The biodice Taverna plugin for clustering and visualization of biological data: A workflow for molecular compounds exploration (Articolo in rivista)

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  • The biodice Taverna plugin for clustering and visualization of biological data: A workflow for molecular compounds exploration (Articolo in rivista) (literal)
Anno
  • 2014-01-01T00:00:00+01:00 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi
  • 10.1186/1758-2946-6-24 (literal)
Alternative label
  • Fiannaca A.; La Rosa M.; Di Fatta G.; Gaglio S.; Rizzo R.; Urso A. (2014)
    The biodice Taverna plugin for clustering and visualization of biological data: A workflow for molecular compounds exploration
    in Journal of cheminformatics
    (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
  • Fiannaca A.; La Rosa M.; Di Fatta G.; Gaglio S.; Rizzo R.; Urso A. (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#url
  • http://www.scopus.com/inward/record.url?eid=2-s2.0-84901697253&partnerID=q2rCbXpz (literal)
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  • 6 (literal)
Rivista
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroFascicolo
  • 1 (literal)
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  • Scopu (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
  • ICAR-CNR, National Research Council of Italy, Viale delle Scienze, ed.11, 90128 Palermo, Italy; ICAR-CNR, National Research Council of Italy, via P. Castellino, 111, 80131 Napoli, Italy; School of Systems Engineering, University of Reading, RG6 6AX, Reading, United Kingdom (literal)
Titolo
  • The biodice Taverna plugin for clustering and visualization of biological data: A workflow for molecular compounds exploration (literal)
Abstract
  • Background: In many experimental pipelines, clustering of multidimensional biological datasets is used to detect hidden structures in unlabelled input data. Taverna is a popular workflow management system that is used to design and execute scientific workflows and aid in silico experimentation. The availability of fast unsupervised methods for clustering and visualization in the Taverna platform is important to support a data-driven scientific discovery in complex and explorative bioinformatics applications. Results: This work presents a Taverna plugin, the Biological Data Interactive Clustering Explorer (BioDICE), that performs clustering of high-dimensional biological data and provides a nonlinear, topology preserving projection for the visualization of the input data and their similarities. The core algorithm in the BioDICE plugin is Fast Learning Self Organizing Map (FLSOM), which is an improved variant of the Self Organizing Map (SOM) algorithm. The plugin generates an interactive 2D map that allows the visual exploration of multidimensional data and the identification of groups of similar objects. The effectiveness of the plugin is demonstrated on a case study related to chemical compounds. Conclusions: The number and variety of available tools and its extensibility have made Taverna a popular choice for the development of scientific data workflows. This work presents a novel plugin, BioDICE, which adds a data-driven knowledge discovery component to Taverna. BioDICE provides an effective and powerful clustering tool, which can be adopted for the explorative analysis of biological datasets. © 2014Fiannaca et al.; licensee Chemistry Central Ltd. (literal)
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