Index

11×N

mapping, 28129X1/SVJ

mouse strain, 222

22D, 214

anisotropic series, 221grid, 313image, 202series, 221

2DG, 201autoradiography, 197

33D, 214

atlas, 220, 224atlas server, 212, 228coordinate system, 226data sets, 220atlas server, 228fMRI, 198motion, 221MRI, 229reconstruction, 211storage format, 228time series, See 4Dviewer, 211volume, 221, 225

3D–3D alignment, 221

44D, 214

55-HT, 145, 147, See serotonin

Aabducent nerve, 74A-beta, 374

Abstract Schema Language, 330ABXD5F2

mouse strain, 222Access, 172, See MS Accessaccuracy, 178ACeDB, 58acetylcholine, See ACh

signaling, 355acetylsalicylic acid, 49, See aspirinACh, 325, See acetylcholineaction potentials, 127activation

time-dependent, 137, 145time-independent, 137voltage-dependent, 145

activation functiontime-dependent, 143voltage-dependent, 137, 143

activation variable, 178Active Data Objects, 31activity profile, 177activity-dependent facilitation, 148activity-dependent Hebbian model, 324AD, 315, 322, 323, 329, 366, See Alzheimer’s

Diseaseadaptive parameter, 309ADO, See Active Data Objectsafferent

damage to pathways, 329synaptic transmission, 325

afferent/efferentneurons, 41

affirmers lexical, 17affirming/negating, 5, 10Affymetrix, 290, 294, 350AFNI, 240, 241, 242, 253, See Analysis

of Functional NeuroImagesAFP, 214AFS, See Andrews File Systemage, 54Agilent, 351, 359agonal state, 347

383

384 Index

agonists, 49AIR, 192, 240, 241, 252, See Automated Image

RegistrationAIR5, 187aldehyde, 207Align Warp module, 191allele frequency disease, 339alleles, 296, 341

disease-related, 342Allen Brain Atlas, 79, 281alpha relaxation state, 328alpha-amino-3-hydroxy-5-methyl-4-

isoxazolepropionic acid, SeeAMPA

ALS, See amyotrophic lateral sclerosisAltaVista, 68alternate average creation, 185Alzforum, 366, 371, See Alzheimer’s Research

ForumAntibody Database, 379

AlzGene, 370, 372Alzheimer Research Forum, See ARFAlzheimer’s Disease, 7, 307, 357, See ADambiguity discrimination, 11amino acid-altering polymorphism, 342ammon horn, 69, 74AMPA, 12, 319amygdala, 74amygdaloid nuclear complex, 74amyloid precursor protein, 368amyotrophic lateral sclerosis, 365Analysis of Functional NeuroImages, 237ANALYZE75, 185anatomic variance, 184Andrews File System, 241Angleman Syndrome, 345ANN, 159, See artificial neural networkantagonist, 49anterior–posterior

olfactory bulb, 197antibody, 372anticholinergic, 49anti-inflammatory drugs, 49antonym, 49API, 70, See Application Programming InterfaceAplysia, 129, 139, 140, 145–147apolipoprotein, 370APP, See amyloid precursor proteinArabidopsis, 289archipallium, 308

archival tables, 14area V1, 282ARF, 377Aricept, 322artificial intelligence, 7artificial neural network, 157artificial neuron, 309artificial scotoma, 319ASCII, 128, 130aspirin, 49aspx, 70associative memory models, 305atherosclerosis, 357atlas

brain, 183digital, 184digital-canonical, 70minimum deformation, See MDAmouse brain, 184construction, 184

attributes, 45–46attribute–value, 50auto-launch, 92automated, 25

nonlinear registration, 223Automated Image Registration, 237automatic deposition, 8autoradiographic, 276autoradiographic mapping, 267autoradiography, 197, 268, 277–278autosomal dominant, 339average

intensity-based, 183activation frequency, 112

axial resistance, 117axon, 111, 207axonal

branches, 98arborizations, 58

Azores, 348

Bbackpropagation, 306BAMM, See Brain Activation and Morphological

MappingBAMMfx, 237BAMS, 81basal

forebrain, 322ganglia, 317

Index 385

basic statistics, 294BatchFtp, 242BaxGrid, 237BBTsyntax, 58behavioral traits, 301Benjamini-Hochberg correction, 356benzaldehyde, 43beta amyloid, 355BIC toolkit, 192bimodal, 139, 144BIMS, See Brain Information Management

Systemsbinary, 51

branch tree, 58BIND, 360biochemical, 104bioinformatics, 287, 337Bioinformatics Research Network, 23biological mechanisms, 306biological pathway, 361

schizophrenia, 357biomarker, 378

for neuropsychiatric disease, 357bipolar

disorder, 308, 340, 345, 357neurons, 80

BIRN, 28, 31, 214–215, See BioinformaticsResearch Network

BIRN-CC, 31BLAST, 6Blue Brain project, 308Boltzman, 130, 132Bonfire, 33–34Boolean, 30, 47–48, 50, 310BPEL, See Business Process Execution

LanguageBPEL4WS, See BPELbrain, 7

atlas, 60, 183comprehensive, 73macaque, 84mouse, 84probabilistic, 183

hierarchy, 71cortex, 196dynamics, 305functions, hierarchical approach to modeling, 315hemispheres, 268images, 235mammalian, 195

map, 271primate, 73, 80mouse, 212

mapping, 195parcellation, 281pH, 347region, 48, 54, 276regions, rat, 59slices, 268spatial normalization, 211structure, 69structures in, 39tissue, 197

