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

UgiChem2CML

The nice thing about a hacksession, is that you have something to write about. Below a screenshot of a Ugi reaction in Bioclipse… note the source tab of the editor, which holds the CML. Now, JChemPaint can do reactions too (I did that in 2003 in Peter’s group, but seems to be offline at this moment), but this was the quick hack to do the CMLReact in Google Docs (or soon to be): less than 1 minute read