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SNNAP TUTORIAL

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88 pages

SNNAP
(SIMULATOR FOR NEURAL NETWORKS AND ACTION POTENTIALS)


Tutorial


January 2003


The University of Texas-Houston Medical School
Center for Computational Biomedicine
Department of Neurobiology and Anatomy
Houston, TX 77030
http://snnap.uth.tmc.edu
© 1993-2003 The University of Texas Health Science Center at Houston Tutorial Manual for Version 8 of SNNAP


Table of Contents
Chapter 1: Introduction to SNNAP................................................................................................................5
Introduction to Tutorial...............................................................................................................................6
Outline...................................................................................................................................................6
Typographic Conventions .....................................................................................................................7
Overview of the Capabilities of SNNAP.....................................................................................................8
Some Example Simulations to Illustrate the Capabilities of SNNAP .........................................................9
SNNAP Parameters and Units ................................................................................................................ 13
Chapter 2: Getting Started...................... 14
Instructions for ...
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SNNAP(SIMULATOR FORNEURALNETWORKS ANDACTIONPOTENTIALS)
Tutorial
January2003
The University of Texas-Houston Medical School Center for Computational Biomedicine Department of Neurobiology and Anatomy Houston, TX 77030
http://snnap.uth.tmc.edu
© 1993-2003 The University of Texas Health Science Center at Houston
Tutorial Manual for Version 8 of SNNAP
Table of Contents
Chapter 1: Introduction toSNNAP................................................................................................................ 5Introduction to Tutorial............................................................................................................................... 6Outline...................................................................................................................................................6Typographic Conventions ..................................................................................................................... 7
Overview of the Capabilities of SNNAP..................................................................................................... 8
Some Example Simulations to Illustrate the Capabilities of SNNAP ......................................................... 9
SNNAP Parameters and Units ................................................................................................................ 13
Chapter2:GettingStarted...........................................................................................................................14
Instructions for Installing SNNAP ............................................................................................................ 15Structure of Tutorial Examples Directory................................................................................................. 19Chapter 3: The Hodgkin-Huxley Neuron Model ........................................................................................... 21Hodgkin-Huxley Model ............................................................................................................................ 21Running the Hodgkin-Huxley Model With SNNAP................................................................................... 23Launching SNNAP .............................................................................................................................. 23Running a Simulation .......................................................................................................................... 24Printing Simulation Results ................................................................................................................. 27Changing Simulation Parameters............................................................................................................ 28Adding Current Injection...................................................................................................................... 28Changing Model Parameters................................................................................................................... 30Changing Model Conductance Parameter .......................................................................................... 31Changing Simulation Duration ............................................................................................................ 34Changing Output Display .................................................................................................................... 35Chapter 4: Bursting Neurons and Central Pattern Generators..................................................................... 38Introduction to Bursting Neurons ............................................................................................................. 39The Morris-Lecar Spiking Neuron Model................................................................................................. 39Simulation of the Morris-Lecar Model.................................................................................................. 40Description of the Morris-Lecar Model ................................................................................................ 41AddingIonicCurrents..............................................................................................................................42Ion Pools ............................................................................................................................................. 46SettingIonEquation............................................................................................................................52Changing Output Screen......................................................................................................................... 57Adding New Output Variable............................................................................................................... 58Multiple Output Graphs ........................................................................................................................... 59Displaying Ion Currents....................................................................................................................... 62
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Tutorial Manual for Version 8 of SNNAP
Central Pattern Generator Modulation..................................................................................................... 65
Chapter 5 Modeling Small Neuronal Networks .......................................................................................... 67
Introduction to Small Neuronal Networks ................................................................................................ 68Running a Small Neuronal Network Simulation .................................................................................. 68Synaptic Connections.............................................................................................................................. 70Changing Synaptic Strength ............................................................................................................... 75Building Networks ................................................................................................................................... 78Adding a Neuron to a Network ............................................................................................................ 79Adding a Synaptic Connection in a Network ....................................................................................... 81Conclusions.............................................................................................................................................85
Appendix: References ................................................................................................................................. 86
Published Studies That Used SNNAP..................................................................................................... 86Literature Cited in Manual ....................................................................................................................... 88
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Tutorial Manual for Version 8 of SNNAP
Disclaimer
SNNAP is distributedas is. This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty ofmerchantability orfitness a particular for purpose. The authors make no claims as to the performance of the program. Individuals who wish access to the source code should contactlgsaB.xaDuotmc.eudter@uth..
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Tutorial Manual for Version 8 of SNNAP
CHAPTER1:INTRODUCTION TOSNNAP
 Recently, there has been a dramatic increase in the number of neurobiologists using computational methods as an adjunct to their empirical studies. As experimental data continue to amass, it is increasingly clear that physiological and anatomical data alone are not enough to infer how neural circuits work. Researchers are recognizing the need for a quantitative modeling approach to explore the functional consequences of neuronal and network features. Computer simulations are an increasingly important tool for neuroscience research.
 
