Download the complete Tutorials package (Tutorials.zip - 54 MB)

CONTENTS

Introduction to Realistic Neural Modeling

David Beeman, University of Colorado, Boulder

This HTML document corresponds to the two-part tutorial given at the WAM-BAMM*05 meeting in San Antonio, Texas.

Part I - Introduction to Realistic Neural Modeling for the Beginner: 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 II - Getting Started with Modeling Using GENESIS: This builds upon the background of Part I 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 (WAM-BAMM 2005 edition)

This tutorial 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 the Advanced Tutorials on Realistic Neural Modeling.

The NEURON simulator - recent developments

This tutorial gives a brief overview of the use of NEURON for realistic neural modeling, with an emphasis on recently added features. The tutorial describes the use of the NEURON ChannelBuilder and graphical specification of inhomogeneous channel density with the CellBuilder.

Advanced Tutorials on Realistic Neural Modeling

These tutorials and slide presentations by various authors were given at the WAM-BAMM*05 workshop on realistic neural modeling, March 31, 2005, San Antonio, TX. They cover the construction of large networks, modeling calcium dynamics and biochemical reactions, modeling case studies, the use of the GENESIS spike train objects, parameter searching, Parallel GENESIS (PGENESIS), the neuroConstruct network construction environment, and the use of XML for model specification.

• Realistic Single Cell Modeling - From experiment to simulation
  Dieter Jaeger, Emory University
• Simulating in vivo-like synaptic input patterns in multicompartmental models
  Jeremy Edgerton, Emory University
• Constructing Large-scale Network Models
  Michael Vanier, California Institute of Technology
• Parameter Searching in Neural Models
  Michael Vanier, California Institute of Technology
• Modeling Calcium and Biochemical Reactions
  Avrama Blackwell, George Mason University
• Parallel (P-) GENESIS: its use and applications
  Greg Hood, Pittsburgh Supercomputing Center (Carnegie Mellon University)
• Building 3D Network Models with neuroConstruct
  Padraig Gleeson, University College London
• XML for Model Specification - a workshop
  Moderator: Sharon Crook, Arizona State University

Other resources for modelers

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 a section on the Hodgkin-Huxley model that might be useful to those who are studying it for the first time, or who need some review.

The GENESIS Reference Manual

This gives information on the local installation of GENESIS and the Tutorials directory, telling you where to find various files, and how to run GENESIS demonstration and tutorial simulations. It is intended to be customized for the local installation.