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chem-bla-ics

chem-bla-ics
Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.
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QsarChimieAnglais
Publié

Amanda had a very nice post on Small molecules that modulate quorum sensing. It’s the perfect read for a Sunday morning, when you have a view looking down on Strasbourg from a hill in the Black Forrest. Biology fascinates me, particularly when small molecules are involved. And the molecular signaling used by these bacteria is just delightful. Make sure to read up on the small squids in 96-well plates too! (And we are worried about varkensflats!

PublishingChimieAnglais
Publié

Rich posted a nice quote the other day on the introduction of the forward pass in football some 100 years ago, and linked that to sciences. I commented with the remark that the outscoring is the problem: Just after that, I read this blog by Antony on survival-of-the-fittest chemical search engine. Even though the measurement of the score is easy, these statistics can easily be obfuscated.

InchiOpenscienceChimieAnglais
Publié

The IUPAC/NIST team made a beta release of the next InChI software release: InChIKey A had heard about the InChIKey extension earlier, and it solves the issue some people have with the InChI: it is too long. Well, molecules can have many atoms indeed. It is important to realize the InChIKey is not a replacement: it simply is not unique. The collision probability is calculated to be rather small, though.

OpenaccessPublishingChimieAnglais
Publié

Peter has been doing an excellent job in advocating ODOSOS , and one of his posts even hit Slashdot. Meanwhile, blogspace has been flooded with dislike of the PRISM intiative (e.g. see also the other Peter’s blog ). The website is so sad, it is almost funny again; but on second thought, it is so sad, you wonder the world will end because of WOIII or because of a total halt of scientific progress.

JchempaintChimieAnglais
Publié

Niels and I held a JChemPaint hack-a-thon today (the IRC log). We had a quite ambitious agenda: make the renderer modular make the controller modular make a controller interface with Swing + SWT implementations All this to make the JChemPaint editor module of the CDK more easily integrate with non-Swing widget environments.

LinuxKdeChimieAnglais
Publié

If you, like me, already upgrade to Ubuntu Gutsy, and use nxclient for remote login (highly recommended, though proprietary code), you might run into the problem that the login no longer works, returning the message “Cannot find KDE environment.”. Ubuntu’s Lauchpad (generally an excellent service) was rather uncooperative and disregarded a bug report about the problem, I found the solution with grep -ri kde /usr/NX:

JchempaintCheminfChimieAnglais
Publié

Rich blogged about Firefly embedding MDL molfiles in PNG images , which I found really cool. Rich and Noel later showed how that metadata can be retrieved again , possibly with Python. But I did not like that Firefly could do this, and JChemPaint not. So, I started hacking. First I discovered I had to get rid of the use of JAI; then I had to adapt the JChemPaintPanel takeSnaphot() API to return a RendererImage;