SNNAP  (Simulator for Neural Network and Action Potentials) was designed as
a tool for the rapid development and simulation of realistic models of single neurons and small neural networks. With SNNAP, all aspects of developing and running simulations are controlled through a user-friendly graphical interface. Thus, no programming skills are necessary to develop and run simulations. The electrical properties of individual neurons are described with either Hodgkin-Huxley type voltage- and time-dependent ionic currents or integrate and fire models. The connections among neurons can be made by either an electrical, modulatory or chemical synapse. The chemical synaptic connections are capable of expressing many forms of plasticity, such as homo- and heterosynaptic depression and facilitation. SNNAP also includes descriptions of intracellular second messengers and ions, which in turn, can be linked to ionic conductances or mechanisms regulating synaptic transmission. Thus, you can use SNNAP to simulate the modulation of cellular and synaptic properties. SNNAP can also be used to simulate the flow of current in multi-compartment models of cell. Many common experimental manipulations can be simulated, such as injecting current, voltage clamping and applying modulatory transmitters. SNNAP (since version 5) was implemented in the Java programming language. Thus, SNNAP can run on virtually any computer and with most operating systems.
 
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Tutorial Manual for Version 8 of SNNAP
INTRODUCTION TOTUTORIAL
This tutorial was designed for non programmers who are interested in carrying out computer simulations of neuroscience experiments. This hand-on tutorial will guide you through several examples using SNNAP. Each chapter was designed to introduce you to several basic SNNAP capabilities in a particular domain of neuroscience. You will learn how to use SNNAP to write mathematical models and run computer simulations in the various domains described in each chapter. This tutorial may complement an introduction to computational neuroscience or be a basis for further investigation.
Outline
This manual is a hands-on tutorial, designed to provide you with experience in using SNNAP as well as introduce you to several topics in computational neuroscience.
Chapter 1: nduroioctntIpresents an overview of SNNAP and this tutorial as well as a short description of SNNAP highlights.
Chapter 2:Getting Starteddescribes how to download and install the SNNAP software.
Chapter 3:Hodgkin-Huxley Neuron Modelpresents the classic neuronal model of Hodgkin and Huxley and shows how to run a simulation using SNNAP. This chapter also describes how to change basic simulation parameters and model parameters.
Chapter 4:Bursting Neurons and Central Pattern Generators a more describes complex model than the Hodgkin-Huxley model, while introducing the concept of an ion pool and second messenger, and how such elements can be used to modulate neuronal behavior with SNNAP.
Chapter 5:Small Networks presents a three neuron network of Hodgkin-Huxley models and shows how to build a network with synaptic connections using SNNAP. The network model can display oscillatory behavior because of the network architecture and synaptic connectivity.
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Typographic Conventions
Tutorial Manual for Version 8 of SNNAP
The following typographic conventions apply throughout this manual:
Code extracts and file names are written inthis typeface. 
Italic type is used to indicate user-specific information. Also, important ideas are
emphasized likethis.
Values that you must fill in (for example, a file name or a path name) also appears in the same typeface as code extracts but slanted to indicate you must supply an appropriate value; for example,SNNAPhome indicates that you must fill in a value forSNNAPhome.
Square brackets ([]) indicate optional items.
Ellipsis (...) indicate that you can repeat the information.
A vertical bar (|) indicates a choice within braces ({}) or brackets ([]).
The following vocabulary is used in this manual to explain how to navigate the menus of SNNAP:
Right-click: click the right mouse button.
Left-click: click the left mouse button.
Click: click either the right or left mouse button.
Menu>SubMenu0>…>SubMenun>Item: menu item identified by the path to access it.
SNNAPhome is the location where you have installed the SNNAP software. All locations presented in the manual start fromSNNAPhome.
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Tutorial Manual for Version 8 of SNNAP
OVERVIEW OF THECAPABILITIES OFSNNAP
 
