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Bioinformatics. 2004 Sep 1;20(13):2075-83. Epub 2004 Apr 1.

Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.

Author information

  • 1Groningen Bioinformatics Center, Faculty of Medical Sciences and Faculty of Mathematics and Natural Sciences, University of Groningen, Groningen, The Netherlands. m.a.swertz@cs.rug.nl

Abstract

MOTIVATION:

Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of appropriate criteria makes any decision on buying or developing a system difficult. Here, we report on the decision process for the case of a molecular genetics group establishing a microarray laboratory.

RESULTS:

Five typical requirements for experimental genomics database systems were identified: (i) evolution ability to keep up with the fast developing genomics field; (ii) a suitable data model to deal with local diversity; (iii) suitable storage of data files in the system; (iv) easy exchange with other software; and (v) low maintenance costs. The computer scientists and the researchers of the local microarray laboratory considered alternative solutions for these five requirements and chose the following options: (i) use of automatic code generation; (ii) a customized data model based on standards; (iii) storage of datasets as black boxes instead of decomposing them in database tables; (iv) loosely linking to other programs for improved flexibility; and (v) a low-maintenance web-based user interface. Our team evaluated existing microarray databases and then decided to build a new system, Molecular Genetics Information System (MOLGENIS), implemented using code generation in a period of three months. This case can provide valuable insights and lessons to both software developers and a user community embarking on large-scale genomic projects.

AVAILABILITY:

http://www.molgenis.nl

PMID:
15059831
[PubMed - indexed for MEDLINE]
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