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Accelerating covering array generation by combinatorial join for industry scale software testing.

ABSTRACT: Combinatorial interaction testing, which is a technique to verify a system with numerous input parameters, employs a mathematical object called a covering array as a test input. This technique generates a limited number of test cases while guaranteeing a given combinatorial coverage. Although this area has been studied extensively, handling constraints among input parameters remains a major challenge, which may significantly increase the cost to generate covering arrays. In this work, we propose a mathematical operation, called "weaken-product based combinatorial join", which constructs a new covering array from two existing covering arrays. The operation reuses existing covering arrays to save computational resource by increasing parallelism during generation without losing combinatorial coverage of the original arrays. Our proposed method significantly reduce the covering array generation time by 13-96% depending on use case scenarios.

SUBMITTER: Ukai H

PROVIDER: S-EPMC9044240 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Accelerating covering array generation by combinatorial join for industry scale software testing.

Ukai Hiroshi H Qu Xiao X Washizaki Hironori H Fukazawa Yoshiaki Y

PeerJ. Computer science 20220211

Combinatorial interaction testing, which is a technique to verify a system with numerous input parameters, employs a mathematical object called a covering array as a test input. This technique generates a limited number of test cases while guaranteeing a given combinatorial coverage. Although this area has been studied extensively, handling constraints among input parameters remains a major challenge, which may significantly increase the cost to generate covering arrays. In this work, we propose ...[more]

PMID: 35494846

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Project description:BackgroundThe genomic information of a species allows for the genome-scale reconstruction of its metabolic capacity. Such a metabolic reconstruction gives support to metabolic engineering, but also to integrative bioinformatics and visualization. Sequence-based automatic reconstructions require extensive manual curation, which can be very time-consuming. Therefore, we present a method to accelerate the time-consuming process of network reconstruction for a query species. The method exploits the availability of well-curated metabolic networks and uses high-resolution predictions of gene equivalency between species, allowing the transfer of gene-reaction associations from curated networks.ResultsWe have evaluated the method using Lactococcus lactis IL1403, for which a genome-scale metabolic network was published recently. We recovered most of the gene-reaction associations (i.e. 74 - 85%) which are incorporated in the published network. Moreover, we predicted over 200 additional genes to be associated to reactions, including genes with unknown function, genes for transporters and genes with specific metabolic reactions, which are good candidates for an extension to the previously published network. In a comparison of our developed method with the well-established approach Pathologic, we predicted 186 additional genes to be associated to reactions. We also predicted a relatively high number of complete conserved protein complexes, which are derived from curated metabolic networks, illustrating the potential predictive power of our method for protein complexes.ConclusionWe show that our methodology can be applied to accelerate the reconstruction of genome-scale metabolic networks by taking optimal advantage of existing, manually curated networks. As orthology detection is the first step in the method, only the translated open reading frames (ORFs) of a newly sequenced genome are necessary to reconstruct a metabolic network. When more manually curated metabolic networks will become available in the near future, the usefulness of our method in network prediction is likely to increase.

Dataset Information

Accelerating covering array generation by combinatorial join for industry scale software testing.

Publications

Accelerating covering array generation by combinatorial join for industry scale software testing.

Similar Datasets

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