With so many ontocat papers published  NBIC has made a newsitem on OntoCAT! n annotating life sciences data, ontologies are quickly gaining importance. Several ontology access resources are available, but these are not always easy to use and the differences in content and mode of operation makes integration with research data difficult. OntoCAT, developed by a team of bioinformaticians at the European Bioinformatics Institute and NBIC faculty member Morris Swertz (University of Groningen) offers a user-friendly interface to query heterogeneous ontology resources. Read all at  http://www.nbic.nl/about-nbic/news-press/bioinformatics-news/detail/article/ontocat-easy-ontology-search/

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 :-)

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  http://www.nytimes.com/2011/12/01/business/dna-sequencing-caught-in-deluge-of-data.html

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  http://www.nlgenome.nl/ (GoNL) and  http://www.bbmriwiki.nl/ (Bioinformatics)

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 http://www.molgenis.org/humanpathwaydb.

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  http://www.bbmriwiki.nl and  http://www.nlgenome.nl elsewhere on this wiki.

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 http://www.molgenis.org/wiki/FormElement and http://www.molgenis.org/wiki/FieldElement.

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.

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  http://code.google.com/p/rest-client/ 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 http://www.molgenis.org/svn/molgenis_distro/3.3/WebContent/WEB-INF/web.xml

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.

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.

In the world of portal research MOLGENIS is known as a data portal for life scientists. Learn more portal technology and how MOLGENIS fits in at the International Workshop on Portals for Life Sciences, 14 - 15 September, e-Science Institute, Edinburgh.

Full story and MOLGENIS slides available at  http://www.nesc.ac.uk/esi/events/1000/

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

A MOLGENIS tutorial day at the BioWise? Information management course in Amsterdam. see  https://wiki.nbic.nl/index.php/BioWiseInformationManagement2009

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.

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