Table Of ContentNEUROSCIENCE DATABASES
A Practical Guide
NEUROSCIENCE DATABASES
A Practical Guide
edited by
RolfKotter
Heinrich Heine University Dilsseldorf
Dilsseldorf Germany
SPRINGER SCIENCE+BUSINESS MEDIA, LLC
Library of Congress Cataloging-in-Publication Data
A C.I.P. Catalogue record for this book is available
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NEUROSCIENCE DATABASES A Practica! Guide / edited by RolfKotter
ISBN 978-1-4613-5384-3 ISBN 978-1-4615-1079-6 (eBook)
DOI 10.1007/978-1-4615-1079-6
Copyright © 2003 by Springer Science+Business Media New York
Originally published by Kluwer Academic Publishers in 2003
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Contents
Contributors ix
Acknowledgements xv
Preface xvii
1 Neuroinformaticsfor C.elegans: RelatingMindand Bodyin
Wormbase 1
NanshengChen,Raymond Y.N. Lee,ZeynepF. Altun,Thomas
Boulin,PaulW. Sternberg,andLincolnD. Stein
2 AGeneExpressionMapofthe MouseBrain.Genepaint.org
-ADatabaseofGeneExpressionPatterns 19
Axel Visel,JamilaAhdidan,andGregorEichele
3 Databasesfor theFunctionalAnalysesofOlfactory
Receptors 37
ChiquitoJ. Crasto, NianLiu,andGordonM. Shepherd
4 Constructionofa Protein-ProteinInteractionDatabase
(PPID)for SynapticBiology 51
HolgerHusiand SethG.N. Grant
vi Contents
5 ModelingtheDynamicsofSecondMessengerPathways 63
KimT. BlackwellandJeanetteHellgrenKotaleski
6 Web-Based NeuronalArchives.NeuronalMorphometric
and ElectrotonicAnalysis 81
DennisA.Turner,RobertC. Cannon,andGiorgioA. Ascoli
7 ModelDB: AResourcefor Neuronaland NetworkModeling 99
AndrewP. Davison,ThomasM. Morse, MicheleMigliore,Luis
Marenco, GordonM. Shepherd,andMichaelL. Hines
8 CoCoDat: CollationofCorticalDataonNeuronsand
Microcircuitry.SystematicStorageandRetrievalof
ExperimentalDataforBiophysicallyRealisticModeling 111
JonasD.-Johnsen,JiirgenMaier,KlaasE. Stephan, andRolf
Kotter
9 ComputerModelsand AnalysisToolsfor Neural
Microcircuits 123
ThomasNatschHiger,HenryMarkram'andWolfgangMaass
10 A PracticalGuidetoInformationAnalysisofSpikeTrains 139
GianniPola, SimonR. Schultz,RasmusS. Petersen, and
StefanoPanzeri
11 AnIntroductiontoCoCoMac-Online.TheOnline-Interface
ofthePrimateConnectivityDatabaseCoCoMac 155
LarsKamper, AhmetBozkurt,KonradRybacki, Andreas
Geissler,InaGerken,KlaasE. Stephan,andRolfKotter
12 GraphTheoryMethodsfor theAnalysisofNeural
ConnectivityPatterns 171
OlafSporns
13 ThePUPS-MOSIXEnvironment: AHomeostatic
Environmentfor Neuro-andBio-informaticApplications 187
MarkA. O'Neill,Gully A.P.CBurns,andClausC. Hilgetag
14 TheNeuroHomologyDatabase: AnOnline-KMSfor
HandlingandEvaluationofthe Neurobiological
Information 203
MihailBotaandMichaelA. Arbib
Contents vii
15 ThefMRI Data Center:SoftwareToolsfor Neuroimaging
DataManagement,Inspection,andSharing 221
JohnDarrellVanHom,Jeffrey B. Woodward, Geoffrey
Simonds,BennetVance,Jeffrey S. Grethe,MarkMontague,
Javed Aslam,DanielaRus,DanielRockmore, andMichael S.
Gazzaniga
16 StatisticalParametricMapping 237
KarlJ. Friston
17 TheBrainPositioningSoftware 251
VolkerSchmitt,Andrzej Wichert,JoGrothe,andFriedrichT.
