I previously wrote about the JavaScript Object Notation (JSON) which has become a de facto standard for sharing data by web services. I personally still prefer something using the Resource Description Framework (RDF) because of its clear link to ontologies, but perhaps JSON-LD combines the best of both worlds. The Open PHACTS API support various formats and this JSON is the default format used by the ops.js library.

I think the authors of the Open PHACTS proposal made a right choice in defining a small set of questions that the solution to be developed could be tested against. The questions being specific, it is much easier to understand the needs. In fact, I suspect it may even be a very useful form of requirement analysis, and makes it hard to keep using vague terms. Open PHACTS has come up with 20 questions (doi:10.1016/j.drudis.2013.05.008;

Yesterday, I received a letter from the Association of Universities The Netherlands (VSNU, @deVSNU) about Open Access. The Netherlands is for research a very interesting country: it’s small, meaning we have few resources to establish and maintain high profile centers, we also believe strong education benefits from distribution, so we we have many good universities, rather than a few excelling universities.

Elsevier is not the only publisher with a large innovation inertia. In fact, I think many large organizations do, particularly if there are too many interdependencies, causing too long lines. Greg Laundrum made me aware that one American Chemical Society journal is now going to encourage (not require) machine readable forms of chemical structures to be included in their flagship. The reasoning by Gilson et al. is balanced.

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. Because if done right, the publishers can even help forward science, despite crippling progress. That sound harsh, and surely they have done a lot of good for science. In fact, we would not be where we are now without the publishers.

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.

Continuing on the theory covered in this course, this part will talk about application programming interfaces (APIs) and web services. Application Programming Interfaces APIs define how programs can be used by other programs. An API defines how methods are called and what feedback you can expect. It basically is the combination of documentation and the program itself.

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.

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.

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. It’s very practice oriented: That should give them enough head start to work on something like this. The material will be more extensive, but I’ll give myself a head start, with some initial content.