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Title: The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button
Authors: Swertz, Morris A.
Dijkstra, Martijn
Adamusiak, Tomasz
van der Velde, Joeri K.
Kanterakis, Alexandros
Roos, Erik T.
Lops, Joris
Thorisson, Gudmundur A.
Arends, Danny
Byelas, George
Muilu, Juha
Brookes, Anthony J.
de Brock, Engbert O.
Jansen, Ritsert C.
Parkinson, Helen
First Published: 21-Dec-2010
Publisher: BioMed Central Ltd
Citation: BMC Bioinformatics 2010, 11(Suppl 12):S12
Abstract: Background: 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. Methods: 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. Results: 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. Conclusions: 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
DOI Link: 10.1186/1471-2105-11-S12-S12
eISSN: 1471-2105
Version: Publisher Version
Status: Peer-reviewed
Type: Published Article
Rights: Copyright © 2010 Swertz et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Description: 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:
Appears in Collections:Published Articles, Dept. of Genetics

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