Sommer
18 Braininfo.AnOnlineInteractiveBrainAtlasand
Nomenclature 259
DouglasM. BowdenandMarkDubach
19 FederationofBrainDatathroughKnowledge-guided
Mediation 275
MaryannE. Martone, AmarnathGupta, BertramLudascher, llya
Zaslavsky,andMarkH. Ellisman
20 FacilitatingDataandSoftwareSharinginthe Neurosciences
-ANeuroinformaticsPortal 293
Raphael Ritz, RainerForster, and AndreasV.M. Herz
Index 307
Contributors
JamilaAhdidan
MaxPlanckInstituteofExperimentalEndocrinology, Feodor-Lynen-Str. 7, D-30165
Hannover, Germany.
ZeynepF. Altun
AlbertEinsteinCollegeofMedicine, DepartmentofNeuroscience, /4/0PelhamParkway
South, R#6/4Bronx, NY/0461-I/01, USA.
Michael A. Arbib
Dept. ofNeurobiology, UniversityofSouthernCalifornia, LosAngeles, CA 90088, USA.
GiorgioA. Ascoli
ComputationalNeuroanatomy, KrasnowInstituteforAdvancedStudyandPsychology,
GeorgeMason University, Fairfax, VA, USA.
JavedAslam
ComputerScienceDepartment, DartmouthCollege,6162MooreHall, Hanover, NH03755,
USA.
Kim. T. Blackwell
KrasnowInstituteofAdvancedStudiesandSchoolofComputationalStudies, GeorgeMason
University, Fairfax, VA22030, USA.
MihailBota
Dept. ofNeurobiology, UniversityofSouthernCalifornia, LosAngeles, CA90088, USA.
ThomasBoulin
ColumbiaUniversity, DepartmentofBiochemistryandMolecularBiophysics,630West168th
Street, New York, NY1003, USA.
x Contributors
DouglasM. Bowden
DepartmentofPsychiatryandBehavioralSciencesandWashingtonNationalPrimate
ResearchCenter, UniversityofWashington, Seattle, WA, USA.
AhmetBozkurt
ComputationalISystemsINeuroscienceGroup, C. & O. VogtBrainResearchInstitute,
HeinrichHeine University, D-40225Dusseldorf, Germany.
Gully A.P.CBums
USC, HedcoNeurosciBldng,3614WattWay, LosAngeles, CA90089, USA.
RobertC. Cannon
TheoreticalBiology, Born-BungeFoundation, UniversityofAntwerp, Wilrijk, Belgium.
NanshengChen
ColdSpringHarborLaboratory, I BungtownRoad, ColdSpring Harbor, NY11724, USA.
ChiquitoJ. Crasto
YaleCenterforMedicalInformatics, Yale UniversitySchoolofMedicine, NewHaven, CT,
USA.
Andrew P. Davison
DepartmentofNeurobiology, Yale UniversitySchoolofMedicine, NewHaven, cr, USA.
Michael S. Gazzaniga
TheJMRIDataCenter, CenterforCognitiveNeuroscience, DartmouthCollege,6162Moore
Hall, Hanover, NH03755, USA.
Jeffrey S. Grethe
TheJMRIDataCenter, DartmouthCollege,6162MooreHall, Hanover, NH03755, USA.
JonasD.-Johnsen
ComputationalISystemsINeuroscienceGroup, C. &O. VogtBrainResearchInstitute,
HeinrichHeine University, D-40225Dusseldorf, Germany.
MarkDubach
DepartmentofPsychiatryandBehavioralSciencesandWashingtonNationalPrimate
ResearchCenter, UniversityofWashington, Seattle, WA, USA.
GregorEichele
MaxPlanckInstituteofExperimentalEndocrinology, Feodor-Lynen-Str. 7, D-30165
Hannover, Germany.
MarkH.Ellisman
NationalCenterforMicroscopyandImagingResearchandDepartmentofNeurosciences,
andSanDiegoSupercomputerCenter, UniversityofCalifornia, SanDiego. SanDiegoCA,
USA.
