NDLI: Heuristic parallelizable algorithm for similarity based biosystems comparison

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Heuristic parallelizable algorithm for similarity based biosystems comparison

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Heuristic parallelizable algorithm for similarity based biosystems comparison

Content Provider	ACM Digital Library
Author	Lushbough, Carol M. Thavappiragasam, Mathialakan Gnimpieba, Etienne Z.
Abstract	Biosystem comparison plays a major role in system biology. Similar biosystems are identified based on the similarity of species naming. Since the species naming does not follow a standard nomenclature, similarity is not easy to formalize. A single metabolite can have different name strings that vary slightly in pattern. Several algorithms have been designed to find similarity between two species using different measures. However, these algorithms failed to achieve good performance in biological species similarity checking due to failure to account for important facts about biological name analysis. We developed ParaABioS, a heuristic, intuitive algorithm for biosystem similarity evaluation. This algorithm integrates sub-name analysis and a symbol management strategy that conserves species name specifications. ParaABioS provides similarity checking between two names that consumes the time O(k!) where k is the number of sub names in worst case. It is implemented in Java and parallelized on a Texas Advanced Computing Center TACC high performance computing (HPC) server and accessed through the iPlant Collaborative Foundation API in order to compare large models. It is available online and also through the BioExtract Server workflow management system (WMS).
Starting Page	782
Ending Page	789
Page Count	8
File Format	PDF
ISBN	9781450328944
DOI	10.1145/2649387.2660849
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2014-09-20
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Edit distance Parallel algorithm Bio systems E-science Workflow Hpc Metabolite naming Similar species
Content Type	Text
Resource Type	Article

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