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

Science Blogging 2008 London was Cool!

Definately not a first post, but here are my experiences of my first blogging conference (see also this and this , the latter using semantic markup for the event): it was fun! My suggested unconference was not chosen, because I, as I usually do, focus to much on how instead of why one wants to do something. Nevertheless, I got to say my things, so I won’t complain. While I have not noted a vivid live coverage in blogosphere of the conference, several people were live covering the meeting on FriendFeed . Really nice, because you can comment on statements the speaker makes, while he is talking. People have been using the sciblog tag, which should give you enough hits in the various aggregators and social sites. 2 minute read

Leaving to Science Blogging 2008 London

Have to leave to the airport any second now for the Science Blogging 2008 in London, so nothing much I shall say. Hope to see you tomorrow at the Royal Institute! less than 1 minute read

MetWare screenshot: propagating XML Schema data types

Just a quick screenshot. Remember our use of SKOS in MetWare ? Steffen has been working on creating integrated JSF pages, while I am focusing on autogeneration of blobs. The below screenshot is such a blob, called a UI component in JSF, which allows easy embedding the the aggregations Steffen is working on. 1 minute read