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      Translational Biomedical Informatics in the Cloud: Present and Future

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          Abstract

          Next generation sequencing and other high-throughput experimental techniques of recent decades have driven the exponential growth in publicly available molecular and clinical data. This information explosion has prepared the ground for the development of translational bioinformatics. The scale and dimensionality of data, however, pose obvious challenges in data mining, storage, and integration. In this paper we demonstrated the utility and promise of cloud computing for tackling the big data problems. We also outline our vision that cloud computing could be an enabling tool to facilitate translational bioinformatics research.

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          Most cited references74

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          Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.

          DAVID bioinformatics resources consists of an integrated biological knowledgebase and analytic tools aimed at systematically extracting biological meaning from large gene/protein lists. This protocol explains how to use DAVID, a high-throughput and integrated data-mining environment, to analyze gene lists derived from high-throughput genomic experiments. The procedure first requires uploading a gene list containing any number of common gene identifiers followed by analysis using one or more text and pathway-mining tools such as gene functional classification, functional annotation chart or clustering and functional annotation table. By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.
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            Ensembl 2012

            The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human genome data as well as data for key model organisms such as mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) and Tasmanian devil (Sarcophilus harrisii) bringing the total number of supported species to 61 as of Ensembl release 64 (September 2011). Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.ensembl.org) with preliminary support. The past year has also seen improvements across the project.
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              Computational analysis of microarray data.

              Microarray experiments are providing unprecedented quantities of genome-wide data on gene-expression patterns. Although this technique has been enthusiastically developed and applied in many biological contexts, the management and analysis of the millions of data points that result from these experiments has received less attention. Sophisticated computational tools are available, but the methods that are used to analyse the data can have a profound influence on the interpretation of the results. A basic understanding of these computational tools is therefore required for optimal experimental design and meaningful data analysis.
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                Author and article information

                Journal
                Biomed Res Int
                Biomed Res Int
                BMRI
                BioMed Research International
                Hindawi Publishing Corporation
                2314-6133
                2314-6141
                2013
                17 March 2013
                : 2013
                : 658925
                Affiliations
                1Center for Systems Biology, Soochow University, Suzhou 215006, China
                2School of Chemistry and Biological Engineering, Suzhou University of Science and Technology, Suzhou 215011, China
                Author notes

                Academic Editor: Ming Ouyang

                Article
                10.1155/2013/658925
                3613081
                23586054
                4a9cc141-7263-4b10-8b82-9f5da23953a2
                Copyright © 2013 Jiajia Chen et al.

                This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 8 December 2012
                : 17 February 2013
                Categories
                Review Article

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