Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics

Irene Kouskoumvekaki, Nour Shublaq, Søren Brunak

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Abstract

As both the amount of generated biological data and the processing compute power increase, computational experimentation is no longer the exclusivity of bioinformaticians, but it is moving across all biomedical domains. For bioinformatics to realize its translational potential, domain experts need access to user-friendly solutions to navigate, integrate and extract information out of biological databases, as well as to combine tools and data resources in bioinformatics workflows. In this review, we present services that assist biomedical scientists in incorporating bioinformatics tools into their research.We review recent applications of Cytoscape, BioGPS and DAVID for data visualization, integration and functional enrichment. Moreover, we illustrate the use of Taverna, Kepler, GenePattern, and Galaxy as open-access workbenches for bioinformatics workflows. Finally, we mention services
that facilitate the integration of biomedical ontologies and bioinformatics tools in computational workflows.
Original languageEnglish
JournalBriefings in Bioinformatics
Volume15
Issue number6
Pages (from-to)942-952
Number of pages11
ISSN1467-5463
DOIs
Publication statusPublished - 2014

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