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.

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.

Chemistry in Second Life. DOI:10.1186/1752-153X-3-14 There are nowadays a lot of people talking about Open, about open access, open data, open source. In fact, some discussion on Twitter resulted in the realization that it is highly unlikely that any scholar has not taken advantage of Open in some way in their research in the last few years. However, this is mostly due to people whom actually do, not by those who talk about it or use it.

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.

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.