The Book of GENESIS
Springer-Verlag New York Inc.
978-1-4612-7224-3 (ISBN)
I Neurobiological Tutorials with GENESIS.- 1 Introduction.- 1.1 Computational Neuroscience.- 1.2 Using This Book.- 2 Compartmental Modeling.- 2.1 Modeling Neurons.- 2.1.1 Detailed Compartmental Models.- 2.1.2 Equivalent Cylinder Models.- 2.1.3 Single and Few Compartment Models.- 2.2 Equivalent Circuit of a Single Compartment.- 2.3 Axonal Connections, Synapses and Networks.- 2.4 Simulation Accuracy.- 2.4.1 Choice of Numerical Integration Technique.- 2.4.2 Integration Time Step.- 2.4.3 Accuracy of GENESIS.- 3 Neural Modeling with GENESIS.- 3.1 What Is GENESIS?.- 3.1.1 Why Use a General Simulator?.- 3.1.2 GENESIS Design Features.- 3.1.3 GENESIS Development.- 3.2 Introduction to the Tutorials.- 3.3 Introduction to the GENESIS Graphical Interface.- 3.3.1 Starting the Simulation.- 3.3.2 The Control Panel.- 3.3.3 Using Help Menus.- 3.3.4 Displaying the Simulation Results.- 4 The Hodgkin—Huxley Model.- 4.1 Introduction.- 4.2 Historical Background.- 4.3 The Mathematical Model.- 4.3.1 Electrical Equivalent Circuit.- 4.3.2 HH Conventions.- 4.3.3 The Ionic Current.- 4.4 Voltage Clamp Experiments.- 4.4.1 Characterizing the K Conductance.- 4.5 GENESIS: Voltage Clamp Experiments.- 4.6 Parameterizing the Rate Constants.- 4.7 Inactivation of the Na Conductance.- 4.8 Current Injection Experiments.- 4.9 Exercises.- 5 Cable and Compartmental Models of Dendritic Trees.- 5.1 Introduction.- 5.2 Background.- 5.2.1 Dendritic Trees: Anatomy, Physiology and Synaptology.- 5.2.2 Summary.- 5.3 The One-Dimensional Cable Equation.- 5.3.1 Basic Concepts and Assumptions.- 5.3.2 The Cable Equation.- 5.4 Solution of the Cable Equation for Several Cases.- 5.4.1 Steady-State Voltage Attenuation with Distance.- 5.4.2 Voltage Decay with Time.- 5.4.3 Functional Significance of ? and ?m.- 5.4.4 The Input Resistance Rin and “Trees Equivalent to a Cylinder”.- 5.4.5 Summary of Main Results from the Cable Equation.- 5.5 Compartmental Modeling Approach.- 5.6 Compartmental Modeling Experiments.- 5.7 Main Insights for Passive Dendrites with Synapses.- 5.8 Biophysics of Excitable Dendrites.- 5.9 Computational Function of Dendrites.- 5.10 Exercises.- 6 Temporal Interactions Between Postsynaptic Potentials.- 6.1 Introduction.- 6.2 Electrical Model of a Patch of Membrane.- 6.2.1 Voltage Response of Passive Membrane to a Current Pulse.- 6.3 Response to Activation of Synaptic Channels.- 6.3.1 The Postsynaptic Current.- 6.3.2 The Postsynaptic Potential.- 6.3.3 Smooth Synaptic Conductance Change: The “Alpha Function”.- 6.4 A Remark on Synaptic Excitation and Inhibition.- 6.5 GENESIS Experiments with PSPs.- 6.5.1 Temporal Summation of Postsynaptic Potentials.- 6.5.2 Nonlinear Summation of Postsynaptic Potentials.- 6.6 Concluding Remarks.- 6.7 Exercises and Projects.- 7 Ion Channels in Bursting Neurons.- 7.1 Introduction.