Harnessing networked workstations as a powerful parallel computer: a general paradigm illustrated using three programs for genetic linkage analysis

• Published in: Bioinformatics Vol. 8; no. 2; pp. 141 - 147
• Main Authors: Miller, Perry L., Nadkarni, Prakash M., Bercovitz, Paul A.
• Format: Journal Article
• Language: English
• Published: Washington, DC Oxford University Press 01.04.1992; Oxford
• Subjects: Algorithms; Biological and medical sciences; Classical genetics, quantitative genetics, hybrids; Computer Communication Networks; Evaluation Studies as Topic; Fundamental and applied biological sciences. Psychology; Genetic Linkage; Genetics of eukaryotes. Biological and molecular evolution; Methods, theories and miscellaneous; Programming Languages; Software; Genetic mapping; Workstation; Parallel algorithm; Linkage; Parallel programming; Computer network; Parallel processing
• ISSN: 1367-4803; 0266-7061; 1460-2059
• DOI: 10.1093/bioinformatics/8.2.141

It is widely accepted that parallel computers, which have the ability to execute different parts of a program simultaneously, will offer dramatic speed–up for many time–consuming biological computations. The paper describes how the use of the machine–independent parallel programming language, Linda, allows parallel programs to run on an institution′s network of workstations. In this way, an institution can harness existing hardware, which is often either idle or vastly underutilized, as a powerful ‘parallel machine’ with supercomputing capability. The paper illustrates this very general paradigm by describing the use of Linda to parallelize three widely used programs for genetic linkage analysis, a mathematical technique used in gene mapping. The paper then discusses a number of technical, administrative and social issues that arise when creating such a computational resource.