Posts in category molgenis

MOLGENIS moved to github

We are delighted to report that all code of MOLGENIS is now in GitHub?. See For those not yet up to speed with github we prepared two tutorials: git commandline and git via Eclipse EGit plugin

PathoKB poster at HVP 2012

First public announcement of PathoKB as poster at the 4th Human Variome Project meeting, Paris. Download as pdf

Observ-OM data model published

Observ-OM and Observ-TAB, the Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information, is published in Human Mutation. Genetic and epidemiological research increasingly employs large collections of phenotypic and molecular observation data from high quality human and model organism samples. Standardization efforts have produced a few simple formats for exchange of these various data, but a lightweight and convenient data representation scheme for all data modalities does not exist, hindering successful data integration, such as assignment of mouse models to orphan diseases and phenotypic clustering for pathways. We report a unified system to integrate and compare observation data across experimental projects, disease databases, and clinical biobanks. The core object model (Observ-OM) comprises only four basic concepts to represent any kind of observation: Targets, Features, Protocols (and their Applications), and Values. An easy-to-use file format (Observ-TAB) employs Excel to represent individual and aggregate data in straightforward spreadsheets. The systems have been tested successfully on human biobank, genome-wide association studies, quantitative trait loci, model organism, and patient registry data using the MOLGENIS platform to quickly setup custom data portals. Our system will dramatically lower the barrier for future data sharing and facilitate integrated search across panels and species. All models, formats, documentation, and software are available for free and open source (LGPLv3) at

CHD7 mutation database published

We are proud with another MOLGENIS for the CHARGE syndrome using Observ-OM published in Human Mutation. CHD7 is a member of the chromodomain helicase DNA-binding (CHD) protein family that plays a role in transcription regulation by chromatin remodeling. Loss-of-function mutations in ICHD7 are known to cause CHARGE syndrome, an autosomal dominant malformation syndrome in which several organ systems, for example the central nervous system, eye, ear, nose and mediastinal organs, are variably involved. In this paper, we review all the currently described ICHD7 variants, including 184 new pathogenic mutations found by our laboratories. In total, we compiled 531 different pathogenic ICHD7 alterations from 515 previously published patients with CHARGE syndrome and 296 unpublished patients analyzed by our laboratories. The mutations are equally distributed along the coding region of ICHD7 and most are nonsense or frameshift mutations. Most mutations are unique, but we identified 96 recurrent mutations, predominantly arginine to stop codon mutations. We built a locus-specific database listing all the variants that is easily accessible at In addition, we summarize the latest data on CHD7 expression studies, animal models and functional studies, and we discuss the latest clinical insights into CHARGE syndrome.

xQTL workbench paper published

See QTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator.

Availability: xQTL workbench runs on all common platforms, including Linux, Mac OS X and Windows. An online demo system, installation guide, tutorials, software and source code are available under the LGPL3 license from

10,000 commits, and the winner is Miranda (AMC)

We are very proud to have had the 10,000 (ten thousand!) commit to the SVN. It has been really incredible how much activity we have seen in the molgenis area the last year with developers from UMCG, RUG, AMC, FIMM, EBI and U Leicester committing regularly!. Also the number of application is raising rapidly such as the mutation databases, compute, research portal, xQTL, NGS. We look forward to the next 10,000 commits :-)

Netherlands Genome project in New York Times

We were proud to read in the New York Times about the Netherlands Genome project. Even a photograph of our beloved colleage Freerk van Dijk is shown whilst carrying a huge amount of hard disk with terabytes of whole genome sequencing data. Read the full story at

GoNL ready for the next level

The BBMRI-NL Rainbow Project Genome of the Netherlands project (GoNL) is ready for the next level. It has completed the alignment of all the DNA reads of the 750 individuals, producing a total of 350 billion reads. Based on these data, further analyses can be performed, enabling the development of new treatments and diagnostic techniques.

The GoNL project offers unique opportunities for science as it gives a close-up look at the DNA of 750 Dutch people—250 trio’s of two parents and an adult child—plus a global genetic profile of large numbers of Dutch people. This information will disclose a wealth of new insights and possible applications.

A reusable analysis pipeline has been assembled based on best practices in the field. Processing 250 trios represents a major computational challenge which was solved with hard work from the BBMRI-NL Biobank Bioinformatics project (eBioank) and with assistance from NBIC, CIT, SARA, Target and BigGrid. Using the storage and computation resources at large infrastructures of Target/CIT and Sara/BigGrid, as well as from the participating institutes, the GoNL project has already produced more than 300 TB of data.

