chem-bla-ics: January 2008

Why chemistry-rich RSS feeds matter...

Peter wrote up an item on Nick's CrystalEye's RSS feed, and I have been enthusiastic about chemistry-enriched RSS feeds for some time. CMLRSS has the chemical data inline in the RSS; see DOI:10.1021/ci034244p, the use of CMLRSS in Chemical blogspace described here and here, and the CMLRSS support in Bioclipse.

Nick's RSS feed does not put the chemistry inline, but does link to the raw CML file:<entry>

<title>No title supplied</title>

<link rel="enclosure" href="http://wwmm.ch.cam.ac.uk/crystaleye/summary//acs/inocaj/2008/3/data/ic702497x/ic702497xsup1_THP4-SINC-publ/ic702497xsup1_THP4-SINC-publ.complete.cml.xml" hreflang="en" />



</entry>The example shown by Peter was nicely chosen: something is wrong with that example.

Jan

My PhD Thesis: in color and grayscale

Wednesday is my regular day off from my metabolomics work, and today I am finalizing the layout of my thesis, which I'll defend on April 2. The print version will feature grayscale images with some of them in color too. However, the PDF version that will end up in our university repository should have color prints. So, while halfway creating suitable grayscale versions of the image, I realized I was not doing it properly. I was replacing the images; so, I lost the color version. Not good.

Jan

Java Server Pages with CDK functionality

Setting up interactive web pages can be done in many way. Java Server Pages are just one of them. They are quite similar to PHP pages or Ruby, and combine plain HTML (and likely any other output) code with fragments of code; Java source code in this case.

Ubuntu's tomcat5.5 package installs quite easily, and sets up a server at port 8180. I still have to figure out how to nicely integrate it with the Apache server on port 80, though. Suggestions much appreciated.

Jan

Be in my Advisory Board #2: JChemPaint development

No idea who the 22 persons are who were willing to join my advisory board, but they advised me to finish the JChemPaint work Niels worked on this summer:

Like my current main hobby project (atom typing in the CDK), the JChemPaint project will be performed in my non-working hours mostly. A reasonable ETA is, therefore, end of this summer. Main discussion on will be done on the cdk-jchempaint mailing list.

Jan

CDK Literature #4

Fourth in the CDK Literature series. Really, a follow up on #3 which I wanted to get out, even though not really finished yet. But, after 3 comes 4, not 3b. Maybe 3.1, but that suggests at least 3.2-3.9 too, let alone full R (that was supposed to the space of all reals...) I'll stick to positive non-zero integers. #1 and #2 are still available too.

Another thing I should remark is that this series does not provide full reviews of the cited papers.

Jan

CDK Literature #3

Third in a series summarizing literature citing one of the two CDK articles. See also #1 and #2.

Reviews

Two reviews have recently appeared which cite the CDK. Ricard Stefani has written a review in Portuguese of the many NMR-based elucidation tools on computer-aided structure elucidation. The CDK is cited as a general chemoinformatics tool. It also cites SENECA which uses CDKs structure generators.

Jan

Open Lab 2007 results

The results for the Open Lab 2007 are out. I participated in this endeavor as judge, and read 75 of the 486 blog items, focusing on the sections chemistry, blogging, publishing, politics of science, and a number of blog items with few reviews when I passed them.

I am happy to see that one of the chemistry submission I made myself made it into the anthology: the Depth-First item on SMILES and Aromaticity: Broken?.

Jan

Collaborative work with Bioclipse

Ola blogged about something he is working on for Bioclipse2. The next major series of Bioclipse releases will use the RCP-based resource architecture, which allows better integrating with other RCP plugins, such as the Subclipse plugin which allows one to browse Subversion repositories directly in Bioclipse. That is cool! Check out the screenshot he posted in his blog.

Now, this kind of integration is important.