Tag Archives: research

Interactive toxicogenomics

If you work in toxicology or drug discovery, you might be familiar with the database Open TG-GATEs, a large transcriptomics database that catalogues gene expression response to well-known drugs and toxins. This database was developed by Japan’s Toxicogenomics Project during many years, as a private-public sector partnership, and remains a very valuable resource. As with […]

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The following is an excerpt from a text I am currently in the process of writing, which may or may not be published in this form.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

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 […]

My Ph.D. Thesis: “Extending the Java Programming Language for Evolvable Component Integration”

After three very hectic first months of 2012, the final version of my Ph.D. thesis has been submitted and I’ve gone through the graduation ceremonies. From the 1st of April I will be a postdoctoral associate in bioinformatics at the National Institute of Biomedical Innovation in Osaka, Japan. I will comment further on my Ph.D. […]

Pointers in programming languages

It is likely that few features cause as much problems as pointers and references in statement-oriented languages, such as C, C++ and Java. They are powerful, yes, and they allow us to control quite precisely how a program is to represent something. We can use them to conveniently compose objects and data without the redundancy […]