Open Data getting more recognition

The OD part of ODOSOS is getting more and more attention, and it seems that Peter’s Open Data battle is paying off (see his original OpenData article in Wikipedia): an open data specific license has reached the beta stage (see this announcement). 1 minute read

I don't blame Individuals in Commercial Chemoinformatics

The comment I left in the ChemSpider blog, was probably a bit blunt. ChemSpider announced having licensed software from OpenEye. I have seen such announcements more often, but am intrigued about the nature of such announcements. Is it bad that ChemSpider is using OpenEye software? Certainly not. But it is surprising that they “announced today they had entered into an agreement that will allow the incorporation of a number of OpenEye’s products into ChemZoo’s online chemistry database and property prediction service, ChemSpider” (emphasis mine). 4 minute read

Tagging, thesauri or ontologies?

Controlled vocabularies, hierarchies, microformats, RDF. Nico Adams pointed me to this excellent video: 2 minute read

Open Source, Open Data at the European Bioinformatics Institute

I was pleased to hear that Christoph will move to the EBI early next year. Christoph has been working on Open Source and Open Data chemoinformatics since at least 1997. I first got in contact with Christoph when I wrote code for JChemPaint (which Christoph developed) to be able to read Chemical Markup Languages (CML). This also got me into contact with Dan Gezelter who is the original author of Jmol, to which I also added CML support. And, of course, with Henry and Peter, who first developed CML. This was before XML was an official recommendation, and I have worked with CML files which you would no longer recognize. It was in Dan’s office that the CDK was founded, where Christoph, Dan and I designed data classes to replace the JChemPaint and Jmol data classes. Both JChemPaint and Jmol were rewritten afterwards, but for Jmol it was later decided that more tuned classes were needed to achieve to required performance for the live rendering of tens of thousands of atoms. 1 minute read

My Open Laboratory 2007 submissions

As promised , here is my list of submission for the Open Laboratory 2007: less than 1 minute read

Web2O, Open Chemistry, and Chemblaics

Chemistry World December issue features a nice item on the future of data in chemistry: Surfing Web2O; Peter gave an excerpt, and Peter commented on it . less than 1 minute read

Be in my Advisory Board #1: being a good Open Science citizen

I recently saw that blogger.com blogs gained a poll feature. From now on, I will try to be a bit more Open Science, in addition to Open Source. From now on, you can be in my Advisory Board. To do so, vote on my next chemblaics (aka Open Source Chemoinformatics) project. The poll can be found on the left side of this blog. Associated which each poll, which I may run more or less frequently depending on the time of year, will be one blog post where I introduce the options. Options not mentioned, or completely different things, you would like to suggest me to do, can be left as comments to these items. 1 minute read