title: Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  http://www.molgenis.nl
authors.affiliation: Groningen 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
authors.forename: Morris A
authors.initials: MA
authors.lastname: Swertz
authors.forename: E O
authors.initials: EO
authors.lastname: De Brock
authors.forename: Sacha A F T
authors.initials: SA
authors.lastname: Van Hijum
authors.forename: Anne
authors.initials: A
authors.lastname: De Jong
authors.forename: Girbe
authors.initials: G
authors.lastname: Buist
authors.forename: Richard J S
authors.initials: RJ
authors.lastname: Baerends
authors.forename: Jan
authors.initials: J
authors.lastname: Kok
authors.forename: Oscar P
authors.initials: OP
authors.lastname: Kuipers
authors.forename: Ritsert C
authors.initials: RC
authors.lastname: Jansen
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D030541:Databases, Genetic; D003661:Decision Support Techniques; D023281:Genomics / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods; D008967:Molecular Biology / Q000379:methods*; D020380:Needs Assessment; D012107:Research Design; D013673:Technology Assessment, Biomedical; D014584:User-Computer Interface