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The GENESIS Neural Modeling Tutorials

Extended Version

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. This version is derived from tutorials used at the first annual meeting of the World Association of Modelers (WAM) Biologically Accurate Modeling Meeting (BAMM), held March 31st - April 2nd 2005, in San Antonio, Texas. It was further developed during use in the Frankfurt Institute of Advanced Studies (FIAS 2006) summer school on theoretical neuroscience and complex systems, and the Latin American School on Computational Neuroscience (LASCON 2006-2014).

Versions of these 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 the neural and cognitive sciences with a particular focus on both education and teaching, and research on the relation between brains, minds and media.

These tutorials are copyright by David Beeman, the GENESIS developers, and others as noted. All are freely distributed and licensed under the terms of the GNU General Documentation License or other compatible licenses. See the Copyright and License Information for details.

Getting Started With Realistic Neural Modeling

This is a guide to using this "extended" version of the Tutorials package, which contains additional material from the GENESIS web site and the GENESIS Users Group (BABEL) archives of models.

Introduction to Realistic Neural Modeling with GENESIS

David Beeman, University of Colorado, Boulder

This HTML document is an expanded version of various presentations on the use of GENESIS for realistic neural modeling given at GENESIS users meetings (GUM 2002, WAM-BAMM 2005 and 2006), the EU Advanced Course on Computational Neuroscience, the Latin American School on Computational Neuroscience (LASCON 2006 and 2008) and the Frankfurt Institute of Advanced Studies (FIAS 2006) summer school on theoretical neuroscience and complex systems.

Part I - Modeling the Brain: Simplified vs. Realistic Models: This gives an overview of realistic neural modeling and the levels of detail that a model may require.

Part II - Brief Overview of Realistic Neural Modeling Techniques: This is a general overview and introduction to compartmental cell modeling and realistic network simulation for the beginner. Although examples are drawn from GENESIS simulations, the tutorial emphasizes the general modeling approach, rather than the details of using any particular simulator.

Part III - Getting Started with Modeling Using GENESIS: This builds upon the background of Part II to describe some deails of how this approach is used to construct cell and network simulations in GENESIS. It serves as an introduction and roadmap to the extended hands-on GENESIS Modeling Tutorial.

GENESIS Modeling Tutorial

This is the main tutorial of the package, and is intended to be a "quick start" to creating simulations with GENESIS. It should give you the tools and enough information to let you quickly begin creating cells and networks with GENESIS, making use of the provided example simulations. Advanced topics are covered by apppropriate links to optional tutorial material in the Advanced Tutorials on Realistic Neural Modeling.

The "README" file

This tells you how to obtain, install, and run GENESIS and the GENESIS Neural Modeling Tutorials package.

The cells/ and networks/ directories

These browseable directories contain GENESIS cell and network models that are used or referenced in the GENESIS Modeling Tutorial.

Introduction to UNIX or Linux

This is a short guide to getting around in the UNIX command line environment for Windows and Mac users.

An Introduction to Computational Neuroscience

These "webified" introductory lectures on computational neuroscience and realistic neural modeling are derived from lecture notes for an introductory biomedical engineering course at the University of Colorado. It has 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.

The GENESIS Reference Manual

PDF version of "The Book of GENESIS"