Brain Activation and MorphologicalMapping, 237

Brain Information Management Systems, 69Brain Surface Extractor, 192Brain Voyager, 237BrainInfo, 67–70, 73–74, 79–80, 84brain-mapping, 184BrainMaps, 79BrainML, 25, 56, 91, 101, 251BrainML/XML, 28BrainPharm, 7BrainPy, 248brainstem, 217BrainSuite, 2, 185, 188, 237BrainVISA/Anatomis, 237BrainVoyager, 241, 250

neuroimaging package, 241branch point, 136, 147BRENDA, 6bridge

table, in databases, 50Bruker

spectrometer, 197BSE, 188burst, 174

duration, 168, 176period, 168, 176spiking, 320

burster, 110conditional, 146

bursting, 174activity, 147discharge frequency, 172neuron, 139

Business Process Execution Language, 243BXA1

mouse strain, 222

386 Index

BXD, 289–291, 293, 298, 300BXD1, 291BXD100, 291

CC++, 64, 170, 238C57BL

mouse strain, 290C57BL/6J

mouse strain, 212–215, 291Ca1

pyramidal cell, 92CA1, 69, 80CA2, 69, 80Ca2+, 139, 144, 147

intracellular concentration of, Seeion channel, 12

Ca2+-dependent K+ current, 146CA3, 69, 80, 121

cell model simulation, 108hippocampal, 121, 326pyramidal, 10pyramidal cell, 122cells, 10

Caenorhabditis elegans, 58calcium

intracellular concentration, 110imaging, 196

cAMPaccumulation of, 147regulation of, 139bimodal regulation of, 144

cancer, 288candidate gene, 337, 342caption, 45Caret

brain mapping program, 198cartesian coordinates, 116CAS, See Chemical Abstracts ServicesCaspase, 355Castor, 64Catacomb, 63, 101Catalyzer, 60catfish, 43CCDB, 49, See Cell Centered DatabaseCDM, See Common Data ModelCelera, 291cell

morphology, 59processing, 24

signalling, 24population, 276

Cell Centred Database, 31CellML, 91CellPropDB, 3–5, 7, 10, 15, 25cellular composition, 347central pattern generator, See CPGcerebellar

cortex, 31Purkinje neuron, See Purkinje

cerebellum, 10–11, 13, 17, 217, 290, 317cerebral cortex, 198cerebral palsy, 315c-fos, 208CGH, 359, See comparative genome

hybridizationCGI-PERL, 11channels, 40, 48Chemical Abstract Services, 202Chiron, 248, 254chlorpromazine

dopamine antagonist, 49Choice_Set_Values, 44Choice_Sets, 44cholinergic, 322

innervation, 325chromosomal

aberrations, 337regions, 341

circuit diagram, 137C-language, 160

vector-oriented, 160class

child, 47parent, 47

Class_Hierarchy, 47classes, 46Classes/Attributes, 51classes/tables, 38

bridge, 41many-to-many, 41

clinical trial, 378cluster map, 293, See QTL cluster mapcluster tree, 299clustering, 157CNFT, See continuum neural field theoryCNS, 230CoCoDat, 268, 269CoCoMac, 81, 267–269, 276, 283Cognex, 322

Index 387

cognition, 24cognitive computational neuroscience, 305cognitive deficits

VCFS, 345cognitive impairment, See Alzheimer’s DiseaseCollation of Receptor Data, See CoReDatcolumn/row, 164combinatorial methods, 338Common Data Model, 26community-building, 374comparative genome hybridization, 361compare correlates, 293, 301complex trait, 296

analysis, See trait analysismodulation, 287

computationallinguistics, 7model, 155, 330

in psychiatry, 305psychiatry, 315simulation, 168speed, 178

Computer Science and Artificial IntelligenceLaboratory, 380

concordance table, 51Condor, 216, 253conductance, 132, 174

cyclic nucleotide gated, 139ion, 134voltage-dependent, 132–133, 136

confocal imaging, 64connectionism, 306connectionist

mode, 309model, 310networks, 310

connexins, 316context, 5, 7–8

statistical, 68contextual, 16continuum neural field theory, 306control current, 132control population, 342controlled vocabulary, 37copy number, 341copy number analysis, 349CORBA, 245, 253CoReDat, 267–269, 276, 283coronally sliced, 217correlation matrix, 293–294, 301

cortexglobal model, 306

corticalareas, 319lesions, 317map reorganization, 318neurons, 319reorganization, 305sublayer, 275volume, 324

cortical columns, 328cortico-basal-ganglia-thalamic-cortical loop, 317cPath, 360CPG, 129, 140, 147–148CPU, 245

Linux, 252cranial nerve, 74craniofacial abnormalities

VCFS, 345cryosection, 268CSAIL, See Computer Science and Artificial

Intelligence LaboratoryCsm, 145curator, 70, 74, 367current, See ionic, reverse potential

external, 132hyperpolarization, Seeintrinsic, See ion channelvoltage-dependent, 137, 146

cvapp, 58cyclic AMP, See cAMPcyclic attractor, 312, 317cyclic nucleotide-gated conductance, 146Cygwin, 104Cygwin-X, 123cytoarchitectonics, 268, 274cytogenetic locui, 355Cytoscape, 348, 358, 360

web link, 357

DDAG, See Directed Acyclic Graphdata

analysis, 267binding, 57complexity, 38conversion, 243copy number, 341definition language triggers, 44derivation, 246diversity, 38

388 Index

elements, 38extraction, 176format conversion, 235genotyping, 351repository, 27, 212haplotype, 341heterogeneity, 23integration, 27–28, 155interoperability, See interoperabilitylineage, 246mediation, 28mediator, 27mining, 155–156model, 38, 271organization, 43pedigree, 246presentation, 44provenance, 251repositories, 27temporal dependencies, 244