With the GoNL project BBMRI-NL expects to increase knowledge about the genetic variation in the Netherlands and complement international resources like the 1000 Genomes and HapMap Projects. The Genome of the Netherlands is an open national consortium of the UMCG, LUMC, Erasmus MC, VUMC, Hubrecht, AMC, RUNMC and UMCU led by Professor Cisca Wijmenga (GoNL) and Paul de Bakker & Morris Swertz (eBiobank). The sequencing work is done by BGI Hong Kong. More information about the project can be found on (GoNL) and (Bioinformatics)

Human metabolic pathway database online

Our collaborator Miranda Stobbe used MOLGENIS to publish a critical assessment of human metabolic pathway databases: a stepping stone for future integration. She compared the genes, EC numbers and reactions of five frequently used human metabolic pathway databases. The overlap is surprisingly low, especially on reaction level, where the databases agree on 3% of the 6968 reactions they have combined! Find the full story at BMC Bioinformatics and the data at

e-BioGrid project for biobanking started

We have proudly joined the e-BioGrid project on a mission to bring nation-wide IT infrastructure for large scale biobanking. First goal is building a model infrastructure for the Dutch Biobank community, BBMRI-NL, that manages resources for the future of biomedical research. See and elsewhere on this wiki.

New XML options: <field xref_cascade and <form hide_fields

We enhanced molgenis with two new features. On a field you can now set xref_cascade="true|false": this will enable cascading deletes which means that is the related element is deleted this entity will be deleted as well. And on form can you now hide fields from view using hide_fields="field1,field2": optional setting to hide fields from view. See and

MOLGENIS at BOSC and ISMB 2010, Boston July 9-13

You can see us at BOSC2010 SIG on Saturday July 10, 14.40 - 15.00 hours, speak to us at posters Q01, E19, E15, P05 on Sunday, July 11: 12.40 - 14.30 and see us at the ISMB technology track, Tuesday, July 13: 12.15 - 12.40.

Added RestApi and javascript to get rid of scrolling

In SVN is now a new MOLGENIS that generates a REST API so you can create AJAX type interactions'. It also contains new javascript that remembers the scroll position between page views so you don't have to scroll that much. Find the list of these services at http://localhost:8080/yourproject/api/rest/?_wadl

Because most browsers don't render JSON, I recommend to use to test your services.

Some people already having a molgenis_distro may have some troubles. If you don't want to check out the molgenis_distro from scratch you can check the following:

1. check web.xml

You need to replace your WebContent/WEB-INF/web.xml with an updated one. The changed two parts around the 'RestServlet?' Find it at

2. library export molgenis

Check if the molgenis project exports its libraries properly

  • right-click your molgenis project and choose properties
  • choose Java EE Module Dependencies
  • make sure that all boxes are selected

Note: this imports all libraries from molgenis to molgenis_distro

3. library import molgenis_distro

Check library references: In Eclipse:

  • right-click your molgenis_distro project and choose properties
  • choose Java Build Path.
  • choose Libraries tab

You should only see two libraries:

  • JRE Systems Library
  • Web App Libraries

All library references to molgenis/lib should be removed. Note that you may have library references you added yourself.

4. project references from molgenis_distro

Check project references from build path

  • right-click your molgenis_distro project and choose properties
  • choose Java Build Path.
  • choose Projects tab

Remove the molgenis project if selected

5. Java EE module depencencies molgenis_distro

Check the Java EE Module Dependencies

  • right-click your molgenis_distro project and choose properties
  • choose Java EE Module Dependencies
  • make sure that the 'molgenis' project is ticket

Note: you may see a long list of blue boxes that also link into MOLGENIS. That is a good thing.

Compact view.

Small enhancement: the ui model one can now say <form compact_view="field1,field2" to initially only show these fields when the form is in edit view. A button is provided to 'show additional fields'. When pushed all the other (hidden=false) fields are shown. This is particularly usefull if one has a large number of fields per entity.


MOLGENIS was at BOSC/DAM meeting and coffee-break demos at the NBIC booth. See BOSC 2009 schedule

Tutorial day at BioWISE

A MOLGENIS tutorial day at the BioWise? Information management course in Amsterdam. see

Release 3.2-testing

Added "AJAX" lookup lists to enable large data sets, alternative CSS styles, and support for many-to-many relationships on import/export using "a|b" in the csv files. All source included.

Release 3.0.3

added PostgreSQL support, generators for plug-ins, and a new type of plugin to customize add,update,delete events.