Elsevier’s new ideas on text mining are getting a lot attention now. Sadly, they get it wrong, again. On the bright side, all other publishers, which are expected to follow this year, can learn from this mistake.

I got a one more source code zip file from the Maastricht Science Programme students (see also the first two screenshots). Vincent and Błażej extended the d3.js tree view, showing classification information from ChEBI (they also submitted three patches to the Open PHACTS ops.js):

Yesterday was the last Programming in the Life Sciences practical day, and the 2nd and 3rd year B.Sc. MSC students presented their results yesterday afternoon. I am impressed with the results that they reached in only six practical days. I have suggested them to upload the presentations to SlideShare or FigShare (with the advantage that you get a DOI), and asked them to send them their tools. Below are some screenshots.

I am happy that I got my first research grant awarded (EU FP7), which should start after all the contracts are signed, etc, somewhere early 2014. The project is about setting up data needs for the analysis of nanosafety studies. And for this, I have the below two position vacancies available now.

HTML (HyperText Markup Language), the language of the web, is no longer the only language of the web. But it still is the primary language in which source code of webpages is shared. Originally, HTML pages were always static: the only HTML source of a web page was that was downloaded from a website. Nowadays, much HTML the is visualized in your web browser, is generated on the fly with JavaScript.

As said, JSON is the format we will use as serialization format for answers given by the Open PHACTS LDA. The API actually supports XML, RDF, HTML, and TSV too, but I think JSON is a good balance between expressiveness and compactness.

Continuing on the theory covered in this course, this part will talk about application programming interfaces (APIs) and web services.

Never underestimate the power of lack of coding standards in code obfuscation. Just try randomly to read code you wrote a year ago or four years ago. You’ll be surprised with what you find. Coding standards are like the grammar in writing: they ensure that our message gets understood.

No course, with some good theory. In this six-day course, I plan to cover this computing theory.

One key feature of programming languages is the following: first, there is linearity. This is an important point that is not always clear to students who just start to program. In fact, ask yourself what the algorithm is for counting the chairs in the room where you are now sitting. Could a computer do that in the same way? How should your algorithm change? A key point is, is that the program is run step by step, in a linear way.

Now that we have the communication working with the Open PHACTS LDA, it is time to make a nice GUI.