Data Source Server, 28–29database, 24, 37, 159, 172

architecture, 4, 37, 271construction, 177construction and analysis, 176data-mining, 156design, 38electrophysiology, 54external, 27federation, 27genetics, 370integration,

centralized, 27mediated, 27

interface, 201mediators, 23neuronal, 40programmer/manager, 70relational, 37schema, 249simulation, 174–175single neuron, 177spatial, 67, 70symbolic, 70text-based, 267transaction, 235transcriptome, 290

databasing, 155receptor distributions, 267simulation-centric, 158

DBA/2Jmouse strain, 290–291

dbCollator, 277DBMS, 26, 28, 44–46dbSNP, 291Decentralized Information Group, 380decision tree, 13decrease-conductance, 143–144

general equation, 142delusion, 339dendrite, 111, 319–320

compartment, 112dendritic

arborizations, 58compartments, 4location, 161morphology, 103

density mechanisms, 96densocellular, 72dentate gyrus, 11, 72, 325depolarization, 142

slow, 146deviation, 178DICOM, 251differential equation

second-order, 139Diffusion Constant, 192digital atlas, 184dimensional stacking, 177

model neuron database, 173Directed Acyclic Graph, 249disease, 337, See infectiousdisease susceptibility, 287disease-induced, 184dissected tissue, 290DNA

alterations, 337damage, 365

Document Object Model, 57DOM, See Document Object Modeldomain, 70domain-dependent, 16dopamine, 49, 292, 317

receptors, 355dorsal, 200dorsal root ganglion, 321dorsolateral prefontal cortex, 361Douglas syntax, 58down-regulate, 145Drosophila, 289

Index 389

drug, 50anti-inflammatory, 49non-steroidal, 49

dsArchweb link, 46

DSS, 29–31, See Data Source ServersDTSearch, 8duty cycle, 171dyslexia, 314

EEAV, 37, 41, 43, 51

triple, 41EAV triplets, 45EAV/CR, 25–26, 28–29, 41–42, 45–46EAV_Flag, 46Edge Constant, 192EEG, 316, 328e-forum, 373electrical

coupling, 132non-synaptic communication, 316

electroencephalogram, See EEGelectrophysiology, 157

button, dialog box, 108database, 54

Em, 117enhancing

score, 11Ensembl, 294

Genome Browser, 296enthorinal, 325Entities/Objects, 42entity, 271

neuroanatomic, 34, 71, 73, 81, 271, 345entity–attribute–value, 41, See EAV, EAV/CRentorhinal cortex, 322Entrez, 41

Gene, 293Nucleotide, 293

environmental risk factors, 288epidemiologic, 378epilepsy, 305, 315epileptic-like discharge, 316episodic memory, 314epistasis, 339EPSP, 142equilibrium potential, 137, 143equivalent electrical circuit, 137erosion size, 192

ESRI GIS, 70EUCOURSE

web link, 105Eutectic, 58excitatory, 311

neuron, 320synaptically activated channel, 111stellate, 320

executive functionsdisturbances in, 322

expert-mediated, 5expression, 288Extended Markup Language Document Object

Model, 31Extensible Markup Language, See XML

Ffalse-negatives, 9false-positive, 68familial AD mutations, 372family-based association, 340FAQ, 302fast indexing, 16FE, See forward Eulerfeedback

loop, 145negative, 146positive, 146

feedback connections, 316feedforward, 306Fiswidgets, 236–238, 240–242, 245

workflow editor, 239flow diagram, 8fMRI, 195, 197, 201–202, 206–208, 235FMRIB, 237forebrain, 80formalin-fixed, 72FormatConvert, 242forward Euler, 135frequency

average activation, 112frontal cortex, 322frontal lobe, 80frontotemporal dementia, 368FScell, 112, 117FSecell, 112FSL, 241FTDP-17, 368, 372functional genomics, 337, 348functional magnetic resonance imaging, 200

390 Index

functionstime-dependent, 142voltage-dependent, 142

GGABA, 319, 356

neurons, 361receptor, 320, 356signalling, 355synthesis, 361

GABAergic, 360signalling, 361

galactose metabolism, 357, 359gamma

bursts, 326rhythm, 326

GenBank, 25gene, 50, 337

amplification, 345effects, 341expression, 291, 338, 357

P-values, 357screens, 341traits, 293

ontology, 287pleiotropy, 288variants, 50, 287

Gene Expression/Genotyping, 359Gene Ontology, 39, 348, 378GeneChip, 356GeneNetwork, See GNGEneral NEural SImulation System, See

GENESISGENESIS, 101, 103, 111, 115, 121, 123, 148,

170, 319, 326, 330Reference Manual, 105scripting, 115simulator, 63software, 58syntax, 105web link, 104

GeneSpring GT, 351, 353–354, 356GeneSpring Network, 361genetic, 337

analysis, 338association, 342complexity, 288correlations, 290, 297covariance, 288disease, 338

makeup, 291manipulation, Seemarkers, 349reference population, 287screen, 349variation, 291

GenMAPP, 360genome

linkage analysis, 337, 343projects, 156

Genome Scan Meta-Analysis, 344schzophrenia, 344

genomics, 24genotype, 291

phenotype relations, 289genotyping, 342Gensat, 281gif, 70Globus, 242

Toolkit, 245glomerular layer, 199, 207glomerulus, 200glutamate, 356

receptors, 12glutamine, 338GN, 287–289, 293, 298, 302GNU, 104GO, See Gene Ontologygoodness-of-fit, 176gradient-echo imaging, 197grammatical analysis, 310graphemes, 309graphical interface, 106gray scale intensities, 251Grid

architectures, 244environment, 252

GRID, 215, 216Grid Services Flow Language, 249GRID-based, 214GridFTP, 242Growth Factor Receptor Bound Protein, 359GRP, 290, 291 See genetic reference populationGSFL, See Grid Services Flow LanguageGUI, 112, 128, 133, 241, 248gyri tracts, 72Gyrus F1, 74

Hhallucination, 339haplotype, 341, 351, 353, 361

Index 391

Hardy–Weinberg Equilibrium, 351HBP, See Human Brain ProjectHD, 338, 357, See Huntington’s DiseaseHDF5, 242hearing defects

