MetWare screenshot: spectrum support #2

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

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MetWare screenshot: spectrum support

Not visually attractive, but that will be solved when Steffen gets his hands on it. For now, I’m happy with a table formatting. Reason: it uses XML Schema to define a dataType, which is recognized by our code generators in MetWare (see also this presentation), and used to create a easy to use Java API, which, in turn, can be used in this JSF snippet:

1 minute read

Profiling the CDK atom typer

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):

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Scientific progress is a primary human need

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.

2 minute read

Mapping Peoples Interest: Google Insight Search

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):

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"The End of Theory: The Data Deluge Makes the Scientific Method Obsolete"

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.

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Online, multiplayer metabolomics game!

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:

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