Introduction to Realistic Neural Modeling

This document corresponds to the tutorial on realistic neural modeling given by David Beeman at WAM-BAMM*05, the first annual meeting of the World Association of Modelers (WAM) Biologically Accurate Modeling Meeting (BAMM) on March 31, 2005 in San Antonio, TX. 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 details 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.

Realistic Single Cell Modeling – from Experiment to Simulation

This tutorial gives a step by step explanation of how one uses experimental data to construct a biologically realistic multicompartmental model. Special emphasis is given on the many ways that this process can be imprecise. The tutorial is intended for both experimentalists who want to get into computer modeling and for computer scientists who use abstract neural network models but are curious about biological realistic modeling. The tutorial is not dependent on the use of a specific simulation engine, but rather covers the kind of data needed for constructing a model, how they are used, and potential pitfalls in the process.

Teaching Cognitive Modeling Using PDP++

PDP++ is a freely available, open source software package designed to support the development, simulation, and analysis of research-grade connectionist models of cognitive processes. It supports most popular parallel distributed processing paradigms and artificial neural network architectures, and it also provides an implementation of the LEABRA computational cognitive neuroscience framework. Models are typically constructed and examined using the PDP++ graphical user interface, but the system may also be extended through the incorporation of user-written C++ code. This article briefly reviews the features of PDP++, focusing on its utility for teaching cognitive modeling concepts and skills to university undergraduate and graduate students. An informal evaluation of the software as a pedagogical tool is provided, based on the author’s classroom experiences at three research universities and several conference-hosted tutorials.