Similar compounds searching system by using the gene expression microarray database.docx
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Similar compounds searching system by using the gene expression microarray database.docx
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Similarcompoundssearchingsystembyusingthegeneexpressionmicroarraydatabase
425articlesfoundfor:
pub-date>2003andtak(((ChemicalDatabase)or(ComputerChemistry)or(databaseChemistry))and((SoftwareDevelopment)or(Largedatabase)or(ApplicationDevelopment)or(visualstudio)orC++orDerivativesor(integrationofmulti-databasesystem)))
计算机化学
计算机软件开发
VS.net或C++
大型数据库
化学专业数据库的开发
应用软件开发
化学数据库
多数据库系统的整合
应用衍生
ComputerChemistry
ComputerSoftwareDevelopment
VS.netorC++
Largedatabase
DevelopmentofthedatabaseChemistry
ApplicationDevelopment
ChemicalDatabase
Theintegrationofmulti-databasesystem
ApplicationofDerivatives
GaussDal:
Anopensourcedatabasemanagementsystemforquantumchemicalcomputations
ComputerPhysicsCommunications
AnopensourcesoftwaresystemcalledGaussDalformanagementofresultsfromquantumchemicalcomputationsispresented.Chemicaldatacontainedinoutputfilesfromdifferentquantumchemicalprogramsareautomaticallyextractedandincorporatedintoarelationaldatabase(PostgreSQL).TheStructuralQueryLanguage(SQL)isusedtoextractcombinationsofchemicalproperties(e.g.,molecules,orbitals,thermo-chemicalproperties,basissetsetc.)intodatatablesforfurtherdataanalysis,processingandvisualization.Thistypeofdatamanagementisparticularlysuitedforprojectsinvolvingalargenumberofmolecules.InthecurrentversionofGaussDal,parsersforGaussianandDaltonoutputfilesaresupported,howeverfutureversionsmayalsoincludeparsersforotherquantumchemicalprograms.
ForvisualizationandanalysisofgenerateddatatablesfromGaussDalwehaveusedthelocallydevelopedopensourcesoftwareSciCraft.
Programsummary
Titleofprogram:
GaussDal
Catalogueidentifier:
ADVT
ProgramsummaryURL:
http:
//cpc.cs.qub.ac.uk/summaries/ADVThttp:
//cpc.cs.qub.ac.uk/summaries/ADVT
Programobtainablefrom:
CPCProgramLibrary,Queen'sUniversityofBelfast,N.Ireland
Computers:
Any
Operatingsystemunderwhichthesystemhasbeentested:
Linux
Programminglanguageused:
Python
Memoryrequiredtoexecutewithtypicaldata:
256MB
No.ofbitsinword:
32or64
No.ofprocessorsused:
1
Hasthecodebeenvectorizedorparallelized?
:
No
No.oflinesindistributedprogram,includingtestdata,etc:
543 531
No.ofbytesindistributionprogram,includingtestdata,etc:
7 718 121
Distributionformat:
tar.gzipfile
Natureofphysicalproblem:
Handlingoflargeamountsofdatafromquantumchemistrycomputations.
Methodofsolution:
UseofSQLbaseddatabaseandquantumchemistrysoftwarespecificparsers.
Restrictiononthecomplexityoftheproblem:
ProgramiscurrentlylimitedtoGaussianandDaltonoutput,butexpandabletootherformats.Generatessubsetsofmultipledatatablesfromoutputfiles.
ArticleOutline
1.Introduction
2.Softwarerequirements
2.1.Relatedsoftware
3.Designandconstruction
3.1.OverallstructureofGaussDal
3.2.Databasestructure
3.3.Technologydecisions
3.4.Visualizationanddataanalysis
3.5.TheSciCraftsystem
3.5.1.Integration
3.5.2.Visualprogramming
3.5.3.TheGaussDalnode
4.TheSQLlanguage
4.1.Relations
4.2.Structuredqueries
4.2.1.SomebasicSQLcommands
5.GaussDalwebsolution
5.1.Webinterface
5.1.1.Submittingcomputations
5.2.PhpPgAdmin
6.Applicationexamples
6.1.Forcefieldparametrization
6.1.1.Descriptionofdataset
6.1.2.QCcalculations
6.1.3.TheSQLquery
6.1.4.DataanalysiswithSciCraft
6.2.Electrophilicadditiontopropene
6.2.1.Descriptionofdataset
6.2.2.QCcalculations
6.2.3.TheSQLquery
6.2.4.DataanalysiswithSciCraft
7.Discussion
8.Outputextract
References
Structurealertsforcarcinogenicity,andtheSalmonellaassaysystem:
Anovelinsightthroughthechemicalrelationaldatabasestechnology
MutationResearch/ReviewsinMutationResearch
Inthepastdecades,chemicalcarcinogenicityhasbeentheobjectofmechanisticstudiesthathavebeentranslatedintovaluableexperimental(e.g.,theSalmonellaassayssystem)andtheoretical(e.g.,compilationsofstructurealertsforchemicalcarcinogenicity)models.Thesefindingsremainthebasisofthescienceandregulationofmutagensandcarcinogens.Recentadvancesintheorganizationandtreatmentoflargedatabasesconsistingofbothbiologicalandchemicalinformationnowadaysallowsforamucheasierandmorerefinedviewofdata.Thispaperreviewsrecentanalysesonthepredictiveperformanceofvariouslistsofstructurealerts,includinganewcompilationofalertsthatcombinespreviousworkinanoptimizedformforcomputerimplementation.TherevisedcompilationispartoftheToxtree1.50software(freelyavailablefromtheEuropeanChemicalsBureauwebsite).TheuseofstructuralalertsforthechemicalbiologicalprofilingofalargedatabaseofSalmonellamutagenicityresultsisalsoreported.
