Using the Grails Object Relational Model tends to work quite well when using conventional, structured data. At that point the type of database you are using, relational or otherwise, doesn't really matter. GORM's dynamic finders [1] are a pleasure[…]

In one of our projects we had reason to combine a Grails-based web application with non-web applications. We were using SpringSource's MongoDB GORM plugin [1] for our Grails-based application. We also had applications that operated on the same[…]

Great news for translational research: Johnson & Johnson recently open sourced their translational medicine datawarehouse, called tranSMART. A paper on tranSMART was published in 2010, and just a few days ago a first version of the source code was[…]

So what does open source mean, really? I would like to skip the legal part and review the community side in this post. What defines and makes a succesful open source project? Why have projects such as Linux, Firefox, Apache, MySQL, Postgres, Plone[…]

When I explain to people what The Hyve does, I try to observe their reactions. This is fun, but it also tells me a lot about how they feel about our business model, which is important feedback to me. Often they smile and nod, until I get to the[…]

What is the major bottleneck in your bioinformatics research when it comes to data and software? I asked this a number of bioinformatics researchers from pharma and food industry at the ISMB conference. It's a very general question, but it never[…]

Battling standardization in metabolomics BETHESDA, MD – Imagine a snow-covered Washington DC, just before Christmas. That was the scene where metabolomics researchers from around the world headed on December 15, 2010. They gathered at the National[…]

Today I want to check out LabKey, an open source software suite which claims to be ‘the best way to manage your biomedical research data’. Its website looks promising, and so does their list of participants and funding parties. When it comes to open[…]

For about a year now, I am technical project manager of the Nutrional Phenotype Database (dbNP)project, which was initiated by The European Nutrigenomics Organisation (NuGO). Nutrigenomics is what I would call ‘applied bioinformatics’. It is[…]