Brief Bioinform. 2014 Nov;15(6):942-52. doi: 10.1093/bib/bbt055. Epub 2013 Aug 1.
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.
随着生成的生物数据量和处理计算能力的增加，计算实验不再是生物信息学家的专利，而是正在向所有生物医学领域扩展。为了使生物信息学实现其转化潜力，领域专家需要能够访问用户友好的解决方案，以便在生物数据库中导航、集成和提取信息，以及在生物信息学工作流程中组合工具和数据资源。在这篇综述中，我们介绍了一些服务，这些服务可以帮助生物医学科学家将生物信息学工具整合到他们的研究中。我们回顾了 Cytoscape、BioGPS 和 DAVID 最近在数据可视化、集成和功能富集方面的应用。此外，我们还说明了如何使用 Taverna、Kepler、GenePattern 和 Galaxy 作为生物信息学工作流程的开放访问工作台。最后，我们提到了一些服务，这些服务可以促进计算工作流程中生物医学本体和生物信息学工具的集成。
