NEUROSCIENCE 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 from the Library of Congress. 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 Softcover reprint of the hardcover 1s t edition 2003 All rights reserved. No part ofthis work may be reproduced, stored in a retrieval system, or trausmitted in auy form or by auy meaus, electronic, mechauical, photocopying, microfilming, recording, or otherwise, without the written permission from the Publisher, with the exception of auy material supplied specifically for the purpose ofbeing entered aud executed on a computer system, for exclusive use by the purchaser of the work. Permission for books published in Europe: [email protected] Permissions for books published in the United States of America: [email protected] Printed on acid-free paper. The Publisher offers discounts on this book for course use and bulk purchases. For further information, send email to<[email protected]> • 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.