chem-bla-ics: December 2011

A Google+ page for the CDK

A week or two ago I created a Google+ page for the CDK, which can be found here and it looks like:

I will use this page to post interesting stories around the CDK. It is not supposed to replace the Planet CDK, which aggregates blog posts from CDK developers and users, but for other, perhaps shorter posts. For example, as can be seen in the above screenshot, I have started to use it as a CDK Literature replacement, which originally was a series of articles in CDK News (the archives), and later hosted in my blog (see CDK Literature #5 for links to the other four).

But, I will (re)share anything I find useful for the CDK community.

Dec

Open Source cancer research (must see video)

Four years ago I wrote up a passionate post about the importance of ODOSOS, and about a year ago written about how research can be open sourced, and how the Open Source Chemistry Development Kit (CDK) fits in. I am proud that the CDK is enabling so many researchers to do novel research! Google Scholar reports over 200 documents and Web of Science gets to over 150 for just the first CDK paper (see also GS vs WoS). That's serious impact.

Dec

Google Scholar versus Web of Science

Web of Science (WoS) is the de facto standard for citation information. It's citation counts are used for many purposes, among which to decide I am a good scientist. Web of Science, however, really expensive, and Joe the Plumber does not have access. No wonder, he doesn't know which scientist to trust (...).

Recently, Google made their Scholar product open to all, allowing you to list your publications (about my list), which Google with augment with citation counts.

Dec

What data is behind this scatter plot?

Dec

Open Science and Non-Commercial licenses (a personal reflection to the Oscar/RSC controversy)

Peter has started a new line of discussion in his blog, referring to a correspondence with representatives from RSC last year, about an annotated literature corpus to (re)train the Oscar3/4 text miner. There are very many sides, and after I reread this post for a second time, I was still not 100% happy about all words: I can only try to express the complexity of the matter and how it started, but do hope to be clear that non-commercial licenses are not useful in Open Science.

Dec

CDK-JChemPaint #9: implicit hydrogens and isotopes

Next in this series (after #1, #2, #3, #4, #5, #6, #7, #8), I'll show how to add implicit hydrogens to a drawing. I actually think the BasicAtomGenerator should cover implicit hydrogens, and the ExtendedAtomGenerator anything that requires more CDK modules than just the interfaces, like isotopes. But I discovered that implicit hydrogens currently also requires the ExtendedAtomContainer too late.

Dec

CDK-JChemPaint #8: rendering of aromatic rings

CDK can render aromatic rings in two ways: with localized double bonds and with a circle reflecting the delocalized nature of the π electrons. Or, graphically:

The following two code snippets are part of full scripts available from my Groovy-JChemPaint repository, and these two drawings are created with CDK 1.4.6.