Computing the brain: a guide to neuroinformatics
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
San Diego [u.a.]
Acad. Press
2001
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XIII, 380 S. Ill., graph. Darst. |
| ISBN: | 0120597810 |
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| 245 | 1 | 0 | |a Computing the brain |b a guide to neuroinformatics |c ed. by Michael A. Arbib ... |
| 264 | 1 | |a San Diego [u.a.] |b Acad. Press |c 2001 | |
| 300 | |a XIII, 380 S. |b Ill., graph. Darst. | ||
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| adam_text | Con
Contributors ix
Preface xi
Part 1
INTRODUCTION
Chapter 1.1
Neurolnformatics: The Issues 3
Michael A. Arbib
1.1.1 Overview 3
1.1.2 Modeling and Simulation 8
1.1.3 Databases for Neuroscience Time Series 14
1.1.4 Visualization and Atlas Based Databases 17
1.1.5 Data Management and Summary Databases 19
1.1.6 The Neurolnformatics Workbench 26
References 27
Chapter 1.2
Introduction to Databases 29
Wen Hsiang Kevin Liao and Dennis McLeod
Abstract 29
1.2.1 An Overview of Database Management 29
1.2.2 Historical View of Key Database Developments 30
1.2.3 Relational Database Model 31
1.2.4 SQL 32
1.2.5 Object Based Database Models 33
1.2.6 Object Relational Database Model 37
1.2.7 An Overview of Federated Database Systems 38
References 39
Part 2
MODELING AND SIMULATION
Chapter 2.1
Modeling the Brain 43
Michael A. Arbib
tents
Abstract 43
2.1.1 Modeling Issues 43
2.1.2 Parietal Premotor Interactions in the Control of
Grasping 46
2.1.3 Basal Ganglia 48
2.1.4 Cerebellum 53
2.1.5 Hippocampus, Parietal Cortex, and Navigation 61
2.1.6 Discussion 67
References 67
Chapter 2.2
NSL Neural Simulation Language 71
Michael A. Arbib, Amanda Alexander, and Alfredo
Weitzenfeld
2.2.1 Modeling and Simulation of Neural Networks 72
2.2.2 NSL Modules and Simulation 74
2.2.3 The NSL System 83
2.2.4 Simulating a Model—The Maximum Selector Model 85
2.2.5 Maximum Selector Model 85
2.2.6 Available Resources 89
References 89
Chapter 2.3
EONS: A Multi Level Modeling System
and Its Applications 91
Jim Shih Liaw. Ying Shu, Taraneh Ghaffar, Xiaping Xie, and
Theodore W. Berger
2.3.1 Introduction 91
2.3.2 EONS Object Library 92
2.3.3 Protocol Based Simulation 98
2.3.4 Conclusion 100
References 100
Chapter 2.4
Brain Imaging and Synthetic PET 103
Amanda BischotT Grethe and Michael A. Arbib
Abstract 103
2.4.1 PET Imaging and Ncurophysiology 103
2.4.2 Denning Synthetic PET 104
2.4.3 Example: A Model of Saccadic Eye Movements 105
V
2.4.4 Synthetic PET for Grasp Control 107
2.4.5 Discussion 111
References 112
Part 3
DATABASES FOR NEUROSCIENCE
TIME SERIES
Chapter 3.1
Repositories for the Storage of
Experimental Neuroscience Data 117
Richard F. Thompson, Jeffrey S. Grethe, Ted Berger,
and X. Xie
3.1.1 Introduction 117
3.1.2 Protocols: A Data Model To Address Schema Complexity in
Neuroscience 118
3.1.3 Considerations of the User Community 119
3.1.4 Building a Time Series Database for In Vivo Neurophysiology:
Cerebellum and Classical Conditioning 120
3.1.5 Building a Time Series Database for In Vitro
Neurophysiology: Long Term Potentiation (LTP) in the
Hippocampal Slice 125
3.1.6 Building a Database for Human Neuroimaging Data 129
3.1.7 Discussion 131
References 132
Chapter 3.2
Design Concepts for NeuroCore and
NeuroScience Databases 135
Jeffrey S. Grethe, Jonas Mureika, and Edriss N. Merchant
3.2.1 Design Concepts for Neuroscience Databases 135
3.2.2 The Three Main Components of the NeuroCore
Database 135
3.2.3 Detailed Description of the NeuroCore Database 137
Conclusion 150
References 150
Chapter 3.3
User Interaction with NeuroCore 151
Edriss N. Merchant, David A.T. King, and Jeffrey S. Grethe
3.3.1 Introduction 151
3.3.2 NeuroCore Schema Browser 153
3.3.3 Java Applet for Data Entry (JADE) 156
3.3.4 Database Browser 157
3.3.5 DataMunch 160
3.3.6 Discussion 161
References 163
Part 4
atlas based databases
Chapter 4.1
Interactive Brain Maps and Atlases 167
Larry W. Swanson
Abstract 167