VCFS, 345Hebbian

model, 324–325hematopoietic stem cells, 290hemorrhagic stroke, 315heptanal, 203heterosynaptic plasticity, 139HH, 128, 135, 137, 148HHRR, 354hierarchies, 17

of modules, 330hierarchy, 5, 7, 9, 80

partitive, 80hindbrain, 80hippocampal, 121

networks, 326hippocampus, 74, 83, 290, 306, 316, 325histological

delineation, 282markers, 283mask, 268

histostained tissue sections, 204HMA, See Human Mapping AssayHodgkin and Huxley, 130, See Hodgkin-HuxleyHodgkin–Huxley, 112, 122, 131, 134, 136, See HHhodological, 81homogeneity

population, 349homology, 282homonyms, 38homosynaptic plasticity, 137, 144Hopfield

autoassociative memory, 324networks, 312

Hopfield network, 312HTML, 54, 57, 70, 105, 247, 249, 302HTTP, 31, 58, 214–215HTTPS, 227Human Brain

Atlas of, 79Human Brain Project, 23, 42human genome

annotation, 347Human Mapping Assay, 350human-readable, 73

human-recognizable, 73label, 74

Huntingtin, 338Huntington, 365

disease, 338HyperCard

Apple/MacIntosh, 81Hyperdoc, 106hyperpolarization current, 92hypertext, 81Hypertext Markup Language, See HTMLhypothalamus, 79

paraventricular nucleus of, 79hypothesis testing, 287hypothetical neuron

equivalent electrical circuit, 139

II/O, 148IATR, See Internet Analysis Tools RegistryIBM, 308Iclamp, 110image

alignment, 220analysis, 306-based query, 211brain, 24histological, 212human-recognizable, 73magnetic resonance microsopy, 183processing, 235radiological, 212registration, 211

Image Queryweb service, 226

imagingfunctional magnetic resonance, See fMRImodality, 211neuroanatomical, 183

impaled recording electrodes, 196inbred strains, 287increase-conductance, 143, 144index

hierarchical, 80string-based, 68

indexing, 3citation, 68neuroanatomical database, 211word, See

inductive database, 155infectious disease, 289

392 Index

inferior temporal cortex, 321informatics, 287information

extraction, 3, 5, 7, 16processing, 309source map, 30

informativeness, 342Ingenuity, 348inheritance modes, 339inhibitory, 311, 320

neuron, 320postsynaptic potentials, See IPSPsynaptically activated channels, 111

input/output, 131, See I/Ointegrate-and-fire

cell, 129, 132integrator Servers, See ISIntegrin signalling, 355Intel Xeon, 70intensity-rescaling, 190interface, 8

constraints, 37graphical, See graphical, interface

intermarker D score, 344Internet Analysis Tools Registry, 250interneurons, 10interoperability, 4, 25, 91, 148, 235InterPro, 348intersection

XML schema approach, 55inter-spike interval, 176intracellular ion pool, 132intracellular pool, 146

multiple, 146ion

channel, 4, 167, 173, 316current, 174pool, 144, 146

intracellular, 136ionic

channel, 320conductances, See channelscurrent, 14, 134

reversal potential, 132IPSP, 142IS, 28, 30ischemic stroke, 315ISM, See information source mapisodisomy, 345isolate, 340

JJ2EE, 213, 216, 224, 227Java, 57, 62, 64, 212–223, 240–241

applet, 70virtual machine, See JVM

Java 2 Enterprise Edition, See J2EEJava Beans, 216Java Message Service, 245, See JMSJava Remote Method Invocation (RMI), 245JAXB, 64Jftp, 242JMS, 245jpeg, See jpgjpg, 70jsp, 70JVM, 129, 133

KK

channels, 122KB, 379, See knowledgebaseKDD, 156, See knowledge discovery and data

miningKEGG, 348, 360keywords, 5, 10

score, 13Kinetikit, 110–111knockout, 287knowledge

base, See KBdiscovery, 155domain, 71management, 365repository, 73

knowledge base, See knowledgebaseknowledge discovery and data mining, 155knowledgebase, 3, 5, 8, 11, 14, 16knowledge-base, See knowledgebaseKnowMe, 34Kohonen network, 313

Llaboratory data management system, 60LabSWAN, 378language skills

degradation of, 322lateral inhibition, 321lateralization, 308late-response, 196

Index 393

layer, 72III, 320IV, 320V, 320

LD, 344, See linkage disequilibriumleak conductance, 134learning

algorithm, 309supervised, 3, 8, 14unsupervised, 3, 11

left–right hemisphere, 308lesions, 317, 318leukocyte, 347, 349, 354lexical, 5

affirmers, 18constraints, 16negators, 18

ligand, 267, 269ligand-binding, 268likelihood ratio statistic, See LRSlimbic, 308, 322limits of detection, 343linguistics, 16linkage, 338, 340linkage calculations, 344linkage disequilibrium, 340Linux, 104, 123, 192, 217LISP, 41list association, 41Load Simulation, 135local voltage, 176locus ceruleus/coeruleus, 74LOD, 350, See limitsof detection

score, 358logical

neuron model, 310typing, 242

long-term potentiation, 320LONI, 79, 185, 190, 192, 224, 237, 251–253, 282

Debabler, 187Pipeline, 189

lower bound, 48LRS, See likelihood ratio stastisticsLTP, See long-term potentiationLycos, 68lymphoblast, 347

MMac, 192Mac OS, 223

Mac OS/X, See OS Xmacaque, 79, 282

atlas, 69machine learning, 159, 306MacOS, 217MacroVoxel, 228Madeira, 348MAGE XML, 64magnetic

field strength, 197resonance imaging, See MRIresonance microscopy image, 183

Magneto and Electroencephalogram, 237major depressive disorder, 345Mann–Whitney

testing, 356map

locus, 287odor, See odor mapsserver, 70

mapping, 267markers, 340Marquardt–Levenberg, 223MAS5, 290mask values, 251MathML, 56, 62MATLAB, 172, 240–241Mauthner, 230maximal conductance, 168MBL, See Mouse Brain LibraryMDA, 184, 185, 186, 187, 191, See minimim

deformation atlasMDT, 190, 191, 192, See minimum deformation

targetMDT2, 191mean, 157mean-square-root

deviation, 176mechanoreceptors, 319medial dorsal nucleus, 72mediator, 67Medical Subject Headings, See MeSHmedium spiny neuron, 12MEG/EEG, See magneto and

electroencephalogrammelanophores, 43membrane, 7

capacitance, 134, 174conductances, 132, 144–146current, 168

394 Index

membrane potential, 177of neurons, 196simulation, 110soma, 116

memory, 306decline, 324loss, 365

Mendelian genetics, 288–289Mercator, 208MERLIN, 351, 353MeSH, 17Message Passing Interface, 240metabolic-vascular state, 197metadata, 12, 16, 23, 25–26, 30–31, 37, 42–44, 45,

