README - Getting started with GENESIS

This README file tells you how to obtain, install, and run GENESIS and the GENESIS Neural Modeling Tutorials package. The main index to the tutorials is here.

If you are unfamilar with the UNIX command line environment, the short Introduction to UNIX or Linux will help you understand the instructions below.

Installing GENESIS

You may install the hypertext GENESIS Modeling Tutorials and the supplementary material for the Advanced GENESIS Tutorials anywhere on your computer, without installing GENESIS. However, you will get the most advantage from the tutorials if you install the GENESIS simulator first, and install the Tutorials in the "genesis" directory.

The first step is to download the latest GENESIS distribution from the GENESIS Web site If you are using Linux, Mac OS/X, or Microsoft Windows with Cygwin (a UNIX-like environment for Windows), you may download the appropriate GENESIS binary distribution that includes a precompiled "genesis" executable file. This will save you the trouble of compiling GENESIS from the source code that is included with the GENESIS source distribution.

The GENESIS distribution may be installed in whatever directory is most convenient. You do not need "root" privileges to install within your home directory. On the other hand, if you want a system-wide installation, /usr/local is a good place to install GENESIS. The distributed compressed tar file will have name like genesis-2.3-src.tar.gz, or if it is a binary distribution, genesis-2.3-linux-bin.tar.gz. It will unpack to produce the directory tree genesis-2.3/genesis and its subdirectories.

Use a terminal window to change to the directory in which you wish the GENESIS directory tree to reside, and (if the file you downloaded is called "genesis-2.3-src.tar.gz") give the Unix command:

    gunzip -c genesis-2.3-src.tar.gz | tar xvf -
For most Linux systems and those with gnu tar, you can simply use:
    tar xvzf genesis-2.3.src.tar.gz

If genesis-2.3-src.tar.gz, is not in this directory, give the full path to it, e.g.

    gunzip -c ~joeuser/downloads/genesis-2.3-src.tar.gz | tar xvf -

Begin by reading the README file in the genesis directory, and then follow the compilation instructions in genesis/src/README. If you are using a package with a precompiled executeable, there will be installation instructions in a README file within the unpacked genesis directory.

Installing the GENESIS Neural Modeling Tutorials

It is likely that the GENESIS Neural Modeling Tutorials have been installed with this file that you are reading. If not, download the Tutorials archive from the GENESIS Web site It is available as either Tutorials.tar.gz, or, which may be extracted with "unzip" or one of the tools used with Windows for extracting zip files. In either case, it extracts to a directory (folder) called "Tutorials". If you have installed GENESIS, you can extract the archive in the genesis directory, alongside the Scripts, Doc, Hyperdoc, and other GENESIS directories. This will allow you to treat it as an extension of the documentation in the GENESIS distribution.

The GENESIS tutorials refer to this "GENESIS Tutorials directory", which contains the tutorials themselves, this README file, and other directories such as the cells directory, which contains cell models that are used by the tutorials. The index.html file in the GENESIS Tutorials directory is the master index to the tutorials. It would be a good idea to set a bookmark to this file in your web browser, so that you will have the links to the tutorials and to the GENESIS documentation easily available.

If you have installed GENESIS, the hypertext GENESIS Reference Manual will be in genesis/Hyperdoc/Manual.html.

If you choose to install the supplementary material for the WAM-BAMM 2005 advanced tutorials, you can copy them into the Tutorials/advanced-tutorials directory. Alternatively, you may download the large "Ultimate GENESIS Tutorial Distribution" package from the GENESIS website This contains an extended version of the tutorials package, including other lengthy advanced tutorials, as well as source and binary distributions of GENESIS.

Running GENESIS simulations

You can try out some of the GENESIS demonstration and tutorial simulations in the genesis/Scripts directory. This directory and its subdirectories each have a README file with information about the files to be found in the directory. For example, assuming that the GENESIS directory is /usr/local/genesis, you can run the "Squid" tutorial on Hodgkin-Huxley channels by giving the commands:

    cd /usr/local/genesis/tutorials/squid
    genesis Squid

Other demos and tutorials that you might want to try are traub91, burster, neurokit, purkinje, and piriform. In some cases, you will want to copy a set of GENESIS simulation scripts into a directory of your own, so that you can modify the scripts or run simulations that create output files. (The permissions of the GENESIS directories are set so that you cannot write into them.) For this you can create your own Scripts directory with "mkdir ~/Scripts" and then copy a directory tree with a command such as

    cp -r /usr/local/genesis/Scripts/purkinje ~/Scripts

You can also try out some of the GENESIS cell and network simulations from the included archives of cell and network simulation scripts.

Once you are able to run these scripts, you can begin to modify them or write your own, using the information in the GENESIS Neural Modeling Tutorials.

Back to the main Tutorials Index.

Last update on: Fri Jun 12 16:25:43 MDT 2009