4.1.1 General Features of Maps 167
4.1.2 Overall Structure of the Brain 168
4.1.3 Experimental Circuit Tracing Methods 169
4.1.4 Atlases: Slice Based Sampling and Standard Brains 169
4.1.5 Transferring Data from Experimental Brain to Standard
(Atlas Reference) Brain 173
4.1.6 Toward Textual and Graphical Databases on
the Web 174
4.1.7 Three Dimensional Computer Graphics Models of the
Brain 174
4.1.8 Two Dimensional Flatmaps: Schematic Circuit Diagrams and
Distribution Patterns 176
4.1.9 The Future: Atlases as Expandable Databases and
Models 176
References 177
Chapter 4.2
Perspective: Geographical Information
Systems 179
Cyrus Shahabi and Shuping Jia
Abstract 179
4.2.1 Introduction 179
4.2.2 Overview of GIS 180
4.2.3 Atlas Based Neuroscientific Data 184
4.2.4 Raster Data 185
4.2.5 Conclusion and Web Resources 186
References 187
Chapter 4.3
The Neuroanatomical Rat Brain Viewer
(NeuARt) 189
Ali Esmail Dashti, Gully A.P.C. Burns, Donna M. Simmons,
Larry Swanson, Shahram Ghandeharizadeh, Cyrus Shahabi,
James Stone, and Shuping Jia
4.3.1 Introduction 189
4.3.2 The NeuARt System 190
4.3.3 Discussion 200
References 200
Chapter 4.4
Neuro Slicer: A Tool for Registering 2 D
Slice Data to 3 D Surface Atlases 203
Bijan Timsari, Richard M. Leahy, Jean Marie Bouteiller, and
Michael Baudry
Abstract 203
4.4.1 Introduction 203
4.4.2 Classification Criteria 204
4.4.3 Intrasubject Image Matching 205
4.4.4 Intersubject Image Matching 206
4.4.5 Neuro Slicer: USCBP Histological Registration Tool 208
References 213
Chapter 4.5
An Atlas Based Database of Neurochemical
Data 217
Rabi Simantov, Jean Marie Bouteiller, and Michael Baudry
Abstract 217
4.5.1 Synaptic Neurotransmission: Molecular and Functional
Aspects 217
4.5.2 Roles of Glutamatergic Synapses in LTP and LTD 218
4.5.3 Glutamate Receptor Regulation and
Synaptic Plasticity 218
4.5.4 How To Build a Useful Neurochemical Database 219
4.5.5 Incorporating Neurochemical Data into the NeuroCore
Repository of Empirical Data 222
4.5.6 Available Resources 225
4.5.7 Conclusion 227
References 227
Part 5
data management
Chapter 5.1
Federating Neuroscience Databases 231
Wen Hsiang Kevin Liao and Dennis McLeod
Abstract 231
5.1.1 Introduction 231
5.1.2 Information Discovery 232
5.1.3 Semantic Heterogeneity Resolution 233
5.1.4 System Level Interconnection 233
5.1.5 Characteristics of Sharing Patterns 234
5.1.6 System Architecture for Sharing Primitives/Tools 236
5.1.7 Federating Neuroscience Databases 237
References 238
Chapter 5.2
Dynamic Classification Ontologies 241
Jonghyun Kahng and Dennis McLeod
Abstract 241
5.2.1 Introduction 241
5.2.2 Heterogeneity 242
5.2.3 Common Ontology 244
5.2.4 Classification 246
5.2.5 Dynamic Classification Ontology 247
5.2.6 Mediators for Information Sharing 250
5.2.7 Conclusions 253
References 254
Chapter 5.3
Annotator: Annotation Technology for
the WWW 255
Ilia Ovsiannikov and Michael Arbib
Abstract 255
5.3.1 Introduction 255
5.3.2 Overview of Existing Annotation Software 256
5.3.3 Annotation Technology: An Integrative Approach 256
5.3.4 Annotator 261
References 263
Chapter 5.4
Management of Space in Hierarchical
Storage Systems 265
Shahram Ghandeharizadeh. Douglas J. Ierardi, and Roger
Zimmermann
Abstract 265
5.4.1 Introduction 265
5.4.2 Target Environment 268
5.4.3 Four Alternative Space Management Techniques 269
5.4.4 Performance Evaluation 276
5.4.5 Analytical Models 280
5.4.6 Conclusions 283
References 283
Part 6
SUMMARY DATABASES AND
MODEL REPOSITORIES
Chapter 6.1
Summary Databases and Model
Repositories 287
Michael A. Arbib and Amanda Bischoff Grethe
Abstract 287
6.1.1 The Database Typology and the Neurolnformatics
Workbench 287
6.1.2 An Overall Perspective 288
6.1.3 General Considerations on Model Repositories 291
6.1.4 Brain Models on the Web 291
6.1.5 NeuroScholar 292
6.1.6 NeuroHomology 294
6.1.7 Future Plans 296
Chapter 6.2
Brain Models on the Web and the Need
for Summary Data 297
Amanda Bischoff Grethe, Jacob Spoelstra, and Michael A.
