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= Welcome to MOLGENIS =

MOLGENIS is an collaborative open source project on a mission to generate great software infrastructure for life science research.

= Using the software =

MOLGENIS applications:

* [wiki:xQTL xQTL Workbench for multi-level QTL mapping]
* [http://www.deb-central.org deb-central mutation database] ([http://www.ncbi.nlm.nih.gov/pubmed/21681854 Human Mutation])
* [XgapStart eXtensible Genotype and Phenotype database (XGAP)]
* [http://gbic.biol.rug.nl/designGG  Design of Genetical Genomics Experiments (designGG)] ([http://www.biomedcentral.com/1471-2105/10/188 BMC Bioinformatics])
* [http://magetab-om.sourceforge.net/ MAGE-TAB microarray gene experiment object model (MAGETAB-OM)] ([http://wwwdev.ebi.ac.uk/microarray-srv/magetab demo])
* [wiki:PhenoFlow Pheno-OM Phenotype observation model] ([http://wwwdev.ebi.ac.uk/microarray-srv/pheno demo])
* [http://bioit.fleming.gr/mrb/ Mouse Resource Browser (MRB) project] ([http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911845 Bioinformatics])
* MOLGENIS as data wrapper in Taverna ([http://www.ncbi.nlm.nih.gov/pubmed/19112082 Briefings in Bioinformatics])
* [http://www.animaldb.org Animal observation database (AnimalDB)]
* [http://www.gen2phen.org/content/gwas-central-curation-tool-solving-bioinformatics-challenges-complex-data-management-molgeni GWAS Central curation tool]
* [http://www.schemalet.org/mediawiki/index.php/FINDIS:Database Finnish disease database (FINDIS)]
* Bacterial microarrays database (MOLGEN-IS) ([http://www.ncbi.nlm.nih.gov/pubmed/15059831 Bioinformatics])

If you think your project should be listed (differently) please [mailto:m.a.swertz@rug.nl let us know]      
= Developing your own 'MOLGENIS' =

Generate [wiki:MolgenisGuide generate your own] in three steps:

 1. Model what you want for your experiment in a simple XML file [http://www.molgenis.org/browser/molgenis_distro/trunk/molgenis_db.xml example db], [http://www.molgenis.org/browser/molgenis_distro/trunk/molgenis_ui.xml example ui]
 1. Run the MOLGENIS generator
 1. Use your web application [http://gbicserver1.biol.rug.nl:8080/demo example].

Each MOLGENIS comes with rich data management interface and plug-in integration of analysis tools in R, Java and web services.




= Getting involved =
[http://gbic.target.rug.nl/trac/molgenis/register Register] and then login to:

 * TracGuide -- Read on how to use this website, and how to add content
 * MolgenisProject -- Who is currently behind MOLGENIS
 * Apply for a MolgenisInternship
 * Add to the MolgenisGuide,
 * brainstorm new ideas on MolgenisEnhancements
 * or hack the MolgenisSourceCode.
 * SequencingWiki

= Partners =
|| [[Image(rug_logo_en.png, align=center, link=http://www.rug.nl/gbic University of Groningen)]] || [[Image(umcg_small.jpg, align=center, link=http://www.geneticsgroningen.nl)]] || [[Image(nbic.png, align=center, link=http://www.nbic.nl)]] ||
|| [[Image(ebi_logo_small.gif, align=center, link=http://www.ebi.ac.uk/fg)]] || [[Image(bbmri.gif, align=center, link=http://www.bbmri.nl] || [[Image{lifelines.gif, align=center, link=http://www.lifelines.nl LifeLines biobank)]] ||
|| [[Image(gen2phen.gif, align=center, link=http://www.gen2phen.org)]] || [[Image(panacea.gif, align=center, link=http://www.panaceaproject.eu)]] ||

The MOLGENIS project is supported by the University Medical Center Groningen [http://www.rug.nl/umcg/faculteit/disciplinegroepen/medischegenetica/research/index UMCG], Groningen Bioinformatics Center [http://www.rug.nl/gbic GBIC], European Bioinformatics Institute [http://www.ebi.ac.uk EBI] and the Netherlands Bioinformatics Center [http://www.nbic.nl NBIC]. Are you curious who is using MOLGENIS, or would like to list your own name, visit the MolgenisUsers page.  Also don't hesitate to add to the MolgenisSystemList