore some of the properties of the model. The file "traub91proto.g" may also be used as an example of the implementation of Ca concentration dependent channels in GENESIS. The README file gives instructions for running the tutorial.

"CPG" is a tutorial on central pattern generator circuits by Sharon Crook (U. of Maryland). The simulation is designed to allow you to study the activation patterns and emergent behavior of a simple neuronal network of four cells. The simulation allows you to set any pattern of connections between the cells, using either excitatory or inhibitory connections, and to vary the cell and channel parameters.

The "piriform" directory contains a "user-friendly" adaptation of the research simulation used by Wilson and Bower to model the processing of olfactory inputs to the piriform cortex. This scaled-down version of the original simulation uses 135 each of pyramidal cells, feedforward and feedback inhibitory interneurons, arranged in a 9 x 15 array. To run the simulation, type "genesis Piriform" and click on the box labeled "help" when it appears.

The "purkinje" tutorial is based upon a GENESIS simulation of a cerebellar Purkinje cell, modeled and fine-tuned by Erik de Schutter. The tutorial assumes that you have a basic knowledge of the Purkinje cell and its synaptic inputs. It gives visual insight in how different properties as concentrations and channel conductances vary and interact within a real Purkinje cell.

The "demos" are intended as examples of simulations which can be built with the package. The demos and their documentation currently include:

The Scripts/tutorials directory contains the GENESIS scripts which are listed in Appendix B of "The Book of GENESIS". These scripts are used in Part II of the book with tutorials which guide the user through the process of constructing GENESIS simulations.

The Orient_tut simulation (in Scripts/orient_tut) is a simplistic version of the Hubel and Weisel orientation selectivity model over a small region of the V1. It is used as an example in Chapter 18 of "The Book of GENESIS" in order to describe the utility functions for setting up large networks. Chapter 22 is also relevant for understanding some of the advanced XODUS features which are used here. It does not have built-in help, but has a detailed README file.

"MultiCell" simulates two simple neurons in a feedback configuration. This simulation, written by Matt Wilson in 1989, illustrates the "old" way of making connections between neurons with the axon and channelC2 objects used in GENESIS versions 1.x. These scripts have been converted to GENESIS 2.0 with the "convert" utility and make use of the X1compat (XODUS 1 compatible) widgets and the Connection Compatibility (oldconn) library. It thus serves as an example of the conversion of a GENESIS 1 simulation to GENESIS 2.

The "neurokit" directory contains one of the most elaborate of the simulations. It provides a number of tools for building and editting complex neurons and uses a sophisticated graphical interface. Although the scripts are quite complicated, the program is easy to use. Type "genesis Neurokit" to start the simulation and, after a while, a command bar will appear at the top of the screen. Click the left mouse button on "help" and follow the directions.

The "kinetikit" directory contains the latest of our "kits" for building simulations with a graphical interface. This program is used for modeling biochemical kinetics reactions, and provides a convienient interface for the use of the objects in the kinetics library. See the README file in this directory for details, or plunge ahead and type "genesis Kinetikit" from within this directory.

The files in genesis/Scripts/channels provide an introduction to the channel editing facilities provided by neurokit, and illustrate the use of the library of prototype channels. This tutorial should be run after the user has tried out Neurokit itself.

The genesis/Scripts/vclamp directory has paradigm files for doing a voltage clamp analysis of ion channels. It is meant as a tutorial on how neurokit can be used to simulate electrophysiological experiments. Familiarity with neurokit is assumed.

The Scripts/int_methods tutorial is a tutorial on the different integration methods accessible through neurokit and available for use in your simulations.

The Scripts/examples directory contains a few short demonstration scripts giving examples of simulations involving new GENESIS features. The Scripts/examples/XODUS subdirectory contains examples illustrating new features of XODUS that have been incorporated into GENESIS 2.0 and later versions. There are several new and revised examples for GENESIS 2.2. The Scripts/examples/README file gives further details.

The Scripts/newlib directory contains sample C source code, header files, and Makefiles for compiling new commands and objects into GENESIS. The procedure is documented in the GENESIS Reference Manual Section "Customizing GENESIS", and in the text files in the genesis/Doc directory, Customizing.txt, NewGenesis.txt, and NewObjects.txt.

The Scripts/param directory contains demonstrations of the parameter search library developed by Mike Vanier, and first introduced in GENESIS 2.2. For an introduction to parameter searching with GENESIS, see the documentation for ParameterSearch and Paramtable and the README file in Scripts/param.

The Scripts/chemesis directory contains tutorial scripts and example scripts to teach how to develop models of second messengers and calcium dynamics. A step-by-step explanation of the Calx.g scripts is provided in CalTut.txt and CalTut.html. 'chemesis' is a library of objects for creating models of biochemical reactions, second messengers, and calcium dynamics that was developed and contributed to the GENESIS 2.4 libraries by K. T. (Avrama) Blackwell. The Scripts/gpython-tools directory contains a collection of stand-alone Python-based graphical utilities for plotting, visualizing, and analyzing the output of GENESIS 2 and GENESIS 3 (G-3) simulations. The scripts are well documented and commented, and may be modified for use with other data.

The Scripts/stdp_rules directory contains both a text and HTML tutorial on using the stdp_rules object, along with example scripts. This new GENESIS 2.4 object has been added for efficiently implementing spike timing dependent plasticity in large networks of hsolved multicompartmental cells.

The Scripts/VAnet2 directory contains an improved hsolved implementation of the dual exponential conductance version of the Vogels-Abbott network model. It serves as a tutorial on how to achieve a speed improvement of 10 to 20 times when using hsolve with network models.

To try out the simulations, cd to the desired directory and look at the README file for information on running the simulation. It is best to do this from a terminal window at the bottom of the screen, so that that it will not be completely covered up by the displays created by the simulations.

IMPORTANT NOTE:

Before running these simulations, make sure that you have added the directory in which GENESIS resides to your search path. You will also need to have a copy of .simrc in your home directory. This file will need to be edited if GENESIS has not been installed in the place specified in the file. In order to access the Neurokit simulation, your .simrc file should use the SIMPATH environment variable to set a path to the neurokit and neurokit/prototypes directories. Normally, the .simrc file will be properly configured during the installation of GENESIS. Further details are given in the src/README file.

To run the simulations, you will need to change into the appropriate directory and follow the directions given in the README file for that directory. In most cases, this will consist of typing "genesis main-script-name", where "main-script-name" is the main simulation script that includes other files in the directory. In a few cases, the simulation will attempt to write data to files when it runs. Usually the README file will warn you of this. If the Scripts directories are installed in a system area for which you do not have write permission, you may need to copy the simulation directory to a directory of your own in which you are allowed to create files.

Return to the GENESIS main index