Arbib
Abstract 297
6.2.1 Storing Brain Models 297
6.2.2 The BMW SDB Relationship 298
6.2.3 Reviewing a Model: The Dart Model of Prism
Adaptation 299
6.2.4 Database Design 300
6.2.5 Accessing the Database 308
6.2.6 Future Plans 316
References 317
Chapter 6.3
Knowledge Mechanics and the
Neuroscholar Project: A New Approach
to Neuroscientific Theory 319
Gully A.P.C. Burns
6.3.1 An Introduction to Knowledge Mechanics 319
6.3.2 Concept of Theory in Neuroscience 320
6.3.3 High Level Software Requirements and Fundamental Design
Concepts of the NeuroScholar System 321
6.3.4 Neuroscholar in Detail 327
6.3.5 The Significance of Knowledge Mechanics 333
References 334
Chapter 6.4
The NeuroHomology Database 337
Mihail Bota and Michael A. Arbib
6.4.1 Introduction: The Definition of the Concept of Homology
in Neurobiology 337
6.4.2 Theory of Degrees of Homology 339
6.4.3 The NeuroHomology Database: Description 340
6.4.4 The NeuroHomology Database: Brain Structures 341
6.4.5 NeuroHomology Database: Connectivity Issues 343
6.4.6 The NeuroHomology Database: Homologies 346
6.4.7 Conclusion and Future Development 348
References 350
Apppendices
Appendix Al
Introduction to Informix 355
Jonas Mureika and Edriss N. Merchant
Informix SQL Tutorial: A Practical Example 355
Appendix A2
NeuroCore TimeSeries Datablade 359
Jonas Mureika and Edriss N. Merchant
Introduction 359
Internal Structure and Description 359
Support Functions 360
Additional SQL Invoked Routines 360
Comparing Data 360
Discussion 361
Appendix A3
USCBP Development Team 363
Appendix Bl
Informix SQL Quick Reference 365
Jonas Mureika and Edriss N. Merchant
Introduction 365
SQL Statements 365
Appendix Cl
USC Brain Project Research Personnel 367
Appendix C2
Doctoral Theses from the USC Brain
Project (May 1997 August 2) 369
Index 371
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| spelling | Computing the brain a guide to neuroinformatics ed. by Michael A. Arbib ... San Diego [u.a.] Acad. Press 2001 XIII, 380 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Brain physiology Computer Simulation Databases, Factual Models, Neurological Neuroinformatics Neuroinformatik (DE-588)4655105-0 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Neuroinformatik (DE-588)4655105-0 s DE-604 Arbib, Michael A. 1940- Sonstige (DE-588)135873517 oth HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009504893&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Computing the brain a guide to neuroinformatics Brain physiology Computer Simulation Databases, Factual Models, Neurological Neuroinformatics Neuroinformatik (DE-588)4655105-0 gnd |
| subject_GND | (DE-588)4655105-0 (DE-588)4143413-4 |
| title | Computing the brain a guide to neuroinformatics |
| title_auth | Computing the brain a guide to neuroinformatics |
| title_exact_search | Computing the brain a guide to neuroinformatics |
| title_full | Computing the brain a guide to neuroinformatics ed. by Michael A. Arbib ... |
| title_fullStr | Computing the brain a guide to neuroinformatics ed. by Michael A. Arbib ... |
| title_full_unstemmed | Computing the brain a guide to neuroinformatics ed. by Michael A. Arbib ... |
| title_short | Computing the brain |
| title_sort | computing the brain a guide to neuroinformatics |
| title_sub | a guide to neuroinformatics |
| topic | Brain physiology Computer Simulation Databases, Factual Models, Neurological Neuroinformatics Neuroinformatik (DE-588)4655105-0 gnd |
| topic_facet | Brain physiology Computer Simulation Databases, Factual Models, Neurological Neuroinformatics Neuroinformatik Aufsatzsammlung |
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