GENESIS Modeling Tutorial

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 appropriate links to the Advanced Tutorials on Realistic Neural Modeling.

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.

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.

Modeling Calcium Concentration and Biochemical Reactions

Almost all regions of the brain receive one or more neuromodulatory inputs, and disrupting these inputs produces deficits in neuronal function. Neuromodulators act through intracellular second messenger pathways to influence the electrical properties of neurons, integration of synaptic inputs, spatio-temporal firing dynamics of neuronal networks, and, ultimately, systems behavior. Second messengers pathways consist of series of bimolecular reactions, enzymatic reactions, and diffusion. Calcium is the second messenger molecule with the most effectors, and thus is highly regulated by buffers, pumps and intracellular stores. Computational modeling provides an innovative, yet practical method to evaluate the spatial extent, time course and interaction among second messenger pathways, and the interaction of second messengers with neuron electrical properties. These processes occur both in compartments where the number of molecules are large enough to describe reactions deterministically (e.g. cell body), and in compartments where the number of molecules is small enough that reactions occur stochastically (e.g. spines). – In this tutorial, I explain how to develop models of second messenger pathways and calcium dynamics. The first part of the tutorial explains the equations used to model bimolecular reactions, enzyme reactions, calcium release channels, calcium pumps and diffusion. The second part explains some of the GENESIS, Kinetikit and Chemesis objects that implement the appropriate equations. In depth explanation of calcium and second messenger models is provided by reviewing code, both in XPP, Chemesis and Kinetikit, that implements simple models of calcium dynamics and second messenger cascades.

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

XML for Model Specification in Neuroscience

One of the main roles of the Neural Open Markup Language, NeuroML, is to facilitate cooperation in building, simulating, testing and publishing models of channels, neurons and networks of neurons. MorphML, which was developed as a common format for exchange of neural morphology data, is distributed as part of NeuroML but can be used as a stand-alone application. In this collection of tutorials and workshop summary, we provide an overview of these XML schemas and provide examples of their use in down-stream applications. We also summarize plans for the further development of XML specifications for modeling channels, channel distributions, and network connectivity.

What is the Relation between Human Practical Action and an Accompanying Discourse? Discussing the Status of Practical Theory

The article discusses the function of an accompanying discourse in relation to the genesis of human practical action. On the one side, theory cannot be taken as the ground for practical action; practical action is not a realisation of intentions. On the other hand, human practical action is accompanied by series of explanations, justifications, declarations of intent, pre‑ and post-rationalisations, motivations etc. These accompanying discourses seem in one way or the other to be necessary for the actual realisation of human practical action. Following Pierre Bourdieu, it is suggested that an accompanying discourse cannot in a meaningful manner be separated from the human practical action, that practical theory should be regarded not as theory but as part of practice, and that practical theory first of all provides a common language for talking about practice and hence for reproducing a fundamentally arbitrary idea of the genesis of human practical action. Parallels are drawn to the education/formal training of semi-professionals.

Die Revolution von 1848 – Kulte um die Toten und die Lebenden

In dem Beitrag wird der Genesis des Totenkults von 1848/49 und ebenso des Kults um lebende Revolutionsheroen sowie den Formen, den Wandlungen und der Funktion der darauf basierenden Erinnerungskulturen nachgegangen. Gezeigt wird u.a. erstens, dass der revolutionäre Totenkult in Deutschland nicht geeignet war, zu einem Nationalmythos zu werden, der die verschiedenen sozialen Gruppen und politischen Strömungen einte. Die öffentliche Erinnerung an die gefallenen Revolutionäre spaltete die Nation vielmehr nachhaltig, in Deutschland, nicht dagegen in anderen europäischen Ländern wie Ungarn oder Italien. Die pathetisch-feierliche Erinnerung an die unterschiedlichen Toten der Revolution von 1848/49 und die jenen unterschobene politische Sendung gab den Parteien jedenfalls in Deutschland überhaupt erst Kontur. Die entstehende Linke wie die Rechte verstanden sich als Testamentsvollstrecker des vermeintlichen politischen Willens der im Kampf gefallenen Revolutionäre bzw. ihrer Kontrahenten, der im Kampf „für König und Vaterland“ getöteten Soldaten. Der Totenkult wurde – erstens – für beide Seiten zum politischen Code; für die Linke markiert er zugleich den Beginn einer Art revolutionärer Familientradition. Der Totenkult, gleich welcher Couleur, implizierte Inklusion – und ebenso Exklusion: War der Totenkult zum politischen Code geworden, wurde ihm als zusätzliches Element das politische und soziale Gegenüber als Feindbild implementiert. Kollektive Ausgrenzung erlaubte, die jeweiligen, zumeist komplexen histo­risch-politischen Konfliktkonstellationen auszublenden bzw. auf griffige und personalisierte Grundmuster zu reduzieren. Zweitens: Obgleich zur ‚Parteisache’ geworden, war der von einer mal kleineren, mal größeren Minderheit zelebrierte Totenkult um die am 18. März 1848 in Berlin gefallenen Barrikadenkämpfer in der gesamtnationalen Erinnerung latent immer präsent. Drittens: Die Totenkulte sowie die politische Funktionalisierung von Begräbnissen sollten nicht den Blick dafür verstellen, dass ihnen schon relativ bald ein gleichfalls quasi-religiös aufgeladener Kult um herausragende lebende Revolutionäre wie Friedrich Hecker u.a. an die Seite trat. Auch dieser überlebte das Revolutionsjahr 1848 um Jahrzehnte, im Grunde – ruft man sich die zahlreichen Hecker-Devotionalien des Jahres 1998 in Erinnerung – bis heute.