Togetherwithbeingarepositoryofthescienceonthechemicalbiologicalinteractionsatthebasisofchemicalcarcinogenicity,theSAshaveacrucialroleinpracticalapplicationsforriskassessment,for:
(a)descriptionofsetsofchemicals;(b)preliminaryhazardcharacterization;(c)formationofcategoriesfore.g.,regulatorypurposes;(d)generationofsubsetsofcongenericchemicalstobeanalyzedsubsequentlywithQSARmethods;(e)prioritysetting.
AnimportantaspectofSAsaspredictivetoxicitytoolsisthattheyderivedirectlyfrommechanisticknowledge.Thecrucialroleofmechanisticknowledgeintheprocessofapplying(Q)SARconsiderationstoriskassessmentshouldbestronglyemphasized.Mechanisticknowledgeprovidesagroundforinteractionanddialoguebetweenmodeldevelopers,toxicologistsandregulators,andpermitstheintegrationofthe(Q)SARresultsintoawiderregulatoryframework,wheredifferenttypesofevidenceanddataconcurorcomplementeachotherasabasisformakingdecisionsandtakingactions.
ArticleOutline
1.Introduction
2.Background
2.1.Themechanisticresearch
2.2.Newdevelopmentsintheorganizationandexploitationofchemicalbiologicaldata
3.Structurealertsandtheirevaluation
4.SAspredictivityandthechangingpatternofchemicalsinuse
5.SAsforcarcinogenicity:
newdevelopments
5.1.TheperformanceofthenewlistofSAs
6.ChemicalbiologicalprofilingofaSalmonellamutagenicitydatabase
7.Finalconsiderations
Conflictofinterest
References
Adecisionsupportgridforintegratedmolecularsolventdesignandchemicalprocessselection
Computers&ChemicalEngineering
Theprocessengineeringdomainmakesaninterestingapplicationareaforgridtechnologiesasproblemsolvinggenerallyinvolvesmultiplesoftwareanddataresourcesandheavycomputations.Therearenumerouscomputationallydemandingapplicationsthatcanbenefitfromgridcomputingsuchasmolecularsimulationsandlarge-scaleoptimizations.Wereportonaprototypegridforintegratedprocessandmoleculardesigntodemonstratethepotentialofgridsintheprocess-engineeringarena.Theprototypeintegratesin-housesolventandprocessdesigntoolswithexternaldistributedcomputationandstorageresourcesaswellasweb-databasesandcomputernetworks.Amiddlewarearchitectureisproposedintheformofaproblem-solvingenvironmentasameansofinterfacingtheheterogeneousgridcomponents.Thegridoperationsandfunctionalitiesareexposedtotheuserthroughaprototypeweb-portalthatenablestheseamlessaccessandutilizationoftheavailableresources.Thedevelopedprototypeisillustratedwithanapplicationcase.
ArticleOutline
1.Introduction
2.Generalconceptsofgridcomputing
3.GridcomputingrelateddevelopmentsinCAPE
3.1.InteroperabilitythroughtheCAPE-OPENstandard
3.2.Agent-basedandservice-orientedapproaches
3.3.Designandoptimizationonthegrid
4.Integratedsolventandprocesssynthesis:
agridcomputingparadigm
4.1.Theintegratedsolventandprocesssynthesisproblem—overview
4.2.Incentivesforgridcomputinginintegratedsolventandprocesssynthesis
5.Thegridcomputingprototypeforintegratedsolventandprocessdesign
5.1.Outlineofprototype
5.2.Availableinfrastructure
5.3.Problem-solvingenvironment—Web/Gridserviceslayer
5.3.1.Workflowgenerator
5.3.2.Queryservices
5.3.3.Deploymentservices
5.3.4.Resourceallocatoranddatamanager:
staticoperation
5.3.5.Jobscheduler
5.4.Workflowandparalleloptimizationstrategies
5.4.1.Workflowstrategiestargetedbytheproposedarchitecture
5.4.2.Targetedparalleloptimizationstrategiesandfuturedirections
5.5.Web-portal
6.Illustrativeexample
6.1.Designproblem
6.2.Targetedsolutionfeaturesanddiscussionofresults
6.2.1.Stochasticoptimalityexperiments
6.2.2.Queryofmoleculesandstorage
7.Concludingremarksandfuturedevelopments
References
Overviewoftheapplicationsofthermodynamicdatabasestosteelmakingprocesses
Calphad
Computerizedthermodynamicdatabasesforsolidandliquidsteel,slagsandsolidoxidesolutions,forlargenumbersofcomponents,havebeendevelopedoverthelastthreedecadesbycriticalevaluation/optimizationofallavailablephaseequilibriumandthermodynamicdata.Thedatabasescontainmodelparametersspecificallydevelopedformoltenslags,liquidandsolidsteelandsolidoxidesolutions.Withuser-friendlysoftware,whichaccessesthesedatabases,complexchemicalreactionsandphaseequilibriaoccurringthroughoutthesteelmakingprocesscanbecalculatedoverwiderangesoftemperature,oxygenpotentialandpressure.Inthepresentarticle,thethermodynamicmodelsanddatabasesformoltenslagandliquidsteelincludedinwell-knownthermochemicalpackagesandtheirapplicationstocomplexsteelmak
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