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MOLGENIS Advanced Application and Computation Framework for the Life Sciences

branch: testing


MOLGENIS is an collaborative open source project on a mission to generate great software infrastructure for life science research. Each app in the MOLGENIS family comes with rich data management interface and plug-in integration of analysis tools in R, Java and web services.

Developing your own

Generate your own in three steps:

1) Clone the MOLGENIS generator and an empty distro:

 git clone
 git clone
 cd molgenis_distro

2) Model what you want for your experiment in a simple XML file example db, example ui:

 <editor> molgenis_db.xml
 <editor> molgenis_ui.xml

3) Run the MOLGENIS generator, after that you're able to use your web application. This depends per app, but in general:

 ant -f build_[APP].xml clean-generate-compile-test
 ant -f build_[APP].xml run

MOLGENIS applications

Many molgenis applications have been developed, a not so short overview:

  • xQTL Workbench for multi-level QTL mapping (project)
  • Dystrophic Epidermolysis Bullosa (deb-central) mutation database (project, publication)
  • eXtensible Genotype and Phenotype database (XGAP) (project, publication)
  • Design of Genetical Genomics Experiments (designGG)] (project, publication)
  • BBMRI-NL biobank catalague (project)
  • MAGE-TAB microarray gene experiment object model (MAGETAB-OM)] (project, demo)
  • Pheno-OM Phenotype observation model (project, demo)
  • Mouse Resource Browser (MRB) project] (project, publication)
  • MOLGENIS as data wrapper in Taverna (publication)
  • Animal observation database (AnimalDB) (project)
  • Nordic GWAS control database (project, publication)
  • GWAS Central curation tool (project)
  • Finnish disease database (FINDIS) (project)
  • Bacterial microarrays database (MOLGEN-IS) (publication)
  • Human Metabolic Pathway Database (project, publication)

If you think your project should be listed (differently) please let us know.

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