title: Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics.
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.
authors.forename: Irene
authors.initials: I
authors.lastname: Kouskoumvekaki
authors.forename: Nour
authors.initials: N
authors.lastname: Shublaq
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
mesh_terms: D064229:Biological Ontologies; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D003627:Data Interpretation, Statistical; D003628:Database Management Systems; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000706:statistics & numerical data; D006801:Humans; D008297:Male; D012984:Software; D057170:Translational Research, Biomedical
keywords: biological networks; biomedical ontologies; data integration; scientific workflows; translational bioinformatics