47, 60, 156, See meta-datameta-data, 250, 253

fields, 251meta-database, 30meta-language, 164metaphysical, 72metathesaurus

UMLS, 84MGH, 376MIAME, 64microarray, 290, 294

data sets, 288Microbrightfield, 58microdletions, 345microsatellite, 291, 341, 349, 350Microsoft Access, 45, 81Microsoft IIS, 201Microsoft Visual C++,

See C++microstructure of cognition, 306midbrain, 80middleware, 246MINC, 187, 189, 251, 253mind objects, 315minimum deformation atlas, 183minimum deformation target, 183, 187misfolded proteins, 365mitochondria, 355MLP, 312model, See Poirazi

compartmentalized cell, 121computational, 129connectionist, 310hierarchical, 81multicompartment, 147networks, 177

neuralspiking, 314

neural systems, 176neuron,

high-dimensional, 178neurons, 177psychiatric, 72single neurons, 103systemic, 81

ModelDB, 91, 100, 129, 148modeling

neuronal, See neuronal, modelingModelView, 91, 93, 96, 100MODm, 144–145modulation, 144modulatory

function, 145relationships, 132synapse, 138, 144–145transmitter, 144–145

moduleAlign Warp, 191Crop, 190Soft Mean

molecular layer, 72mollusc, 129Mollweide, 208monozygotic twins, 339mood instability

VCFS, See velocardiofacial syndromemood swings, 308MorphML, 53, 56, 58, 100–101

schema, 59viewer, 60

morphology, 53, 184dendritic, 103

mossy fibers, 10motor

cortex, 317function

disturbances in, 322mouse brain, 212mouse brain atlas, 281Mouse Brain Library, 79, 217

Project, 214Mouse Pheromone Database, 291movement disorders, 195MPI, See Message Passing InterfaceMRI, 183–184, 188, 197, 201, 235MRM, 186–187, 191

Index 395

mRNA, 341expression, 290transcripts, 342

MS Access, 25, 269MS Access XP® „ 271MS Excel, 25MS Windows, 70, 92, 104MS-SQL, 70Mulit-layer perceptron feedforward network, 311multi-compartmental models, 310multifactorial analysis, 269Multilayer Perceptron, 311Multiple Interval Mapping, 299multiple mapping, 293Multiple QTL Mapping, 300multi-point downstream linkage analysis, 351Multipoint Engine for Rapid Likelihood Inference,

See MERLINmultivariate analysis, 269mutant

mice, 183mutation, 368

disease-causing, 339myeloarchitectonics, 268MySql, 25MySQL, 269MySQL® 4,1,10, 271MySWAN, 378

NNa

channel, 118, 122nanoAmps, 110narrow distribution, 176N-ary, 43NAS, See Network Attached StorageNational Alliance for Research on Schizophrenia

and Depression, See NARSADNational Center for Biotechnology Information, See

NCBINational Library of, 39National Library of Medicine, 15, 84, 201natural language processing, 35Nature

journal, 371NCBI, 41, 348NDG, See Neuroscience Database Gatewaynegating

contextually, 12score, 11

negatorslexical, 17

neocortex, 306, 308, 316neostriatum, 12nerve bundle, 207nerve cell, See neuronnervous system, 23NetCDF, 189NetOStat, 223–226, 229

Brain Atlas Navigator, 226Netscape, 244network

graph, 293Hopfield, 312nodes, 309non-rhythmic, 174rhythmic, 174simulations, 161

Network Attached Storage, 242network databases, 170

model, 170Network File System, See NFSNeuoinformatics Information Framework, 23neural

activities, 198cell assemblies, 308circuits, 128, 196function, 127information processing, 310model, 309, 326network, 305, 311, 128, 140, 147,

155, 167networks, 24, 127, 130, 316plasticity, 306processes, 305query system, See NQSsimulation, 103, 157–158, 314system, 127

complex, 177function, 167

systems, 24Neural Simulation Language, 330neuregulin1, See NRG1neuroanatomical, 288

informatics, 211neuroanatomist, 79neuroanatomy, 59, 67, 71–72

hierarchy, 80database

indexing, 211

396 Index

microscopic, 72texts and atlases, 69

Neurobase, 377neuroConstruct, 63neurodegenerative, 7neurodegenerative disorders, 365, 371neurodynamic, 315neurodynamics, 315neurogenetics, 287neuroimaging, 185, 235, 246, 249

Informatics, See NIfTIsize and complexity of, data, 243

Neuroimaging Informatics Technology Initiative,See NIfTI

neuroinformatics, 3, 53–54, 67, 83, 129, 148, 211,235, 305

Neurokit, 107, 111neurological, 7

diseases, 195terminology, 72

Neurolucida, 58NeuroML, 53, 55–56, 101

Development Kit, 56, 60, 62neuromodulation

acetylcholine, 326neuromorphic devices, 306neuron, 7, 14, 17, 30, 40, 48, 130

activation, 309activity

bursting, 168afferent, Seeafferent/efferent, 41biophysical and biochemical properties, 128bipolar, 80computational element, 136electrical coupling between, 147excitability, 162HH-type, 132, 136large-scale networks, 55medium spiny, 34, Seepyramidal, 80reticular, 4thalamic reticulartonically spiking, 176tracing system (software), 58two-compartment, 111two-state, 312

