Programming in the Life Sciences #19: debugging

Debugging is the process find removing a fault in your code (the etymology goes further back than the moth story, I learned today). Being able to debug is an essential programming skill, and being able to program flawlessly is not enough; the bug can be outside your own code. (… there is much that can be written up about module interactions, APIs, documentation, etc, that lead to malfunctioning code …) 4 minute read

Programming in the Life Sciences #17: The Open PHACTS scientific questions

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. 3 minute read

On Open Access in The Netherlands

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. Mind you, this clouds that we absolutely do have excelling research institutes and research groups; they just are not concentrated in one university. 7 minute read

Slow publishing innovation: SMILES in ACS journals

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. It is also 15 years too late. This question was relevant at the end of the last century. The technologies were already more advanced than what will now be adopted. 15 years!!! Seriously, that’s close to the time it takes to bring a new drug on the market! 2 minute read

Elsevier's new text mining initiative is a step sideways

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. 7 minute read

Looking for a PhD and a Postdoc to work on Open Science Nanosafety

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. If you are keen on doing Open Science (CDK, Bioclipse, OpenTox, WikiPathways, …, …), working within the European NanoSafety Cluster, and have an affinity with understanding the systems biology of nanomaterials, then you may be interested in applying. less than 1 minute read

Programming in the Life Sciences #9: APIs and Web Services

Continuing on the theory covered in this course, this part will talk about application programming interfaces (APIs) and web services. 2 minute read