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!

Update: live coverage at Friend Feed.

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.

Autogeneration of web content benefits greatly from well defined input, including data types.

As promised yesterday, here's the pretty visualization of the mass spectrum, using JavaScript from the PRIDE project:

Note the manual adding of peaks at 10 and 100 m/z to get the real peaks somewhere in the middle instead of on the left and right border of the graph.

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):
3

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.

The question is about getting return-on-investment: if I developed a new algorithm (or new efficient implementation), how can I make some money with that, to feed me, continue development, maybe just maintenance. And, how does that work for scientific software, which can best be opensource? So I replied:Deepak, did not have time to read it earlier.

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):

More interesting is that the interest in chemoinformatics only comes from India:

This tool holds for both flavors too.
3

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.

How can he say that?! There is no analysis of data anymore?!? Don't we need to understand why X correlated with Y?!? Etc etc.
5

I was just organizing my toreads, when I found this link: metabolaspel.nl, an online, multiplayer metabolomics game! It's in Dutch, but I guess anyone will get the idea :) Two teams, each may have two players, fight each other in sugar-fat conversion, by tuning the metabolism parameters:

The game board should look familiar:

I finally found a worthy follow up for Civilization :)
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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!
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