In addition to the large amount of documentation available for GENESIS, there are many tutorials that have been written by GENESIS developers and users. Some of these teach general principles of neuroscience, illustrated with GENESIS simulations. Others teach both basic and advanced neural modeling. Finally, there a number of well-documented GENESIS research simulations that are available through the BABEL model archives, or that are included in the "Ultimate CD ROM" package described below.

Tutorials provided with the GENESIS distribution

The GENESIS distribution includes a number of demonstration simulations in the form of "user-friendly" tutorials. Several of these have been adapted from recent research simulations, in order to let the user have convenient access to the simulations. As the full simulation scripts are provided, they may be modified and used to create one's own simulations. The Book of GENESIS uses these simulations to teach concepts in computational neuroscience, as well as the use of GENESIS.

These are some of the tutorial simulations provided with GENESIS

• Tutorial 1 - extensible neuronal cable.
• Tutorial 2 - voltage clamp experiments on a compartment containing Hodgkin-Huxley channels.
• Tutorial 3 - neuronal tutorial to explore temporal & spatial summation of synaptic inputs.
• Tutorial 4 - burst firing in molluscan neurons.
• Tutorial 5 - Traub multi-compartmental CA3 pyramidal cell model.
• Tutorial 6 - small networks of neurons studied with a simulation based on central pattern generator circuits.
• Tutorial 7 - a piriform cortex simulation.
• Tutorial 8 - biochemical modeling with Kinetikit
• Tutorial 9 - Cerebellar Purkinje cell model.

Tutorials from the GENESIS web site

The GENESIS Neural Modeling Tutorials

The GENESIS Neural Modeling Tutorials are an evolving package of HTML tutorials intended to teach the process of constructing biologically realistic neural models with the GENESIS simulator. The most recent versions are derived from the supplementary material provided with the introductory GENESIS modeling tutorials at WAM-BAMM*05, and further refined during the 2006 Latin American School on Computational Neuroscience (LASCON).

View the GENESIS Neural Modeling Tutorials

Download the Tutorials package: Tutorials.tar.gz or Tutorials.zip

The GENESIS Neural Modeling Tutorials, and many of the Advanced Tutorials from WAM-BAMM*05, have been published in article form (both in browseable HTML and downloadable PDF format) in the November 2005 special issue on Realistic Neural Modeling in the electronic journal Brains, Minds, and Media (http://www.brains-minds-media.org/ ). Brains, Minds, and Media is an open access (free) eJournal for interactive and visual media in the neural and cognitive sciences. The journal provides peer-reviewed articles, software and interactive media for interactive and visual media in the neural and cognitive sciences. The journal provides peer-reviewed articles, software and interactive media for the neural and cognitive sciences with a particular focus on both education and teaching, and research on the relation between brains, minds and media.

The Ultimate GENESIS Modeling Tutorial Distribution

This is the latest version of a complete self-paced GENESIS modeling course that has been packaged for distribution on a CDROM, or installation on a hard drive. It brings together material that is available as separate downloads from the GENESIS web site and through the GENESIS Users Group. It includes several simulator-independent tutorials on biologically realistic neural modeling, as well as both tutorial and research simulations that have been implemented with GENESIS.

This collection is based on an extended version of the GENESIS Neural Modeling Tutorials package that contains other tutorials, the Book of GENESIS, GENESIS 2.3 source and binary distributions, and additional GENESIS network simulation scripts taken from the archives of BABEL, the GENESIS Users Group. These include the Nenadic, Ghosh and Ulinsky large scale model of turtle visual cortex, and the Menne, et al. hippocampal network model. A "Getting Started With Realistic Neural Modeling" guide has been added to this extended Tutorials package, with suggested exercises for self-paced study.

Browse the contents of the Ultimate GENESIS Modeling Tutorial Distribution, and the included cell and network simulation directories.

Download the Ultimate CDROM package as:

• Ultimate_CDROM.iso.zip - A zip-compressed CDROM image, ready for burning to CDROM after unzipping.

• Ultimate_CDROM.zip - A zip-compressed archive of the CDROM contensts, ready to unzip to a hard drive.

• Ultimate_CDROM.tar.gz - A gzipped tar archive of the CDROM contents, ready to extract to a hard drive.

These all have the same contents, and are each about 40 MB in size. This material is all freely distributable under the terms of various GNU licenses, so you are encouraged to copy it and pass it around to anyone who might want to incorporate it into a neuroscience or modeling course, or to give to a student as a start on an independent modeling project.

What is biologically realistic neural modeling?

These are introductory lectures on computational neuroscience and realistic neural modeling, illustrated with GENESIS tutorial simulations. There are sections on the Hodgkin-Huxley model and compartmental modeling that might be useful to those who are studying them for the first time, or who need some review. They are included in the "Ultimate CD ROM" package.

Download the set of lectures: cnslecs.tar.gz or cnslecs.zip.

View them here.

Contributed Tutorials from BABEL

This is a collection of tutorials submitted by members of the GENESIS Users Group, BABEL. The contents are described in the README, and may be viewed or downloaded from the index file. It includes the latest version of the Purkinje cell tutorial, which implements the full De Schutter and Bower (1994) detailed Purkinje cell model. This is an update to the version that is ncluded in the GENESIS 2.3 genesis/Scripts/purkinje directory.

The WB*05 Advanced Tutorials

Slides from the Advanced Tutorials on Neural Modeling presented at WAM-BAMM*05, March 31 - April 2, 2005,San Antonio, TX.

The GUM*02 Tutorials

Introductory through Advanced Tutorials on Neural Modeling presented at GUM*02, Nov. 8, 2002, San Antonio, TX.

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