NEURON, 91–92, 101, 148, 155, 157–160, 164,170, 330

software, 58

neuron databasesmodel, 170

neuronalactivity

odor-stimulated, 196compartment, 8, 10compartments, 14death, 322membrane properties, 4model, 55modelingmorphology, See morphologynetwork, 155, 167pathways, 49, 81signals, 195

neuronal excitability, 134NeuroNames, 33, 67, 69–72, 74, 79–80, 82, 84,

212, 224, 251NeuronDB, 3–5, 7, 10, 15, 25, 48, 49neuropharmacological, 288neurophysiology, 155, 329neuropil, 33neuropsychiatric

diseases, 356disorders, 345

neuropsychological syndromes, 305neuropsychopharmacology, 314neuroscience, 267, 305, 315, 330

ontologies, 67Society For, 71XML in, 55

NeuroscienceJournal of, 3, 8, 14

Neuroscience Database Gateway, 267Neuroscience Information Framework, 71neurosimulator, 130, 148neurosimulators, 128NeuroSys, 25, 27, 60NeuroTerrain, 212, 224–225

Atlas Server, 228mouse atlas, 229

NeuroText, 3, 5, 7– 8, 10–11, 13, 15–16, 19web link, 3

neurotransmitter-receptor transcripts, 356neurotransmitters, 4, 10, 14neurotransmitters/neuromodulators, 48Nevin, 58nextToken, 57NFS, 214, 241NIF, See Neuroscience Information Framework

Index 397

NIH, 379NIH Blueprint for Neuroscience

Research, 71NIMH, 307Nissl-stained, 72, 212, 230, 282

atlas, 223NLP, 7, 18, See Natural Language ProcessingNMDA, 319

channel, 320receptor, 320–321, 374

NMOD, 158nodes, 306nodulation, 138nomenclature, 70Nomina Anatomica, 72non-declarative memory, 327nonparametric linkage, 343

analysis, 351nonspecific hybridization, 294nonspiking neurons, 307non-steroidal drugs, 49noradrenaline, 38norepinephrine, 38normal

genetic pathwaysdisruption, 183

maps, 320probability plot, 294

normalizedcorrelation, 205fluorescence, 294

NPAIRS, 237NPL Z score, 353, See nonparametric linkage Z

scoreNQS, 155, 157–161, 163–164NTDB, 6NT-SDK, 229numerical

classification, 157simulation, 178

OOB, 198, 207–208, See Olfactory Bulbobesity, 289object, 271

class, 55objects/entities, 50octanal, 203odds ratio test, 14

ODE, 148, See ordinary differentialequation

odor, 43map, 195, 198, 200–202, 204–205mapping, 197–198stimuli, 196, 202, 207

OdorDB, 201OdorMapBuilder, 198, 200, 206–207OdorMapComparer, 195, 202–203, 206OdorMapDB, 195, 201–202, 206olfaction, 24olfactory

bulb, 195, See OBreceptor, 207

interactions with odor, 202signals, 208

olivary nucleus, 39OME, See open microscopy environmentOMIM, 292, 293ontological, 23ontology, 27, 29, 33, 50, 67–68, 157, 287

neuroanatomical, 72neuroscientific, 68XTM databases, 82

Ontology Server, See OSOpen Microscopy Environment, 242open reading frames, 347OpenGL, 185Openmicroscopy, 64OpenPBS

workflow, 216optimization algorithm

stacking order, 177Oracle, 25, 27, 44ORDB, 201ordinary differential equation, 136ORF, See open reading framesorthographical representations, 314OS, 28, 30–31OS X, 92overtransmission, 340oxidative phosphorylation, 355

Ppair-scan, 297pair-scan mapping, 296paleomammalian, 308PANTHER, 292Parallel Distributed Processing,

See PDP

398 Index

parameterchange

minimization, 178combination, 174–175space, 174

parametric linkage, 343paranoid delusions, 322paraventricular nucleus, 75–76, 79Parkinson, 365Parkinson’s, 7Parkinson’s disease, 315, 329, 345, 373Parkinsonism, 315, 368parsing

contextual, 3fine-grained, 11lexical, 3semantic, 3syntactic, 6

partitive, See partitive, hierarchyparvalbumin, 361pathogenesis

Alzheimer’s Disease, 323pathogenic event, 378pathologic change, 378pathophysiologic, 378Pathway Assist

commercial software, 348pattern recognition, 306PDGene, 376PDNN, 299, See position-dependent nearest

neighborPDP, 306PDP++, 330per burst

interval, 176peripheral

leukocytes, 347, 356nervous system, 196receptor, 207

PERL, 8, 64Perlegen/NIEHS

resequencing project, 291perturbation, 378pFam, 348pH, 347phantom limb, 320, 321phase relations, 310phenothiazine

chlorpromazine, 49phenotype, 288, 291, 299–300, 337, 342

phonemes, 309–310phonological, 314phonology, 314phosphorylation, 357

regularion pathway, 359photomicrographs, 184PHP, 57, 64physiological traits, 301physiopathology, 24PIC, See Portuguese Island Collectionpipeline, 211, 214, 228, 235, See LONI

image_processing, 214NeuroTerrain, 213

piriform, 110pivoting, 43plasticity

function, 140heterosynaptic, 145homosynaptic, 142, 145

plateau potentials, 148pleiotropic, 299plexiform layer, 199PNAS

journal, 371point attractor, 312point processes, 96Poirazi model, 93polygenic

disease, 288traits, 289

polymorphism, 50, 356amino acid-altering, 342

population isolate, See isolatePortuguese Island Collection, 354position-dependent nearest neighbor, See PDNNposterior parietal cortex, 321PostgreSQL, 25, 213, 215post-processing, 10, 11postscript, 249postsynaptic