- 7.2 General Properties of Molluscan Neurons.- 7.3 Ionic Conductances — The Dance of the Ions.- 7.3.1 Action Potential Related Conductances.- 7.3.2 Control of Bursting Properties.- 7.4 A Model Molluscan Neuron.- 7.4.1 Adrift in Parameter Space.- 7.4.2 Implementation of the Model.- 7.4.3 Modeling the Channels.- 7.5 The Molluscan Neuron Simulation.- 7.5.1 Using Neurokit.- 7.5.2 Understanding the Results.- 7.6 The Traub Model CA3 Pyramidal Cell.- 7.6.1 Experiments with the Traub Model.- 7.6.2 Firing Patterns.- 7.7 Exercises.- 8 Central Pattern Generators.- 8.1 Introduction.- 8.2 Two-Neuron Oscillators.- 8.2.1 Phase Equation Model of Coupled Oscillators.- 8.2.2 Simulation Parameters.- 8.2.3 Initial Conditions.- 8.2.4 Synaptic Coupling.- 8.2.5 Non-Phase Equation Models.- 8.3 Four-Neuron Oscillators.- 8.3.1 Chains of Coupled Oscillators.- 8.3.2 Simulation Parameters.- 8.3.3 Modeling Gaits.- 8.4 Summary.- 8.5 Exercises.- 9 Dynamics of Cerebral Cortical Networks.- 9.1 Introduction.- 9.2 Piriform Cortex.- 9.3 Structure of the Model.- 9.3.1 Cellular Complexity.- 9.3.2 Network Circuitry.- 9.4 Electroencephalography.- 9.5 Using the Tutorial.- 9.5.1 Getting Started.- 9.5.2 Generating Simulated Data.- 9.5.3 Initial Look at Simulated Activity.- 9.5.4 Observing Network Behavior.- 9.5.5 Varying Network Parameters.- 9.6 Detailed Examination of Network Behavior.- 9.7 Summary.- 9.8 Exercises.- 10 The Network Within: Signaling Pathways.- 10.1 Introduction.- 10.1.1 Nomenclature.- 10.1.2 A Short Short Course in Biochemistry.- 10.1.3 Common Signaling Pathways.- 10.2 Modeling Signaling Pathways.- 10.2.1 Theory.- 10.2.2 Sources of Data.- 10.2.3 Figuring Out the Mechanisms.- 10.2.4 Reaction Rate Constants.- 10.2.5 Enzyme Rate Constants.- 10.2.6 Initial Concentrations.- 10.2.7 Refining the Model.- 10.3 Building Kinetics Models with GENESIS and Kinetikit.- 10.3.1 The kinetics Library.- 10.3.2 Kinetikit.- 10.3.3 A Feedback Model.- 10.3.4 Beyond Kinetikit.- 10.3.5 Connecting Kinetic Models to the Rest of GENESIS.- 10.4 Summary: Molecular Computation.- 10.5 Exercises.- II Creating Simulations with GENESIS.- 11 Constructing New Models.- 11.1 Structurally Realistic Modeling.- 11.2 The Modeling Process.- 11.2.1 Single Neurons or Networks.- 11.2.2 Modeling Steps.- 12 Introduction to GENESIS Programming.- 12.1 Simulating a Simple Compartment.- 12.2 Getting Started with GENESIS.- 12.3 GENESIS Objects and Elements.- 12.3.1 Creating and Deleting Elements.- 12.3.2 Examining and Modifying Elements.- 12.4 Running a GENESIS Simulation.- 12.4.1 Adding Graphics.- 12.4.2 Linking Elements with Messages.- 12.4.3 Adding Buttons to a Form.- 12.5 How GENESIS Performs a Simulation.- 12.6 Exercises.- 13 Simulating a Neuron Soma.- 13.1 Some GENESIS Script Language Conventions.- 13.1.1 Defining Functions in GENESIS.- 13.2 Making a More Realistic Soma Compartment.- 13.2.1 Some Remarks on Units.