Git mirror for the CDK

While slowly merging with Sweden , and ADSL which should reach my house in some two weeks, I am enjoying my new office space and Git to upload patches to the CDK. Christoph wondered if we should switch CDK from SVN to Git. A few developers objected, for various reasons: no native Windows clients (though msysgit might be the solution), no (stable) plugins for Eclipse, IDEA(?), etc. 1 minute read

Moved to Sweden: Post-doc in the Bioclipse group of Prof. Jarl Wikberg

The reason why I have not been able to blog much lately, is that my family and I have been moving to Uppsala/Sweden, where I’ll start a postdoc in the group of Jarl Wikberg @ BMC @ Uppsala University, where I’ll work on chemoinformatics in drug design, and the use of CDK and Bioclipse in particular. less than 1 minute read

FriendFeed for the Chemistry Development Kit

FriendFeed is a nice aggregation service allowing discussion of items posted from delicious, blogs, and any other RSS-based feed (e.g. my feed). It also has a room concept, where people can post stuff around a topic, such as a conference such as Science Blogging 2008 London, or the CDK: less than 1 minute read

CDK development with branches using Git

Christoph pointed me to a video on Git by Linus. CDK is now using branches extensively in development, and just set up a branch for the upcoming 1.2.0 release later this year (end of October, see cdk-1.2.x). Christoph has just reviewed the branch containing the API move to Iterable. This patch now allows to do this (which would really deserve a blog item by itself): 4 minute read

Ubiquity fun: entering semantic markup as easy as running a Ubiquity command

Now, the DOI ubiquity scripts I just blogged about, was just the beginning of things. Me exploring the environment and learning the JavaScript language. 1 minute read

Ubiquity fun: resolving DOIs

Now, I’m really after something else, but here’s my first Ubiquity scripts. It allow you to select a DOI on any web page (which really only makes sense if it is not already a hyperlink), you hit ALT-SPACE (Linux), CTRL-SPACE (Windows), or whatever the shortcut is on your operating system, and type resolve-doi and it will automatically convert the DOI into a hyperlink to look up the paper. 1 minute read

Creating CMLReact from UsefulChem Ugi Reactions

Cameron, Jean-Claude and I were invited to Peter’s place in Cambridge, where we are now hacking on CMLReact for the Ugi reactions Jean-Claude has been working on. I just finished a script that uses the CDK and Sam’s interface to the InChI library to convert a list of four reactants and one Ugi product into CMLReact (doi:10.1021/ci0502698). The full BeanShell script looks like: 2 minute read