The latest news from The Hyve on Open Source solutions for bioinformatics

Set up a tranSMART Postgres development environment

March 26, 2013 | By Kees van Bochove 2
Earlier, I blogged about how to set up a tranSMARTdevelopment environment - this was the GPL 1.0 release which has Oracle as a prerequisite. Nowadays, we have a version that runs on Postgres - it still has some problems, but it is promoted as the[…]
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Set up a tranSMART development environment

September 27, 2012 | By Kees van Bochove 0
In an earlier post, I shared my experiences with installing tranSMART on Amazon, but there are now AMI's availabe for the tranSMART 1.0 GA version, which makes that post obsolete. However, I like to be able to code on the road when I have to travel,[…]
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Phenotype Database installation guide, GSCF

August 21, 2012 | By Taco Steemers 0
This post will assist you with installing (parts of) the Phenotype Database project [1] . We will be using a CentOS installation [2] . CentOS uses the source code from the commercial Red Hat Enterprise Linux project [3] . Currently the project's[…]
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Combining Grails with less-structured data: GORM or no GORM?

August 16, 2012 | By Taco Steemers 0
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[…]
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Using the same MongoDB database with Grails and non-Grails applications

August 08, 2012 | By Taco Steemers 0
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[…]
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How to run the tranSMART open source package for translational research on Amazon AWS

February 25, 2012 | By Kees van Bochove 0
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[…]
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Why open source? (2)

October 13, 2011 | By Kees van Bochove 0
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[…]
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Why open source? (1)

August 12, 2011 | By Kees van Bochove 0
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[…]
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A business case for semantic data integration in Bioinformatics

August 02, 2011 | By Kees van Bochove 0
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[…]
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From compound spectra to online games

December 16, 2010 | By Kees van Bochove 0
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[…]
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