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MOLGENIS Advanced Application and Computation Framework for the Life Sciences

branch: testing

Merge pull request #470 from paraiko/master

merge back active changes in the fwn-production branch to the molgenis legacy branch
latest commit bae67e7c4f
RoanKanninga RoanKanninga authored
Octocat-spinner-32 .settings fixed bug, that was caused by wrong path April 09, 2013
Octocat-spinner-32 TestWorkflow small changes to pilot September 20, 2012
Octocat-spinner-32 WebContent Add support for Dymo labels in breeding plugin. December 20, 2013
Octocat-spinner-32 apps added remark option to genotype and edit litters on Vibeke's request. January 06, 2014
Octocat-spinner-32 doc doc reflects inputdir issue April 04, 2013
Octocat-spinner-32 modules enhancement: Added the option to also use panels as targets in the August 22, 2013
Octocat-spinner-32 publicdata Repacked the TAR without lock file, example data now readable under L… November 26, 2012
Octocat-spinner-32 test Fixed helloWorld test for compute4 to make the sun shine again in Hud… May 17, 2013
Octocat-spinner-32 .classpath.template.xml fix for missing 'molgenis' dependency in .classpath.template October 18, 2012
Octocat-spinner-32 .gitattributes changed gitattributes September 14, 2012
Octocat-spinner-32 .gitignore added new eclipse kepler .metadata folder to .gitignore August 19, 2013
Octocat-spinner-32 .pmd rename gcc project to more informative molgenis_apps March 27, 2011
Octocat-spinner-32 .project removed all jars in favor of using IVY to automatically download jars… September 07, 2012
Octocat-spinner-32 .project.template created working templates of the .settings files, ignore the real July 04, 2012
Octocat-spinner-32 README.md added description on how to build and run apps under (3) December 07, 2012
Octocat-spinner-32 build_animaldb.xml merge master March 07, 2013
Octocat-spinner-32 build_bbmri.xml removed load January 17, 2013
Octocat-spinner-32 build_bioshare.xml add _deprecated to path in order to make old code work January 15, 2013
Octocat-spinner-32 build_catalogue.xml give a name to project in the build scripts October 18, 2012
Octocat-spinner-32 build_cbm.xml improved the performance of harmonization February 12, 2013
Octocat-spinner-32 build_chado.xml give a name to project in the build scripts October 18, 2012
Octocat-spinner-32 build_chd7.xml give a name to project in the build scripts October 18, 2012
Octocat-spinner-32 build_col7a1.xml push upstream changes December 18, 2012
Octocat-spinner-32 build_common.xml update buildscript: change name of molgenis dirs to molgenis-legacy. March 11, 2013
Octocat-spinner-32 build_compute.xml Fixed compute4 helloWorld test and improved makedistro Ant task to ad… May 21, 2013
Octocat-spinner-32 build_designgg.xml push upstream changes December 18, 2012
Octocat-spinner-32 build_euratrans.xml give a name to project in the build scripts October 18, 2012
Octocat-spinner-32 build_examples.xml give a name to project in the build scripts October 18, 2012
Octocat-spinner-32 build_filemanager.xml give a name to project in the build scripts October 18, 2012
Octocat-spinner-32 build_gcc.xml give a name to project in the build scripts October 18, 2012
Octocat-spinner-32 build_gcc_jpa.xml give a name to project in the build scripts October 18, 2012
Octocat-spinner-32 build_gonl.xml add variant search service test January 22, 2013
Octocat-spinner-32 build_gonl_pheno.xml give a name to project in the build scripts October 18, 2012
Octocat-spinner-32 build_hemodb.xml give a name to project in the build scripts October 18, 2012
Octocat-spinner-32 build_ibdportal.xml give a name to project in the build scripts October 18, 2012
Octocat-spinner-32 build_knowledgecenter.xml give a name to project in the build scripts October 18, 2012
Octocat-spinner-32 build_lifelinesresearchportal.xml push upstream changes December 18, 2012
Octocat-spinner-32 build_myo5b.xml push upstream changes December 18, 2012
Octocat-spinner-32 build_ngs.xml give a name to project in the build scripts October 18, 2012
Octocat-spinner-32 build_old.xml [partial commit] creation of 'apps' folder; with one subfolder per ap… July 18, 2011
Octocat-spinner-32 build_omicsconnect.xml call xjc instead of xjc.exe December 04, 2012
Octocat-spinner-32 build_patho.xml fix patho app January 16, 2013
Octocat-spinner-32 build_pheno.xml give a name to project in the build scripts October 18, 2012
Octocat-spinner-32 build_phenoflow.xml add _deprecated module December 20, 2012
Octocat-spinner-32 build_plantqtl.xml Fixed plantqtl build by adding deprecated module January 14, 2013
Octocat-spinner-32 build_sandbox.xml give a name to project in the build scripts October 18, 2012
Octocat-spinner-32 build_scrum.xml give a name to project in the build scripts October 18, 2012
Octocat-spinner-32 build_wormqtl.xml Added homepage template for private wormqtl January 27, 2013
Octocat-spinner-32 build_xqtl.xml push upstream changes December 18, 2012
Octocat-spinner-32 build_xqtl_zip.xml Updated references to TJWS January 10, 2013
Octocat-spinner-32 c3p0.properties maybe it is needed, properties file for c3p0 November 21, 2012
Octocat-spinner-32 demo.txt further development July 05, 2012
Octocat-spinner-32 ivy.xml update selenium to 2.35 to fix compatibility with recent versions of October 08, 2013
Octocat-spinner-32 molgenis.test.properties Cleanup and refactor for removal of MolgenisServlet and rework of gen… September 17, 2012
Octocat-spinner-32 pom_animaldb.xml Removed warnings from CHD7 app & refactoring. October 02, 2012
Octocat-spinner-32 pom_gids.xml Added pom_gids.xml. September 26, 2012
Octocat-spinner-32 pom_lifelines.xml Merge branch 'testing' of https://github.com/molgenis/molgenis_apps July 27, 2012
Octocat-spinner-32 pom_omicsconnect.xml Added pom_omicsconnect.xml. September 26, 2012
Octocat-spinner-32 pom_patho.xml Added missing files / dependencies to patho. October 25, 2012
Octocat-spinner-32 pom_phenoflow.xml Added pom_phenoflow.xml. September 26, 2012
Octocat-spinner-32 pom_variant.xml Changed pom with respect to moving resources back to WebContent folder. November 07, 2012
Octocat-spinner-32 pom_xqtl.xml Removed warnings from CHD7 app & refactoring. October 02, 2012
Octocat-spinner-32 status.txt Try to fix git problems... March 05, 2013
README.md

MOLGENIS

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 https://www.github.com/molgenis/molgenis.git
 git clone https://www.github.com/molgenis/molgenis_distro.git
 cd molgenis_distro

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

 <editor> molgenis.properties
 <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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