Comparison of Computational Tools for Protein-Protein Interaction (PPI) Mapping and Analysis

Leong, Geok Wei; Lee, Sheau Chen; Lau, Cher Chien; Klappa, Peter; Shamsir, Mohd Shahir

doi:10.11113/jt.v63.1226

Cited by 2 publications

(1 citation statement)

References 19 publications

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“…Gephi software is open-source and free. It has been used to explore data and analyze the SLR s for different authors in various areas of study (Wei Leong et al, 2013;Deng et al, 2016;Hurst et al, 2016;Montoya Restrepo et al, 2016;Venkatesakumar and Pachayappan, 2017;Rajagopal et al, 2017).…”

Section: Methodsmentioning

confidence: 99%

Evaluation of value stream mapping (VSM) applicability to the oil and gas chain processes

Lobo

Calado

Conceição

2018

IJLSS

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Purpose Lean approach has overcome the boundaries of the automotive and manufacturing industry and has achieved many different sectors of the economy, including services. In this context, this paper aims to investigate the applicability of value stream mapping (VSM) tool in processes of the oil and gas chain. Also, this paper investigates if there is a specific framework currently being used by organizations belonging to this chain to map the value stream of its processes. Design/methodology/approach A detailed systematic review of the literature is done by using a set of relevant keywords based on peer-reviewed journal articles and conference papers available in the Scopus database, analyzing data from 2012 to 2017. Content analysis methodology involving a four-step process (identification, screening, eligibility and inclusion) suggested by Moher et al. (2009) was adopted for this study. Findings The number of studies in literature on VSM applicability to the oil and gas chain processes is low when compared to studies regarding the application of lean tools and methods in general in this area. Also, there is no specific framework that has been used by the oil and gas chain companies to carry out the VSM, which is a research gap that can be further explored. Research limitations/implications Sample size for this research consists of 42 studies, thereby limiting the generalizability of the research studies. However, the analysis presented in this paper was based only on Scopus database, which is a remarkable and broad base, which provided robustness to the data found. Practical implications Practicing managers of oil and gas chain who are planning to transform their processes can use the VSM for it. Researchers can explore the research gap found in this study and develop a specific framework to implement VSM in the oil and gas chain processes. Originality/value This is the first paper to evaluate the VSM tool applicability to the oil and gas chain processes based on an systematic literature review and understand if this is possible and if there is a specific framework to carry out this task.

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Section: Methodsmentioning

confidence: 99%

Evaluation of value stream mapping (VSM) applicability to the oil and gas chain processes

Lobo

Calado

Conceição

2018

IJLSS

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Integrated web visualizations for protein-protein interaction databases

2015

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BackgroundUnderstanding living systems is crucial for curing diseases. To achieve this task we have to understand biological networks based on protein-protein interactions. Bioinformatics has come up with a great amount of databases and tools that support analysts in exploring protein-protein interactions on an integrated level for knowledge discovery. They provide predictions and correlations, indicate possibilities for future experimental research and fill the gaps to complete the picture of biochemical processes. There are numerous and huge databases of protein-protein interactions used to gain insights into answering some of the many questions of systems biology. Many computational resources integrate interaction data with additional information on molecular background. However, the vast number of diverse Bioinformatics resources poses an obstacle to the goal of understanding. We present a survey of databases that enable the visual analysis of protein networks.ResultsWe selected M =10 out of N =53 resources supporting visualization, and we tested against the following set of criteria: interoperability, data integration, quantity of possible interactions, data visualization quality and data coverage. The study reveals differences in usability, visualization features and quality as well as the quantity of interactions. StringDB is the recommended first choice. CPDB presents a comprehensive dataset and IntAct lets the user change the network layout. A comprehensive comparison table is available via web. The supplementary table can be accessed on http://tinyurl.com/PPI-DB-Comparison-2015.ConclusionsOnly some web resources featuring graph visualization can be successfully applied to interactive visual analysis of protein-protein interaction. Study results underline the necessity for further enhancements of visualization integration in biochemical analysis tools. Identified challenges are data comprehensiveness, confidence, interactive feature and visualization maturing.

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Comparison of Computational Tools for Protein-Protein Interaction (PPI) Mapping and Analysis

Cited by 2 publications

References 19 publications

Evaluation of value stream mapping (VSM) applicability to the oil and gas chain processes

Evaluation of value stream mapping (VSM) applicability to the oil and gas chain processes

Integrated web visualizations for protein-protein interaction databases

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