A brief list of some of the capabilities of SNNAP (version 8) is provided below:
9simulate networks of up to 10000 neurons with electrical, chemical and modulatory synapticSNNAP can connections. SNNAP can simulation networks containing both Hodgkin-Huxley type neurons and Integrate-and-Fire 9 type cells. Moreover, the synaptic contacts among integrate-and-fire cells can incorporate learning rules that modify the synaptic weights. The User is provided with a selection of several non associative and associative learning rules. 9SNNAP can simulate the flow of current in multi-compartment models of neurons, which in turn, can be incorporated into neural networks. 9SNNAP can simulate intracellular pools of ions and / or second messengers that can modulate neuronal processes such as membrane conductances and transmitter release. Moreover, the descriptions of the ion pools and second-messenger pools can include serial interactions as well as converging and diverging interactions. For example, the synthesis of a second messenger (e.g., cAMP) can be regulated by both a modulatory transmitter and the levels of intracellular Ca2+. 9The number of ionic conductances as well as the number of intracellular pools of ions and second messengers that can be incorporated into a neuron is dynamically allocated. The User can add as many elements to a model as may be necessary to describe a given neuron. Thus, models of neurons can achieve a high level of sophistication. 9Chemical synaptic connections have User-defined kinetics (i.e., fast or slow), can produce either increases or decreases in postsynaptic conductance, can be excitatory or inhibitory, can have multiple components (e.g., fast and slow components, increase and decrease conductance components, excitatory and inhibitory components, etc.), and can manifest homosynaptic plasticity (i.e., depression, facilitation, or both). Chemical synaptic connections can include a description of a pool of transmitter that is regulated by 9 depletion and / or mobilization and that can be modulated by intracellular concentrations of ions and second messengers. Thus, the User can simulation heterosynaptic plasticity. synapses (both chemical and modulatory) can include a voltage-dependent component.Descriptions of 9 For example, a synapse can include a NMDA-like conductance. 9SNNAP can simulate asymmetrical electrical coupling between cells. 9number of experimental manipulations, such as injecting current into neurons,SNNAP can simulate a voltage clamping neurons, and applying modulators to neurons. In addition, SNNAP can simulate noise within any conductance (i.e., membrane, synaptic, or coupling conductances) and SNNAP can simulate a novel procedure for clamping a state variable in which the magnitude of a specified membrane current(s) can be clamped to a specified value at any given time. 9SNNAP includes aBatch Modeto assign any series of values toof operation, which allows the User any given parameter or combination of parameters. TheBatch Mode reruns the automatically simulation with each new value and displays, prints, and / or saves the results. 9The on-screen display can plot any combination of state variables in either the time domain and / or as a phase plane (i.e., one state variable vs. another). Moreover, the results of a simulation can be printed,
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Tutorial Manual for Version 8 of SNNAP
stored as a postscript file or stored as data file. The data file is in ASCII format and can be used by other software packages and / or by theOff-Line Viewerthat is provided with SNNAP. 9capabilities of SNNAP and that canSNNAP includes a large suite of example simulations that illustrate be used as a tutorial for learning how to use SNNAP or as an aid for teaching neuroscience. 9In addition to the example simulations, other supplemental information and software that is included with SNNAP including an electronic version (i.e., *.pdf) of the Users Manual, numerous Excel® spreadsheets, illustrates of simulations, and new program called CellMatrix. CellMatrix is a data-management tool for organizing empirical data that describe synaptic connections among identified neurons. This tool can be useful in developing models of small neural networks that are based on a large body of published literature. SNNAP was implemented in Java and can run on virtually any computer and under most operating 9 systems. 9 software, example files andSNNAP is freely available and can be downloaded via the internet. The Users manual are available atNNPAu.htt.cme.udhttp://S.
SOMEEXAMPLESIMULATIONS TOILLUSTRATE THECAPABILITIES OFSNNAP