Contributors xi
RainerForster
InstituteforTheoreticalBiology, Humboldt-UniversitiitzuBerlin, InvalidenstrafJe43,D
101l5Berlin, Germany.
Karl1.Friston
WellcomeDept. ofImagingNeuroscience, UCL, UK.
AndreasGeissler
ComputationalISystemsINeuroscienceGroup, C. &0. VogtBrainResearchInstitute,
HeinrichHeine University, D-40225DUsseldorf, Germany.
InaGerken
ComputationalISystemsINeuroscienceGroup, C. &O. VogtBrainResearchInstitute,
HeinrichHeineUniversity, D-40225DUsseldorf, Germany.
SethG.N. Grant
CentreforNeuroscience, UniversityofEdinburgh, Edinburgh,EH8912, UK.
JoGrothe
DepartmentofPsychiatrylll, UniversityofVIm, D-89075Ulm, Germany.
AmarnathGupta
SanDiegoSupercomputerCenter, UniversityofCalifornia, SanDiego, SanDiegoCA, USA.
JeanetteHellgrenKotelski
RoyalInstituteofTechnologyandKarolinskaInstitute, S100-44Stockholm, Sweden.
Andreas V.M. Herz
InstituteforTheoreticalBiology, Humboldt-UniversitiitzuBerlin, InvalidenstrafJe43,D
101l5Berlin, Germany.
Claus C. Hilgetag
InternationalUniversityBremen, CampusRing1, D-28759Bremen, Germany.
MichaelL. Hines
DepartmentofNeurobiology, YaleUniversitySchoolofMedicine, NewHaven, CT, USA.
HolgerHusi
CentreforNeuroscience, UniversityofEdinburgh, Edinburgh, EH89J2, UK.
LarsKamper
ComputationalISystemsINeuroscienceGroup, C. & O. VogtBrainResearchInstitute,
HeinrichHeineUniversity, D-40225DUsseldorf, Germany.
RolfKotter
ComputationalISystemsINeuroscienceGroup, C. & O. VogtBrainResearchInstitute,and
InstituteofAnatomy11, HeinrichHeine University, D-40225DUsseldorf, Germany.
xii Contributors
Raymond Y.N. Lee
HowardHughesMedicalInstitute. DivisionofBiology. California InstituteofTechnology.
Pasadena. CA91125. USA.
NianLiu
YaleCenterforMedicalInfonnatics, Yale UniversitySchoolofMedicine. NewHaven. CT.
USA.
BertramLudascher
SanDiegoSupercomputerCenter, UniversityofCalifornia. SanDiego. SanDiegoCA, USA.
WolfgangMaass
InstituteforTheoreticalComputerScience. Technische UniversitiitGraz, Graz, Austria.
JtirgenMaier
ComputationalISystemsINeuroscienceGroup, C. &O. VogtBrainResearchInstitute.
Heinrich Heine University. D-40225Dusseldorf, Gennany.
LuisMarenco
CenterforMedicalInfonnatics, Yale UniversitySchoolofMedicine, NewHaven, CT. USA.
HenryMarkram
BrainMindInstitute, EcolePolytechniqueFederaledeLausanne, Lausanne, Switzerland
MaryannE. Martone
NationalCenterforMicroscopyandImagingResearchandDepartmentofNeurosciences.
UniversityofCalifornia, SanDiego, SanDiegoCA, USA.
MicheleMigliore
DepartmentofNeurobiology, Yale UniversitySchoolofMedicine. NewHaven. CT. USA, and
InstituteofAdvancedDiagnosticMethodologies. NationalResearchCouncil, Palermo. Italy.
MarkMontague
ThefMRIDataCenter, ComputerScienceDepartment. DartmouthCollege, 6162MooreHall.
Hanover, NH03755, USA.
ThomasM. Morse
DepartmentofNeurobiology. Yale UniversitySchoolofMedicine, NewHaven, CT. USA.
ThomasNatschHiger
InstituteforTheoreticalComputerScience. Technische UniversitiitGraz, Graz.Austria.
MarkA. O'Neill
DepartmentofPsychology. UniversityofNewcastleuponTyne, NewcastleuponTyne. NE2
4HH. UK.
