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.
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!
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.
As promised yesterday , here’s the pretty visualization of the mass spectrum, using JavaScript from the PRIDE project:
Not visually attractive, but that will be solved when Steffen gets his hands on it. For now, I’m happy with a table formatting.
I was doing some profiling (YourKit and Eclipse3.4) of the CDK atom typer, and it turns out that most time is spend on the perception of nitrogen atom types, which seems to be caused by the loadClassInternal() method of the JVM (java-1.5.0-sun-1.5.0.16 on Ubuntu Hardy):
Deepak asked me to comment on his blog post Is your web service open source?. With a slight delay, I did on FriendFeed. I’ll copy it here.
Google has a new service: Google Insight Search, and I was wondering if it could tell me to use chemoinformatics or cheminformatics… No, it can’t. In both there is a declining interest (only chemoinformatics shown):
The thought triggering editorial “The End of Theory: The Data Deluge Makes the Scientific Method Obsolete” by Chris Anderson can’t have escaped your attention. I was shocked when I read the title and the comments made on the blogosphere and on FriendFeed.
I was just organizing my toreads, when I found this link: metabolaspel.nl, an online, multiplayer metabolomics game!
Time flies. Another CDK Literature (see also #1 , #2 , #3 , #4 ). Quite a few papers have been published again, and I’ll briefly discuss a few of them. Detection of IUPAC names Klinger et al. have written a paper on detection of IUPAC names. As long as semantic markup languages are not the default, this remains important. Remaining problems include correctly finding boundaries in summaries of chemical.