 Detailed descriptions of the capabilities of SNNAP are provided inChapter 3 and Appendix B, which describe the equations incorporated into SNNAP and the example simulations that are distributed with SNNAP. To briefly illustrate some capabilities and potential uses of SNNAP, a few example simulations are presented below. Figure 1 illustrates how SNNAP can be used to simulate the biophysical properties of neurons, including relatively simple models of the action potential and neuronal excitability (e.g., the Hodgkin-Huxley model of the squid giant axon) and more complex models of autonomous bursting, intracellular second messengers, and modulation (e.g., the Butera et al. model of the R15 neuron inAplysia).
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Tutorial Manual for Version 8 of SNNAP
Fi ure 1.1. Usin SNNAP to model neurons with relativel sim le ro erties e. ., the s uid iant axon or to model neurons with more complex properties such as autonomous bursting, second messengers and modulation (e.g., R15). The equivalent circuit diagrams for both models are illustrated (A1 andB1). In addition, the intracellular regulatory pathways of the R15 model are illustrated (B1).A: Simulation of the Hodgkin and Huxley model of an action potential in the squid giant axon. This model has only two voltage-and time-dependent conductances.A2 SNNAP simulation illustrates the: TheBatch Modeof operation. In theBatch Modeare repeated automatically while systematically varying parameter, simulations values. In this exam le the ma nitude of the in ected de olarizin current ulse arrows was increased with each simulation and the results of each simulation were su erim osed. The SNNAP in ut files used to generate this simulation are included in the H type neurons/Examples /H _ _ _ /Biophysics 01subdirectory.B: Simulation of the Butera et al. model of the bursting neuron R15 in _ A l sia. orates addition, it incor In conductances.This model incor orates six volta e- and time-de endent two intracellular ools i.e., an ion ool of calcium and a ool of the second messa e cAMP . These ools, in turn, modulate several membrane conductances.B2: an variable allows the User to lot SNNAP in a model, such as the membrane volta e, intracellular concentration of calcium and s ecific membrane currents. The SNNAP input files used to generate this simulation are included in the/Examples /H H type neurons /R15subdirectory. _ _ _
In addition to simulating the complex biophysical properties of neurons (Figure
1), SNNAP can simulate the complexities of synaptic connections and synaptic plasticity
(both homo- and heterosynaptic plasticity). Several examples are illustrated in Figure
1.2. SNNAP can simulate synaptic connections with homosynaptic facilitation and / or
depression, synaptic connections with multiple components (e.g., fast and slow PSPs),
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Tutorial Manual for Version 8 of SNNAP
synaptic connections that produce decreased postsynaptic conductances as well as synaptic connections that are modulated via heterosynaptic connections. In addition, SNNAP can simulate modulatory synaptic connections (i.e., synaptic connections that drive the synthesis of second messengers in the postsynaptic neuron, not shown) and synaptic connections that are both voltage- and time-dependent (not shown). For example, SNNAP can simulate NMDA-type synaptic responses.
Fi ure 1.2. Simulatin s na tic connections and s na tic lasticit with SNNAP. Man different t es of s na ses and lasticit can be modeled. For exam le, homos na tic facilitation or de ressionA can be simulated. B includin a second messen er s stem that modulates transmitter release, heteros na tic lasticitB le com onses that have multi na tic res SNNAP can simulate s onentscan be simulated.Csuch as fast and slow otentials, and s na tic res onse that induce conductance decreasesD. The /Examples /Synaptic connections contains simulations similar to those subdirectory _ illustrated in this figure.
 Although SNNAP was designed to simulate neurons as a single, isopotential compartment, it can also simulate neurons as multi compartmental structures (Figure 1. 3). The fundamental computational unit of a SNNAP simulation is the *.neu file (i.e., neuron file). The *.neu files can be used to represent a single neuron or to represent individual compartments of a multi-compartment neuron. To develop a multi compartment model, the properties of the *.neu files are adjusted to match the morphological features of the neuronal compartments. These *.neu files are then linked together so as to reflect the branching structure of a given neuron. SNNAP incorporates several tools that help the User develop multi compartmental models. For example, the User can enter geometric parameters (e.g., the diameter and length of
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