- 13.2.2 Building a “Squid-Like” Soma.- 13.2.3 GIGO (Garbage In, Garbage Out).- 13.3 Debugging GENESIS Scripts.- 13.4 Exercises.- 14 Adding Voltage-Activated Channels.- 14.1 Review.- 14.2 More Fun With XODUS.- 14.3 Voltage-Activated Channel Objects.- 14.3.1 The hh_channel Object.- 14.3.2 Adding Hodgkin—Huxley Na and K Channels to the Soma.- 14.4 Final Additions and Improvements.- 14.4.1 Use of the Compartment initVm Field.- 14.4.2 Overlaying GENESIS Plots.- 14.5 Extended Objects.- 14.6 Exercises.- 15 Adding Dendrites and Synapses.- 15.1 Adding a Dendrite Compartment.- 15.2 Providing Synaptic Input.- 15.3 Connections Between Neurons.- 15.4 Learning and Synaptic Plasticity.- 15.4.1 Continous Modification of the Synaptic Weight.- 15.4.2 Use of the MOD Message.- 15.4.3 Hebbian Learning with the hebbsynchan.- 15.4.4 Customizing the synchan or hebbsynchan.- 15.5 Where Do We Go from Here?.- 15.6 Exercises.- 16 Automating Cell Construction with the Cell Reader.- 16.1 Introduction.- 16.2 Creating a Library of Prototype Elements.- 16.2.1 Future Changes in the Cell Reader.- 16.2.2 The protodefs.g Script.- 16.3 The Format of the Cell Descriptor File.- 16.4 Modifying the Main Script to Use the Cell Reader.- 16.5 The Neurokit Simulation.- 16.6 Exercises.- 17 Building a Cell with Neurokit.- 17.1 Introduction and Review.- 17.2 Customizing the userprefs File.- 17.2.1 Step 1.- 17.2.2 Step 2.- 17.2.3 Step 3.- 17.3 The Cell Descriptor File.- 17.4 Some Experiments Using Neurokit.- 17.5 Exercises and Projects.- 18 Constructing Neural Circuits and Networks.- 18.1 Introduction.- 18.2 The Orient_tut Simulation.- 18.3 Running the Simulation.- 18.4 Creating a Network Simulation.- 18.5 Defining Prototypes.- 18.6 Creating Arrays of Cells.- 18.7 Making Synaptic Connections.- 18.7.1 Specifying Individual Synaptic Connections.- 18.7.2 Commands Involving Groups of Synapses.- 18.7.3 Utility Functions for Synapses.- 18.8 Setting Up the Inputs.- 18.9 Summary.- 18.10 Exercises.- 19 Implementing Other Types of Channels.- 19.1 Introduction.- 19.2 Using Experimental Data to Make a tabchannel.- 19.2.1 Setting the tabchannel Internal Fields.- 19.2.2 Testing and Editing the Channel.- 19.3 Using Equations for the Rate Constants.- 19.4 Implementing Calcium-Dependent Conductances.- 19.4.1 Calculating the Calcium Concentration.- 19.4.2 The AHP Current.- 19.4.3 The C-Current.- 19.4.4 Other Uses of the table Object.- 19.4.5 The vdep_gate Object.- 19.4.6 Using the tab2Dchannel Object.- 19.5 NMDA Channels.- 19.6 Gap Junctions.- 19.7 Dendrodendritic Synapses.- 19.8 Exercises.- 20 Speeding Up GENESIS Simulations.- 20.1 Introduction.- 20.2 Some General Hints.- 20.3 Numerical Methods Used in GENESIS.- 20.3.1 The Differential Equations Used in GENESIS.- 20.3.2 Explicit Methods.- 20.3.3 Implicit Methods.- 20.3.4 Instability and Stiffness.- 20.3.5 Implementation of the Implicit Methods.- 20.4 The setmethod Command.