Mar
30
Reporting missing atom types...
About a month ago, I blogged about how to report new atom types the CDK has no knowledge about yet.
Mar
28
Google Summer of Code 2011: some cool ideas
The Google Summer of Code is a now yearly event where university students (including PhD students) can work on open source project, and get payed fairly well (mentors only get a T-shirt :). A few years ago I was mentor for the KDE project, supervising work on Strigi-Chemistry. Various open source science projects participate again this year (no, no chemistry projects, I'm afraid), but a few come close.
Mar
28
CDK 1.2.8: the changes, the authors, and the reviewers
CDK 1.2.8 is one more bug fix release in the 1.2 series.
The changes
The changes include another few new atom types and fixes of recognition of earlier defined atom types, further widening the scope of chemistry recognized by the 1.2 series. It also has a few other minor fixes, as listed below.
The changes
The changes include another few new atom types and fixes of recognition of earlier defined atom types, further widening the scope of chemistry recognized by the 1.2 series. It also has a few other minor fixes, as listed below.
Mar
24
Supplementary files, publishing, and standards #2
You must read this previous post first.
Now, it is important to realize there are standards at many levels. Open specifications allow people to implement the specification without having to pay fees, run into patents, etc. To me, an Open Specification is something you can take, modify, and propose to the community as new Standard.
Now, it is important to realize there are standards at many levels. Open specifications allow people to implement the specification without having to pay fees, run into patents, etc. To me, an Open Specification is something you can take, modify, and propose to the community as new Standard.
Mar
24
Supplementary files, publishing, and standards
The publishing world is slowly changes. Things a small community has been screaming for more than a decade now (and possible before that), that data standards in publishing are inadequate. PDF has not helped (fortunately there are replacement initiatives).
Mar
23
Tutorials around the OpenTox standard
Just a quick forward. Roman posted this announcement for tutorials around the Open OpenTox Standard:The first tutorial will be held Wednesday, 30 March, at 15:00 CET, and aiming at Java developers who want to learn how to build an OpenTox API compliant Web service (some acquaintance with Restlet, and basic knowledge of the OpenTox REST API, is necessary). Participation in these online events involves no registration fee.
Mar
23
Why I like Linux, it's fast! Or, a quick typo fix in the CDK.
Last week there was a short git tutorial, resulting in a small test patch (feel free to ping me, if you like git training for the CDK too). Gaev some commit and review fame to Jules and Gilleain. I ran onto another 'Contructs' typo today, and decided to fix it.
Mar
15
Open Standards (Or: "the long list of things that we weren’t required to do")
Hot on the heels of a presentation I give today in a ToxBank virtual meeting on (Open) Standards (I'll blog the points as soon as possible), I just ran into this great blog post by the makers of the OWL reasoner Pellet (license:GPL), which we use in Bioclipse. It is spot on on what happens if you use Open Standards: "That's notable not only because it took so little time, but also because of the long list of things that we weren’t required to do in order to make it happen".
Mar
15
Chemometrics with R
I just heard that my supervisor's book Chemometrics with R was released, and I immediately requested our library to get a copy. Ron introduced me to R at a time that most at our department were still using Matlab. In fact, I had be maintaining Matlab scripts used in the departments chemometrics courses, and wrote my own philogenetic tree visualization code for Matlab, using a I-no-longer-remember line notation system for the trees.
Mar
13
Unfortunate (CDK) decisions
Sometimes you make decisions which turn out unlucky. Christoph, Dan, and I made one about 10 years ago (see this photo from Dan with his whiteboard where we wrote down our thoughts). The one I am talking about is not bad in itself, but the implementation is bad; bad in the sense that it makes it easy for other toolkits to make a difference in size and performance (see also Quo vadis, CDK?).
