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The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button

By 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 and Helen Parkinson


This is the published article. It is reproduced here under the Creative Commons Attribution License. The article is also freely available from the publisher's website at:\ud There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed.\ud \ud Methods:\ud The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS’ generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This ‘model-driven’ method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software.\ud \ud Results:\ud In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist’s satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the ‘ExtractModel’ procedure.\ud \ud Conclusions:\ud The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at http://www.molgenis.orgPeer-reviewedPublisher Versio

Publisher: BioMed Central Ltd
Year: 2010
DOI identifier: 10.1186/1471-2105-11-S12-S12
OAI identifier:

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  9. (1998). Little languages, little maintenance? doi
  10. (1986). Little languages. doi
  11. (2007). Micklem G: FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biol doi
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  13. (2008). NW: Data capture in bioinformatics: requirements and experiences with Pedro. doi
  14. Omixed: customisable storage system for scientific data.
  15. OntoCAT: ontology common API (application programming interface) toolkit. doi
  16. Open Bioinformatics Foundation doi
  17. (2002). Patterns of Enterprise Application Architecture.
  18. Rails: open source web framework in the Ruby language. doi
  19. (2007). RC: Beyond standardization: dynamic software infrastructures for systems biology. Nat Rev Genet doi
  20. (2009). RC: designGG: an Rpackage and web tool for the optimal design of genetical genomics experiments. doi
  21. (2004). RC: Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases. Bioinformatics doi
  22. (2010). RC: XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. Genome Biol doi
  23. (2010). Ripatti S: NordicDB: a Nordic pool and portal for genome-wide control data. doi
  24. (1981). Software construction using components. Irvine: PhD Thesis,
  25. (2004). Software Factories: Assembling Applications with Patterns, Models, Frameworks, and Tools. doi
  26. (2008). Solutions for data integration in functional genomics: a critical assessment and case study. Brief Bioinform doi
  27. (2004). Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics doi
  28. (2010). The full contents of the supplement are available online at Author details 1Genomics Coordination Center, Groningen Bioinformatics Center,
  29. (1995). The Mythical Man Month: doi
  30. (1999). Thomas D: The pragmatic programmer: from Journeyman to Master. doi
  31. (2008). Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges. Nat Rev Genet doi

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