MOLGENIS Research : Advanced bioinformatics data software for non-bioinformaticians

作者: K Joeri van der Velde , Floris Imhann , Bart Charbon , Chao Pang , David van Enckevort

DOI: 10.1093/BIOINFORMATICS/BTY742

关键词: SoftwareSource codeBioinformaticsGenomeProcess (engineering)Container (abstract data type)Biological dataOmicsGenomicsComputer scienceVolume (computing)

摘要: Motivation The volume and complexity of biological data increases rapidly. Many clinical professionals biomedical researchers without a bioinformatics background are generating big '-omics' data, but do not always have the tools to manage, process or publicly share these data. Results Here we present MOLGENIS Research, an open-source web-application collect, analyze, visualize large complex datasets, need for advanced skills. Availability implementation Research is freely available (open source software). It can be installed from code (see http://github.com/molgenis), downloaded as precompiled WAR file (for your own server), setup inside Docker container http://molgenis.github.io), requested Software-as-a-Service subscription. For public demo instance complete installation instructions see http://molgenis.org/research.

参考文章(19)
H.V. Jagadish, Big Data and Science: Myths and Reality ✩ Big Data Research. ,vol. 2, pp. 49- 52 ,(2015) , 10.1016/J.BDR.2015.01.005
Sarah Bowdin, Peter N. Ray, Ronald D. Cohn, M. Stephen Meyn, The Genome Clinic: A Multidisciplinary Approach to Assessing the Opportunities and Challenges of Integrating Genomic Analysis into Clinical Care Human Mutation. ,vol. 35, pp. 513- 519 ,(2014) , 10.1002/HUMU.22536
Roger Higdon, Rachel K. Earl, Larissa Stanberry, Caitlin M. Hudac, Elizabeth Montague, Elizabeth Stewart, Imre Janko, John Choiniere, William Broomall, Natali Kolker, Raphael A. Bernier, Eugene Kolker, The promise of multi-omics and clinical data integration to identify and target personalized healthcare approaches in autism spectrum disorders. Omics A Journal of Integrative Biology. ,vol. 19, pp. 197- 208 ,(2015) , 10.1089/OMI.2015.0020
Geoffrey Ginsburg, Medical genomics: Gather and use genetic data in health care. Nature. ,vol. 508, pp. 451- 453 ,(2014) , 10.1038/508451A
Tomasz Adamusiak, Helen Parkinson, Juha Muilu, Erik Roos, Kasper Joeri van der Velde, Gudmundur A. Thorisson, Myles Byrne, Chao Pang, Sirisha Gollapudi, Vincent Ferretti, Hans Hillege, Anthony J. Brookes, Morris A. Swertz, Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information. web science. ,vol. 33, pp. 867- 873 ,(2012) , 10.1002/HUMU.22070
T. A. Down, M. Piipari, T. J. P. Hubbard, Dalliance: interactive genome viewing on the web Bioinformatics. ,vol. 27, pp. 889- 890 ,(2011) , 10.1093/BIOINFORMATICS/BTR020
Morris A Swertz, Martijn Dijkstra, Tomasz Adamusiak, Joeri K van der Velde, Alexandros Kanterakis, Erik T Roos, Joris Lops, Gudmundur A Thorisson, Danny Arends, George Byelas, Juha Muilu, Anthony J Brookes, Engbert O de Brock, Ritsert C Jansen, Helen Parkinson, The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button BMC Bioinformatics. ,vol. 11, pp. 1- 9 ,(2010) , 10.1186/1471-2105-11-S12-S12
Wullianallur Raghupathi, Viju Raghupathi, Big data analytics in healthcare: promise and potential health information science. ,vol. 2, pp. 3- 3 ,(2014) , 10.1186/2047-2501-2-3
Chao Pang, Dennis Hendriksen, Martijn Dijkstra, K Joeri van der Velde, Joel Kuiper, Hans L Hillege, Morris A Swertz, BiobankConnect : software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing Journal of the American Medical Informatics Association. ,vol. 22, pp. 65- 75 ,(2015) , 10.1136/AMIAJNL-2013-002577
Morris A Swertz, K Joeri Velde, Bruno M Tesson, Richard A Scheltema, Danny Arends, Gonzalo Vera, Rudi Alberts, Martijn Dijkstra, Paul Schofield, Klaus Schughart, John M Hancock, Damian Smedley, Katy Wolstencroft, Carole Goble, Engbert O de Brock, Andrew R Jones, Helen E Parkinson, Ritsert C Jansen, , , XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments Genome Biology. ,vol. 11, pp. 27- ,(2010) , 10.1186/GB-2010-11-3-R27