1992
Parallel Computation for Medicine and Biology: Applications of Linda At Yale University
Sittig D, Shifman M, Nadkarni P, Miller P. Parallel Computation for Medicine and Biology: Applications of Linda At Yale University. The International Journal Of High Performance Computing Applications 1992, 6: 147-163. DOI: 10.1177/109434209200600203.Peer-Reviewed Original ResearchComparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison
Miller P, Nadkarni P, Pearson W. Comparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison. Bioinformatics 1992, 8: 167-175. PMID: 1591612, DOI: 10.1093/bioinformatics/8.2.167.Peer-Reviewed Original ResearchConceptsDatabase of sequencesBiological sequence comparisonParallel computationMachine-independent parallel programming languageParallel programming languageHypercube parallel computerProgramming languageSoftware platformParallel computersParallel machinesExpressive powerBiological sequencesParallelizationPlatform programComputationModest sacrificeBenchmark testsLogicDatabaseCase studyComputerPortabilityMachineLindaRelative advantages
1991
Parallelizing genetic linkage analysis: A case study for applying parallel computation in molecular biology
Miller P, Nadkarni P, Gelernter J, Carriero N, Pakstis A, Kidd K. Parallelizing genetic linkage analysis: A case study for applying parallel computation in molecular biology. Journal Of Biomedical Informatics 1991, 24: 234-248. PMID: 1868693, DOI: 10.1016/0010-4809(91)90046-y.Peer-Reviewed Original ResearchConceptsParallel computersSequential programsMachine-independent parallel programming languageParallel programming languageDifferent parallel machinesLengthy computation timeParallel programsProgramming languageAvailable processorsDifferent processorsParallel computationParallel machinesSequential versionParallel versionComputational loadComputation timePerformance benchmarksComputerProcessorsCase studyDifferent piecesIterative programsLINKMAPComputationParallel formsParallel computation and FASTA: confronting the problem of parallel database search for a fast sequence comparison algorithm
Miller P, Nadkarni P, Carriero N. Parallel computation and FASTA: confronting the problem of parallel database search for a fast sequence comparison algorithm. Bioinformatics 1991, 7: 71-78. PMID: 2004277, DOI: 10.1093/bioinformatics/7.1.71.Peer-Reviewed Original ResearchConceptsSequence comparison algorithmAmount of computationMachine-independent parallel programming languageComparison algorithmsDisk I/OParallel programming languageParallel program runsO bottleneck problemDifferent parallel machinesBiological sequence comparisonNumber of processorsTime-consuming computationProgramming languageParallelization strategyParallel computationParallel machinesProgram design strategiesProgram runBottleneck problemFASTA algorithmFASTAAlgorithmComputationBottleneckGeneral problemParallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube.
Nadkarni P, Miller P. Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube. AMIA Annual Symposium Proceedings 1991, 404-8. PMID: 1807632, PMCID: PMC2247563.Peer-Reviewed Original ResearchConceptsMachine-independent parallel programming languageIntel HypercubeVirtual parallel machineParallel programming languageBiological sequence comparisonNumber of processorsParallel programmingParallel programsProgramming languageParallel computationDesktop workstationsParallel machinesProgramming commandsApplication areasPortable modelProcessorsLindaBenchmark testsNative modelsHypercubeParallelizationCase studyWorkstationsVersionMachine