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Category Archives: Bioinformatics

Equipmental visibility and barriers to understanding

The following is an excerpt from a text I am currently in the process of writing, which may or may not be published in this form. The text is concerned with the role of software in the scientific research process, and what happens when researchers must interact with software instead of hardware equipment, and finally […]

Posted 12 July 2013 † johan § Computer science § Philosophy § Software development ‡ Comments (0) ° Tagged: , , ,

Is our ability to detect fractals underdeveloped?

Fractals appear in many places in biology and ecology, in society, in man-made artefacts. Yet the concept itself is quite new. Fractal phenomena existed for a long time before Benoit Mandelbrot formally investigated them as such. Amazingly, the Greeks, who did so much, do not seem to have had the notion of a fractal. In […]

Posted 08 March 2013 † johan § Philosophy ‡ Comments (0) ° Tagged: , ,

The limitations and fundamental nature of systems are not understood

Recently, I’ve become more and more aware of the limitations of conscious thought and formal models of entities and systems. We don’t understand how political systems make decisions, how world events occur, or even how we choose what to wear on any particular day. Cause and effect doesn’t exist in the form it is commonly […]

Posted 22 December 2012 † johan § Computer science § Philosophy § Software development ‡ Comments (0) ° Tagged: , , , ,

The “Friedrich principles” for bioinformatics software

I’ve just come back from Biohackathon 2012 in Toyama, an annual event, traditionally hosted in Japan, where users of semantic web technologies (such as RDF and SPARQL) in biology and bioinformatics come together to work on projects. This was a nice event with an open and productive atmosphere, and I got a lot out of […]

Posted 13 September 2012 † johan § Computer science § Software development ‡ Comments (0) ° Tagged: , , , , , , ,

Entering into bioinformatics

As of now, I have been working with bioinformatics in the Mizuguchi lab at NIBIO, Osaka, for about two weeks. The lab environment is stimulating and I feel quite fortunate to be here. It is interesting to compare computer science and bioinformatics with just the hindsight of this short period. In computer science and electronics, […]

Posted 14 April 2012 † johan § Life ‡ Comments (0) ° Tagged: , , ,