- 20.5 Using the hsolve Object.- 20.5.1 Modes of Operation.- 20.5.2 Rules for Table Dimensions.- 20.6 Setting up hsolve.- 20.6.1 The findsolvefield Function.- 20.6.2 The DUPLICATE Action.- 20.7 Experiments with the hsolve Object.- 20.8 Exercises.- 21 Large-Scale Simulation Using Parallel GENESIS.- 21.1 Introduction.- 21.2 Classes of Parallel Platforms.- 21.3 Parallel Script Development.- 21.4 Script Language Programming Model.- 21.4.1 Parallel Virtual Machine.- 21.4.2 Namespace.- 21.4.3 Execution (Threads and Synchronization).- 21.4.4 Simulation and Scheduling.- 21.4.5 Node-Specific Script Processing.- 21.4.6 Asynchronous Simulation.- 21.4.7 Zones and Node Identifiers.- 21.4.8 Remote Function Call.- 21.4.9 Asynchronous Remote Function Call.- 21.4.10 Message Creation.- 21.5 Running PGENESIS.- 21.5.1 The pgenesis Startup Script.- 21.5.2 Debug Modes.- 21.6 Network Model Example.- 21.6.1 Setup.- 21.6.2 Simulation Control.- 21.6.3 Lookahead.- 21.7 Parameter Search Examples.- 21.8 I/O Issues.- 21.9 Summary of Script Language Extensions.- 21.9.1 Startup/Shutdown.- 21.9.2 Adding Messages.- 21.9.3 Synaptic Connections.- 21.9.4 Remote Command Execution and Synchronization.- 21.9.5 PGENESIS Objects.- 21.9.6 Modifiable PGENESIS Parameters.- 21.9.7 Unsupported and Dangerous Operations.- 21.10 Exercises.- 22 Advanced XODUS Techniques: Simulation Visualization.- 22.1 Introduction.- 22.2 What Can Your User Interface Do for You?.- 22.3 Draw/Pix Philosophy.- 22.4 Meet the Cast.- 22.4.1 The Draw Widget Family.- 22.4.2 The Pix Family.- 22.5 XODUS Events.- 22.5.1 Returning Arguments to Script Functions.- 22.6 Using Advanced Widgets: A Network Builder.- 22.6.1 The Library Window.- 22.6.2 Making Prototype Cells.- 22.6.3 The Work Window.- 22.6.4 Editing Cells.- 22.6.5 Connecting Cells.- 22.6.6 Plotting Cell Activity.- 22.6.7 Running Netkit.- 22.6.8 Extending Netkit.- 22.7 Interface vs. Simulation.- 22.8 Summary.- A Acquiring and Installing GENESIS.- A.1 System Requirements.- A.2 Using the CD-ROM.- A.3 Obtaining GENESIS over the Internet.- A.4 Installation and Documentation.- A.5 Copyright Notice.- B GENESIS Script Listings.- B.1 tutorial2.g.- B.2 tutorial3.g.- B.3 tutorial4.g.- B.4 tutorial5.g.- B.5 hhchan.g.- B.6 hhchan_K.g.- B.7 userprefs.g.- B.8 cellproto.g.- Index of GENESIS Commands.- Index of GENESIS Objects.
Zusatzinfo | 10 Tables, black and white; 34 Illustrations, black and white; XXIV, 458 p. 34 illus. With CD-ROM. |
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Verlagsort | New York, NY |
Sprache | englisch |
Maße | 178 x 254 mm |
Gewicht | 920 g |
Themenwelt | Mathematik / Informatik ► Informatik ► Software Entwicklung |
Informatik ► Theorie / Studium ► Künstliche Intelligenz / Robotik | |
ISBN-10 | 1-4612-7224-6 / 1461272246 |
ISBN-13 | 978-1-4612-7224-3 / 9781461272243 |
Zustand | Neuware |
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