Simulating in vivo-like Synaptic Input Patterns in Multicompartmental Models

In the laboratory of Dr. Dieter Jaeger at Emory University, we use computer simulations to study how the biophysical properties of neurons—including their three-dimensional structure, passive membrane resistance and capacitance, and active membrane conductances generated by ion channels—affect the way that the neurons transfer synaptic inputs into the action potential streams that represent their output. Because our ultimate goal is to understand how neurons process and relay information in a living animal, we try to make our computer simulations as realistic as possible. As such, the computer models reflect the detailed morphology and all of the ion channels known to exist in the particular neuron types being simulated, and the model neurons are tested with synaptic input patterns that are intended to approximate the inputs that real neurons receive in vivo. The purpose of this workshop tutorial was to explain what we mean by ‘in vivo-like’ synaptic input patterns, and how we introduce these input patterns into our computer simulations using the freely available GENESIS software package (http://www.genesis-sim.org/GENESIS). The presentation was divided into four sections: first, an explanation of what we are talking about when we refer to in vivo-like synaptic input patterns

Using P-GENESIS for Parallel Simulation of GENESIS Models

P-GENESIS is an extension to the GENESIS neural simulator that allows users to take advantage of parallel machines to speed up the simulation of their network models or concurrently simulate multiple models. P-GENESIS adds several commands to the GENESIS script language that let a script running on one processor execute remote procedure calls on other processors, and that let a script synchronize its execution with the scripts running on other processors. We present here some brief comments on the mechanisms underlying parallel script execution. We also offer advice on parallelizing parameter searches, partitioning network models, and selecting suitable parallel hardware on which to run P-GENESIS.

VR Based Visualization and Exploration of Plant Biological Data

This paper investigates the use of virtual reality (VR) technologies to facilitate the analysis of plant biological data in distinctive steps in the application pipeline. Reconstructed three-dimensional biological models (primary polygonal models) transferred to a virtual environment support scientists' collaborative exploration of biological datasets so that they obtain accurate analysis results and uncover information hidden in the data. Examples of the use of virtual reality in practice are provided and a complementary user study was performed.