Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.
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
Swertz
Morris A
MA
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
De Brock
E O
EO
Van Hijum
Sacha A F T
SA
De Jong
Anne
A
Buist
Girbe
G
Baerends
Richard J S
RJ
Kok
Jan
J
Kuipers
Oscar P
OP
Jansen
Ritsert C
RC
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