platform day
TRANSCRIPT
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PlatformDay2008
홍창범국립보건연구원유전체센터
2008.5.30
광우병과대용량데이터처리플랫폼
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전문가가되어버리다
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M/MMethionine=Met,Valine=Val
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영국인은40%한국사람은95%
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gtg/atg
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dbSNP
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단지하나차이일뿐인데...
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단일염기다형성(SNP,SingleNucleotide
Polymorphism)
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모두23쌍의염색체를지님인간은누구나서로99.9%의유전정보가동일
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한인구집단의유전체에서1%이상의빈도를보이는염기서열의변이
대머리의56%가가족력존재
22%가유당분해효소결핍증44%가귓볼존재 알츠하이머의19%가가족력존재
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30억염기쌍이라는거대한책의색인을작성
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인간유전체연구
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여자3명,남자2명의DNA샘플을시작으로휴먼지놈프로젝트
시작
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영국,미국,캐나다,일본,나이지리아및중국에서약200여과학자들
아시아,아프리카및미국에서약269명의DNA표본을이용
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1000명유전체프로젝트(1000GenomesProject)
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한국인만명에대한...
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2003년휴먼지놈프로젝트$27억2004년크레이그벤터박사$1억
2008년왓슨박사$100만5년후$100
-MITTechnologyReview2008년4월17일뉴스-
30억염기서열쌍이라는대용량데이터생산과분석이현실다른오믹스(단백체,발현체,대사체등)정보와의통합분석
을구현할시점
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점점커져가는데...
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대량의연구를빠른시간에...
SequencingMicroarrays
HighthroughputGenotypingPowerfulComputation
LabAutomation
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생물학데이터에대해서
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자료구조의관점
1차원배열형태의서열데이터다차원배열형태의구조데이터매트릭스형태의발현데이터네트워크형태의상호작용데이터문서형태의텍스트데이터
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서열데이터
DNA,RNA등의유전체데이터EST서열
SNP데이터
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구조데이터
단백질3차구조데이터질량분석기데이터
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발현데이터
마이크로어레이데이터arrayCGHChIP-chip
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네트워크형태
pathwayproteininteraction
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텍스트데이터
논문,문헌정보
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유전체연구
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DatabaseHardware
Agent
Machine LearningAlgorithm
InformationRetrieval
IT와유전체연구
Genomic Variation Research
Personalized Medicine
GeneBankSWISS-PROT
Super ComputerCluster
ClusteringPattern recognition
Classfication
Sequence alignment
Biomedical text analysis
Information filteringMonitoring agent
Personal Genome
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SequenceAlignment-SimulatedAnnealing-GeneticAlgorithms
StructureandFunctionPrediction-HiddenMarkovModels-MultilayerPerceptrons
-DecisionTreesMolecularClusteringand
Classification-SupportVectorMachines
-NearestNeighborAlgorithmsExpressionAnalysis
-Self-OrganizingMaps-BayesianNetworks
MachineLearning
TobySegaranBiotechsoftwarecompany
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SequenceSearchwithMPI
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GPU를이용한병렬서열정렬
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웹서비스를이용한생물학매쉬업(Taverna,Myexperiment)
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컴퓨팅파워제공(Folding@Home,Korea@Home)
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집단지성을이용한퍼즐맞추기-foldit
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시맨틱웹(FreeBase)
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유전체연구플랫폼
50만개의SNPPorbe를포함하고있는AffymetrixGenome-Wide
HumanSNPAssay5.0고밀도SNParray
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MultidimensionalScaling(MDS)북부및서유럽(CEU),나이지라아계열(YRI),일본계(JPT),중국한족(CHB)
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한국인SNP
2,978개의유전자에대한12,995개의SNP
KARE로생산된9,603명(Genotype데이터18GB)
후속13,000명생산중
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임상,역학데이터
12개질환군별센터(심혈관,뇌신경질환,당뇨,피부,불임,선
천성기형등등)안산(대도시),안성(농촌)코호트등등
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질병관련연관성연구
정상,환자의시료를이용한표현형(phenotype)에연관된SNP발굴
질환가계및질환형제자매를이용한연구
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역학정보변수
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KSNP(KoreanSNP)Browser
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질병예측
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GenomeBrowserwithGoogleMapsAPI
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BioBlogRSS:전세계의생물학블로거
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모든것은바로컴퓨터의힘!
SimulationDataAnalysis
DataAcquisitionDataManagement
DataArchiving->ScientificResults,
Publication
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유전체센터의컴퓨팅파워
18NodeIA2Cluster 32NodeX86Cluster
100NodePPCCluster
NAS,DASStorageWorkstation
pc
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해결해야할문제점
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단일플랫폼
Capacity&Size증가데이터생산의가속화
데이터부족
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다중플랫폼
비용문제지리적문제
협업을통한시너지창출컴퓨팅리소스
누구도접근해보지못한
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...ATTAGGACCAATAAGTCT...
...ATTAGGAGCAATAAGTCT...
...ATTAGGAGCAATAACTCT...
...ATTAGGAGCAATAAGTCT...
Person 1 +
Person 2 -
Single locus Pair of locii
(+,-)Cost = 0.5M x 5k x 10k
(+,-)Cost = 1/2 x 0.5M x 0.5M x 5k x 10k
0.5M SNP, cohort of 5K individuals, 10k random data set
1 day 120 yr
Computationalproblem
Text
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기상청
지역별관측소자료+작년도오늘날씨=
내일비올확률40%
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RealisticSolution
머리카락+몸무게+키+음주습관=
다음주당뇨
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구글과생명공학의만남
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GoogleHealthBETA
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SNP정보
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유전자정보
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나는누구인가?
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얼마나유사한가?
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원하는것은?
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Google검색엔진->Google플랫폼Nutch검색엔진->Hadoop플랫폼
분석도구의손쉬운접근새로운알고리즘의개발과적용대용량의데이터의접근
->생물학데이터처리를위한플랫폼
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플랫폼그이상의플랫폼
모든연구자들이아무런댓가없이자신의연구를수행하고
서로의의견을교류할수있는그런...
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