Abstract

The proposed research project will explore the parallelization of algorithms used in molecular biology, focusing primarily on algorithms for 10 genetic sequence analysis and 2) genetic linkage analysis. A key aspect of the proposal involves the use of the machine-independent parallel programming language Linda. Genetic Sequence Analysis: We propose to continue work currently in progress to explore design issues in parallelizing algorithms for genetic sequence analysis. This research will focus on 1) the intrinsic parallelizing of an algorithm, and 2) the """"""""parallel database search"""""""" and """"""""load balancing"""""""" issues involved in running an algorithm simultaneously on many sets of input. Genetic Linkage Analysis: Using the machine-independent parallel programming language Linda, we will explore how the complex algorithm for performing genetic linkage analysis is best parallelized, and will test and refine the parallelized version using data from the laboratory of Dr. Kenneth Kidd of the Yale Department of Human Genetics and the Human Gene Mapping Library in New Haven. An Online Library for Use by Molecular Biology Researchers: As parallelized versions of the algorithms are developed, they will be incorporated into an online library whose use by molecular biology researchers at Yale and elsewhere will be encouraged. This online use of the parallelized algorithms will let us obtain concrete feedback to help guide our efforts.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Library of Medicine (NLM)
Type
Research Project (R01)
Project #
5R01LM005044-02
Application #
3374150
Study Section
Biomedical Library and Informatics Review Committee (BLR)
Project Start
1989-09-01
Project End
1992-08-31
Budget Start
1990-09-01
Budget End
1991-08-31
Support Year
2
Fiscal Year
1990
Total Cost
Indirect Cost

  Institution

Name
Yale University
Department
Type
Schools of Medicine
DUNS #
082359691
City
New Haven
State
CT
Country
United States
Zip Code
06520

  Publications

Shifman, M A; Windemuth, A; Schulten, K et al. (1992) Molecular dynamics simulation on a network of workstations using a machine-independent parallel programming language. Comput Biomed Res 25:168-80
Miller, P L; Nadkarni, P M; Pearson, W R (1992) Comparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison. Comput Appl Biosci 8:167-75
Miller, P L; Nadkarni, P M; Bercovitz, P A (1992) Harnessing networked workstations as a powerful parallel computer: a general paradigm illustrated using three programs for genetic linkage analysis. Comput Appl Biosci 8:141-7
Goradia, T M; Lange, K; Miller, P L et al. (1992) Fast computation of genetic likelihoods on human pedigree data. Hum Hered 42:42-62
Sittig, D F; Foulser, D; Carriero, N et al. (1991) A parallel computing approach to genetic sequence comparison: the master-worker paradigm with interworker communication. Comput Biomed Res 24:152-69
Nadkarni, P M; Miller, P L (1991) Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube. Proc Annu Symp Comput Appl Med Care :404-8
Shifman, M A; Windemuth, A; Schulten, K et al. (1991) Molecular dynamics simulation on a network of workstations using a machine-independent parallel programming language. Proc Annu Symp Comput Appl Med Care :414-8
Miller, P L; Nadkarni, P M; Carriero, N M (1991) Parallel computation and FASTA: confronting the problem of parallel database search for a fast sequence comparison algorithm. Comput Appl Biosci 7:71-8
Miller, P L; Nadkarni, P; Gelernter, J E et al. (1991) Parallelizing genetic linkage analysis: a case study for applying parallel computation in molecular biology. Comput Biomed Res 24:234-48
Foulser, D E; Core, N G (1990) Parallel computation of multiple biological sequence comparisons. Comput Biomed Res 23:310-31