chem-bla-ics: May 2008

Development of the new JChemPaint

A quick screenshot, after some work on the JChemPaint code based on CDK trunk/. Nothing much to see, but a rather small code base, which is good. Today, I have set up cdk/cdk/trunk/ and cdk/jchempaint/trunk as Eclipse plugins, allowing the second to depend on the first. So, no more use of svn:externals. This is what it now looks like, and basically formalizes the end result of Niels' work of last year:

A possible spin of is that Bioclipse2 can use these plugins too, instead of defining plugins itself.

To reproduce the above screenshot, just import cdk/cdk/trunk and cdk/jchempaint/trunk into Eclipse, and run the TestEditor from the JChemPaint plugin.

May

Metware Status Report

Following many, many others, I finally got myself a SlideShare account and uploaded a recent presentation on MetWare, our metabolomics data warehouse project. Some spoilers: SQL, RDF/SKOS, JSF.

May

John Wilbanks replies to the ChemSpider/OpenData discussion

Not long after I posted my view on things, John posted his reply on the ChemSpider/OpenData discussion. His comment was merely to illustrate an internal advice to some organization, which got accidentally leaked. Anyway, a must read, with two good links to further reading on open data licensing.

His blog mentions the concept of public domain, where data might be dumped, but I always understood that the US public domain concept is different from that of mainland-EU, German law in particular.

May

Does ChemSpider really violate Open Data with CC SA?

ChemSpider is afraid they are doing something bad because they release their data as CC-BY-SA. Because, John Wilbanks says in Peter's blog:I would add to it that I'd like to see a meaningful discussion of the

risks of Share Alike and Attribution on data integration.

May

Re: What should a Nature Chemistry paper look like?

Neil wondered "what a Nature Chemistry paper should look like", and asked the following questions. Below are my answers.

1. HTML vs PDF: does anyone read the HTML articles? Do you read the PDF on-screen or print it out?

I typically read the HTML to scan if a paper is interesting for me. But because electronic paper is still too expensive, I typically make a print of the PDF. I would love to print the HTML instead, if only it was not clouded with advertisement, link menu's etc.

May

Wicked chemistry and unit testing

After a discussion on starting development releases for CDK on cdk-devel, the discussion continued on the state of the CDK atom typer. Dan and Rajarshi have done tests in the past against PubChem and its DTP/NCI subset. Rajarshi made his analysis part of CDK Nightly, and provides but a summary (which seems broken: zero fails) and a detailed list.

Dan, do I understand correctly that those Structure Evaluation:No Comparision - Unparameterized Atom - S.

May

Comparing JUnit test results between CDK trunk/ and a branch #2

I reported earlier on how to compare unit test results between CDK trunk and a branch. Later, I noted that the diff typically overestimates the fail count, when unit tests had been moved to a different module. Therefore, a sort has to be added.