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Enlighten Your Research Global Award: Virtual Machine Images for Life Science Research

Denver (USA) 18 November 2013 – One of the four prestigious "Enlighten Your Research Global" has been awarded to an idea developed by an ELIXIR working group for the sharing of virtual machines over research and education networks.

  • Posted: 2015-04-03 15:06 (Updated: 2015-04-03 15:07)
  • Author: george
  • Categories: MCF
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MOLGENIS/compute at IWSG-2013

MOLGENIS/compute was presented at 5th International Workshop on Science Gateways, IWSG 2013, Zurich, Switzerland

Visual Analytics for Bio-Workflows at NBIC-2013

Towards visual analytics of bio-workflows presentation was given at the NBIC-2013 conference, Lunteren, Netherlands

  • Posted: 2013-06-04 10:01 (Updated: 2013-06-04 10:05)
  • Author: george
  • Categories: MCF
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Visual Analytics for Bio-Workflows at BIOINFORMATICS-2013

"Visualization of bioinformatics workflows for ease of understanding and design activities" paper will be presented at the BIOSTEC-BIOINFORMATICS-2013 conference, on February 11th, 2013, Bercelona, Spain. Download paper

  • Posted: 2013-01-31 10:57 (Updated: 2013-01-31 10:59)
  • Author: george
  • Categories: MCF
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MOLGENIS/compute workshop at BioAssist meeting

MOLGENIS/compute workshop took place at the NBIC Bio Assist meeting, in Utrect, Oct.12, 2012

  • Posted: 2012-11-22 13:41 (Updated: 2012-11-22 13:42)
  • Author: george
  • Categories: MCF
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MOLGENIS/compute at IWSG-Life 2012

MOLGENIS/compute demo was given at the 4th International Workshop on Science Gateways for Life Sciences, May 23-25 2012, Amsterdam, Netherlands

MOLGENIS/compute at NBIC-2012

MOLGENIS/compute demo was given at the NBIC-2012 conference in Lunteren, Netherlands, Apr.23, 2012

MOLGENIS/compute at BIOINFORMATICS-2012

MOLGENIS/compute was accepted as a full paper and presented at the International Conference on Bioinformatics Models, Methods and Algorithms, Algarve, Portugal, Feb.3 2012. (BIOINFORMATICS 2012 received 109 submissions, of which 14% were accepted as full papers) Download paper

  • Posted: 2012-11-22 13:17 (Updated: 2013-01-31 10:50)
  • Author: george
  • Categories: MCF
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MOLGENIS moved to github

We are delighted to report that all code of MOLGENIS is now in GitHub?. See http://www.github.com/molgenis. 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 http://www.observ-om.org.

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 www.CHD7.org. 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 http://bioinformatics.oxfordjournals.org/content/28/7/1042. 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 http://www.xqtl.org.

GenomeNL variation database

The first version of the GenomeNL database is online. Now researchers can already sneak peak the GoNL variant data to verify whether variants observed in their own sample are unique against 25 million SNPs observed in the panel of 500 parents. By April we expect this set to be updated with a high quality SNP set based on the full panel of 770 individuals (and their genotype frequencies) while the unique trio structure to filter false positives. Also we will include a collection of structural variations. The database will be enriched with an optimized search interface and reference annotations on each variant to disclose a wealth of new information, new insights, and possible applications the development of new treatments and diagnostic techniques. See http://application32.target.rug.nl/gonl

OntoCAT easy ontology search

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/

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

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 http://www.nlgenome.nl/ (GoNL) and http://www.bbmriwiki.nl/ (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 http://www.molgenis.org/humanpathwaydb.

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