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

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 a...

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Bibliographic Details
Published in:Briefings in bioinformatics 2014-11, Vol.15 (6), p.942-952
Main Authors: Kouskoumvekaki, Irene, Shublaq, Nour, Brunak, Søren
Format: Article
Language:English
Subjects:
Bioinformatics
Biological Ontologies
Biomedical research
Computational Biology - methods
Computational Biology - trends
Data base management
Data Interpretation, Statistical
Database Management Systems
Female
High-Throughput Nucleotide Sequencing - statistics & numerical data
Humans
Information management
Male
Ontology
Software
Translational Medical Research
Visualization
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Summary: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.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bbt055