The power of big numbers

Contributions to open data do not have to be large, as long as many people are doing it. The Wikipedia is a good example, and PubChem accepts contributions of small databases too (I think). The result can still be large and rather useful, even scientifically.

less than 1 minute read

Chemo::Blogs #2

Because no one picked up my Chemo::Blogs suggestion, I will now officially claim the blog series title. However, unlike the original Bio::Blogs series, I will not summarize interesting blogs, but just spam you with websites I recently marked as toblog on del.icio.us.

2 minute read

Code coverage: making sure your code is tested

Recently I discussed JUnit testing from within Eclipse , and blogged at several occasions about it in other situations. I cannot stress enough how useful unit testing is: it adds this extra set of eyeballs to make bugs shallow. And it does that, indeed.

1 minute read

German Conference on Chemoinformatics 2006: Day 3

Just some short quites note about the third day (see day 1 and 2 ). Today’s program of the German Conference on Chemoinformatics started with a presentation by Rzepa about his work on a semantic wiki (DOI:10.1021/ci060139e), which might be online here. (He recorded a podcast, but I have not seen it online yet.) I wish I could see the sources of those wiki pages, to see how that system integrates RDF, but at least Jmol is running fine. The presentation by Couch showed the status of the Materials Grid project, and how a guy called AgentX does all the hard work. Ihlenfeldt updated us about the status of PubChem, and mostly on what they had to do to keep the system from dying from its own success, for example using something called minimol. Googling does not seem to help, as that points to a number of things, but not any PubChem webpage. I am still waiting for a European organization to set up a mirror.

1 minute read

German Conference on Chemoinformatics 2006: Day 1 and 2

The 2nd German Conference on Chemoinformatics started yesterday, with two chemoinformatics tutorials: one on industrial chemoinformatics (I saw this presentation before… not sure when), with a good overview on integrating different information sources; the second one was about opensource chemoinformatics by Christoph Steinbeck (being involved in opensource chemoinformatics for almost 10 years now!), which included a Bioclipse demo (by me) and a demo by Thomas Kuhn on the CDK based chemoinformatics plugin to Taverna. Other opensource projects of the Blue Obelisk movement were mentioned and a few outside it too.

2 minute read

Organic chemists can now tune properties without changing the molecular structure??

Paul Bracher and Joshua Finkelstein pointed my attention to a nice discussion in Nature on the future of chemistry, in What Chemists Want to Know, by Philip Ball. Paul and Joshua already reviewed it thoroughly, but I could not resist commenting in it too. Having chosen chemistry as specialization when I went to university, and with a minor in supramolecular chemistry, this is a something I do relate to.

2 minute read

When is open source chemoinformatics successfull?

Open source chemoinformatics has become a common phenomenon, though many projects are small in nature: source code is developed by only few developers, or even in a closed manner and released when considered done. Within open source software there is room for distinguishing a subset of open development chemoinformatics, that is, Bazar-like, instead of Cathedral-like (see ESR famous writing).

1 minute read