cell, 139, 145potentials, 143

multicomponent, 142receptor, 161

potassium channel, 110, 112, 118gene, 292

POW, 370PowerBuilder, 45PowerPoint, 302Prader-WIlli Syndrome, 345

Index 399

precision, 8prefrontal cortex, 317presenilin-1, 368, 372presenilin-2, 368, 372presynaptic

activity, 138, 142cell, 161

spikes, 142primates, 281probabilistic brain atlas, 183probe, 294process

non-linear, 167process management, 248processing

natural language, 3projection pathways, 196Protégé, 27protein interactions, 55proteomics, 24protocols

standardized, 24prototype

library, 118provenance, 253pruning, 323PSD95, 374PSM, 140PSP, 142, 143, See postsynaptic potential

time-dependent, 143voltage-dependnet, 143

psychological, 315psychology, 315psychotic features, 322PubMed, 3, 15, 17, 25, 74, 290, 357, 367, 375, 379pull-down, 45purine metabolism, 357, 359Purkinje, 10, 13, 17, 110

dendrites, 33neurons, 33

putamen, 317P-value, 298pyramidal neurons, 80, 316Python, 64, 237

QQC, 219, 220QIS, 28, 30–31QTL, 287–288

cluster map, 293, 299

quasi-stable statesattractor networks, 315

querylanguage, 158translation, 28web-service, 214

Query Integration System, 29Query Integrator System,

See QIS

Rradial separation, 204radioactively labeled, 268radioactivity, 268random number variable, 137, 143rate-constant equation

HH-type, 132RDBMS, 28, 212, 215–216, 227RDF, 16, SeeReactome, 360readcell, 116reading, 306recall, 8receptor, 4, 10, 14, 40, 43, 48, 278

binding, 276ligands, 268table, 279

recessive allelesdisease-causing, 345

recombinant inbred, See RIrecombination events, 342recording-site, 54red/green/blue, 201reference atlas, 211regulators

intracellular, 139regulatory agents

intracellular, 137, 142relational database, 267relational database management system, See

RDBMSrelationship

binary, 41many-to-many, 40

resequencing project, 291Resource Description Framework, See RDF,

See RDFresting conductance, 142resting potential, 171

400 Index

retrieval, 68information, 74precision, 68

reversal potential, 132RGB, 203, See red/green/bluerheumatoid arthritis, 357rhythmic network, 176RI, 297–298, See recombinant inbredribosomal, 355rigidity, 316RMA, 356, See robust multichip analysis or robust

multiarray averagingRMI, See remote method invocationRobust Multiarray Averaging, See RMArobust multichip analysis, 290rodents, 281Roget’s Thesaurus, 10, 18RPPL, 248Ruby scripts, 216rule-based systems, 310Run Pipeline in Parallel, See RPPLrun simulation, 135

SSAMBA, 214Sao Miguel Azores, 348SAX, 31, See Simple Application Programming for

XMLXML parser, 63

SBML, 56scalability, 246Scalable Vector Graphics, 31schema, 40, 44

complex-database, 39continually evolving, 38global, 28mixed, 45RDF, 378simplification, 40SWAN, 379

schematic, 139schizophrenia, 289, 316, 337–339, 345–346, 349,

356–357, 361Schizophrenia Research Forum, 376Science

journal, 371SCIL, 216scotoma, See artificial scotomascreen-scraping, 25scrolling lists, 14

SDP, See strain distribution patternsecond messenger, 132, 138, 145

pool, 144second messengers, 144secondary database, 176secondary dendrites, 230sectioning, 184segmentation, 185

errors, 219layer, 223

Selbst-Erhaltungs-Therapie, See Self-MaintenanceTherapy

self organized mapping networks, 318Self-Maintenance therapy, 327self-organizing, 309

networks, 321Self-Organizing Mapping, See SOMsemantic, 5

-based indexes, 68data models, 23data-types, 251inverse/reciprocal, 49metadata annotations, 23phrases, 11reciprocal, 49relationship, 11Web, 35web services, 26relationships, 8

Semantic Web Applications in Neuromedicine, SeeSWAN

Semantic Web in Life Sciences, 377senile plaque, 325SenseLab, 4, 7, 14–15, 42, 46, 48–49,

92, 158sensitivity, 8, 9, 10sensory perceptions

abnormal, 195sentence processing, 306sequence, 24, 50serotonin, 139, See 5-HT

signalling, 355shared cluster, 175short oligomer microarrays, 290sigmoidal, 310signal

analysis, 306encoding, 195neuronal, See neuronal signals

Index 401

silentdischarge frequency, 172neuron model, 175

Simple Application Programming Interface, 57Simple Application Programming Interface for

XML, 31simple interval mapping, 295Simple Object Access Protocol, See SOAPSimToolDB, 158simulation, 118–119, 155, 159, 168

full network, 178large networks, 104program, 174time, 174

simulator for neural networks and action potentials,See SNNAP

singlehidden layer, 311neuron excitability, 161spikes, 309

single-chromosome Map Viewer, 296single-nucleotide polymorphism, See SNPsingle-point

downstream linkage analysis, 351slower synaptic learning, 318SMART ATLAS, 224smell

perception of, 196SNNAP, 127–128, 130, 133, 135–136, 143,

147–148Tutorial Manual, 129, 133web link, 129

SNP, 291, 338, 341, 351, 353, See single nucleotidepolymorphism

database, 291genotype, 349genotyping, 349haplotype, 342haplotyping, 349LOD scores, 357–358

