Category Archives: Software development

Small Tools for Bioinformatics

Pjotr Prins has published a Small Tools Manifesto for Bioinformatics, which is well worth a read for anyone who develops bioinformatics software. In essence it’s about increased adoption of the Unix design philosophy. I fully support the manifesto, which in many ways is reminiscent of the ideas that me and Gabriel Keeble-Gagnere presented in our […]

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The following is an excerpt from a text I am currently in the process of writing, which may or may not be published in this form.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 […]

Piety, self-examination and the purification of software

This writer is not a believer in Christianity. However, I am interested in trying to understand the history of and heritage from Christianity, as it is a major component of Western culture. Of particular interest to me is the heritage from protestantism, which also happens to be the official religion of Sweden, the society that […]

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 […]

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 […]