SOAP, 26sodium

channel, 112Soft Mean module, 190SOM, 313, 318soma, 111–112, 117, 319somatosensory cortex, 318–319, 320spatial

correlation, 205coefficient, 203

discretization, 94distributed markers, 268frequency, 220indexer, 211normalization, 183–184, 212, 220

species, 54specificity, 10speech perception, 306spike, 112, 174

activity, 145–146, 161, Seecount, 176duration, 142frequency, 171, 310

histogram, 173generator, 112, 118per burst, 171propagation, 136

spiketrain, 115spiking

discharge frequency, 172membrane conductances, 174neural models, 314neurons, 314

SPM, 241, 248SQL, 39, 43–44, 81, 82, 160

server, 25squashing functions, 310squid, 110Squid_Na, 130squid-like channels, 112SRB, 214, 227, See Storage Resource BrokerS-shape, 294, See sigmoidalstacking order, 177staining, 184staining-method, 54standard deviation, 157startElement, 63statistical evaluation, 290statistics, 157, 306steady state, 175stereological, 288stimulus

modulatory, 132stimulus current

extrinsic, 134storage

information, 74Storage Request Broker, See SRBStorage Resource Broker, 242strain, 291

402 Index

strain distribution pattern, See SDPstriatum, 290structure

anatomical, 184, 195chemical, 50dendritic, 111genotyping, 351long name, 79pedigree, 351primary, 71superficial, 72

Structured Query Language, See SQLstudy population, 340sub-cellular, 103sub-nuclei, 72sub-ontologies, 84sub-schema, 39sub-structures, 72Sun Grid Engine, 253superior frontal gyrus, 74susceptibility gene, 344SVG, See Scalable Vector GraphicsSWAN, 377–378, 380

schema, 379Sybase, 44SymAtlas, 292symbolic

description, 315information processing, 310

synapse, 161chemical, 132–134, 142database, 292electrical, 134modulatory, 133strength, 174time-dependent, 132voltage-dependent, 132

synapses, 130network, 128

synaptic, 311activation, 143compensation, 323conductances, 143

time-dependent activation, 139connection, 142

exponential growth of, 325connections, 323

per unit cortical volume, 324current, 143deletion, 323

input, 112integration, 92isolation, 177loss, 326plasticity, 128potentials and integration, 137receptors

activation of, 167strength, 139transmission, 128, 142transmissions, 196

synaptic runaway model, 325synaptophysin, 215synchrony, 316SynDB, 292synonym, 5, 10, 42synonyms, 38, 49, 72syntax, 68synuclein, 355systematic reasoning, 310systemic, 81systems

biology, 337, 338genetics, 288theory

non-linear, 168Systems Biology Markup Language, See SBML

TT1, 187

MRI component, 197T1-weighted, See T1T2

MRI component, 197table

bridge, 40column, 161create/alter, 44lookup, 40objects, 41reciprocal attributes, 49

tables/classes, 44tactile, 319tags, 54tal

Fiswidgets application interface, 241tau, 372

gene, 368mutation, 368

taxonomic, 157

Index 403

TCP/IP, 26Telemakus, 370template workflow, 249temporal gradients

memory decline, 324terminological, 67Terms/Synonyms, 50Tesla, 197text

human-readable, 73mining, 3, 348-based databases, 267

TEXTAREA, 48thalamic, 4, 318

interneuron, 319nuclei, 319relay cell model, 319

thalamo-cortical, 318thalamus, 75, 319, 320theta rhythm, 326tiff, 216, 225time constant, 139tonic spikers, 173tonically spiking, 174

neuron, 176Tools/FXParse, 238Topic Maps, 82topographical, 309

map, 313, 318trait

analysis, 287regulation, 299

transcript expression, 287transcriptional

change, 342level, 342profiling, 347

transcriptome database, 290transcripts, 290transgenic, 184, 287transmitter, 132, 136, 144

pool, 146transQTL, See QTLtremor, 316TrialDB

web link, 43trinucleotide repeat, 338triplets, See EAV tripletstriune, 308true-negatives, 14

true-positives, 14t-test, 157tutorial, 103, 106two-state neurons, 312

UUbiquitin, 355UCSC, 294, 348

Genome Browser, 296UMLS, 17, 29, 31, 33–34, 39, 41, 50, 84UniGene, 292, 293uniparental isodisomy, 345unirelational

concepts, hierarchical models, 81Unix, 216, 223, 228, 240UNIX, 104, 107, 123, 192, 228UNIX/Linux, 92upper bound, 48up-regulate, 145URL, 25, 30user, 45

interface, 38, 70

Vvalidation, 8, 13

constraints, 37values, 42VCFS, 359, See velocicardiofacial syndromevelocardiofacial syndrome, 345ventral posterior lateral, See VPLventroposterolateral, See VPLvibration, 319View/Query Designer, 34virtual datasets, 249Virtual Knife, 225, 229Virtual RatBrain Project, 59VisANT, 34Visome, 329visual cortex, 282, 319visualization

dimensional stacking, 173Vm, 117vocabulary

default, 74controlled, 39, 73

VOI, 225voltage

maxima, 174minima, 174

voltage trace, 171, 173

404 Index

per burst, 171voltage-activated

channels, 112voltage-dependent gating, 167volumes of interest, See VOIVoxBo, 237voxel, 251VPL, 79, 319

WW3C, 26, 377WAMBAMM

web link, 105warping algorithm, 204wavelet-based registration, 222Web Service Description Language, See WSDLWeb Services Interoperability Organization, See

WS-IWebGestalt, 299WebQTL, 295, 300

Map Viewer, 296WebStart, 224Wellcome-CTC, 291WFMS, 235–236, 238, 241–242, 245, 248, 252white blood cell, 354Whole Brain Atlas, 79Wikipedia, 379Windows, 123, 217Windows 2000, 185Windows XP, 185

WIRM, 25word morphology, 306word-indexing, See indexingworkbench, 236workflow, 235, 244

for genetic analysis, 351management system, See WFMSneuroimaging, 235verification, 252

working memory, 314wrapper function, 240WS-I, 227

XX Windows, 107XDTM, 243, 252XML, 16, 26, 29–31, 53, 54, 62, 82, 100–101,

238, 251libraries, 57schema, 55

XML Dataset Type and Mapping, See XDTMXML DOM, 31XML Pull Parser, 57XODUS, 106, 121, 123

web link, 104XPP, See XML Pull ParserXTM, 76, 82

ZZ score, 343, 357, 358