Today Ola, Jonathan and I have a mini-hack session on getting JChemPaint support ported from Bioclipse1 to Bioclipse2. And, we made some progress:

I'm sure there is still a lot to do, but this is promising... :)

Oh, and BTW, this is based on the JChemPaint 2.3 / CDK 1.0.2 branch, in case you are interested in those details.
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Via Carbon-Based Curiosities's blogroll I found a number of new blogs (on top of the list I posted yesterday), and just added them to Chemical blogspace. This is something I found in Infiniflux!:

Blog comments? No, Peer Reviews! Nice thought, Joel! I'll copy that, if you don't mind.
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bbgm was rethinking software access. The blog observes:current commercial licensing is unfriendly towards home sciencebench tools do not easily allow mash upsAbout 1

Actually, much of the work I have been doing in opensource chemoinformatics was done as 'home' science; I started as organic chemist student, and later data analyst, while the CDK/Jmol/JChemPaint was something I did at home because I liked, and needed it.

Via Rich' blog, I was informed about the work by goesLightly on CampDepict, a Ruby-based application which uses the CDK for SMILES parsing and 2D diagram generation. With cdk-20060714.jar it's using pretty ancient code, and I have not seen a screenshot.

Some publishers hesitate a bit, but others go full speed ahead into the electronic publishing era. Noel comment on my post about OA/OD inviting added value:I heard a talk by the RSC at the ACS, saying that their RSS feeds contain InChIs now! Just thought I'd throw that out there :-) The RSC Project Prospect is ahead of other publishers, for over a year already.

Two companies recently showed two things:open access and open data allow adding valueadding value is easier by forking Rich' MetaMolecular set up Chempedia which combines a substructure-searchable chemical Wikipedia. There is also a page to make links to new Wikipedia monographs. Not sure why Rich chose CAS instead of the InChI, given the recent controversy on validity of CAS numbers in Wikipedia...
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While I do not agree in details on the statement made by Klaus, I agree with his intentions, and happy to propagate the mantra, like others did before me:MAKE ALL RESEARCH RESULTS CC-BY

The details I disagree with:no need for shouting; we can all perfectly well read it in lower caseCC-BY is not required; any open data license will do

Now, I know some of you disagree, and I understand the costs for maintaining and curating a database.
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Today starts the MetWare developers meeting, hosted by Steffen Neumann, at the Leibniz-Institut für Pflanzenbiochemie. Steffen's group and the Applied Bioinformatics group where I now work, are co-developing an opensource platform for metabolomics data management. Not really a full LIMS system, but a system to keep track of all the facts about the experiments and samples we would use when analyzing the data in order to find new chemistry, biomarkers, etc (see this earlier blog too).

As announced earlier, Miguel, Velitchka, Christoph and I held a small CDK/Metabolomics/Chemometrics unconference. We started late, and did not have an evening program, resulting in not overly much results. However, we did do molecular chemometrics.

We used the R statistics software together with Rajarshi's rcdk package (an R wrapper around the CDK library) and Ron's (my PhD supervisor) PLS package (see this paper), to predict retention indices for a number of metabolites.
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In reply to Peter's news that the NIH's PubMed Central (PMC) does not allow machine retrieval of content, I was wondering about this section in the CC license of much of the PMC content, such as our paper on userscripts (section 4a of the CC-BY 2.0):You may not distribute, publicly display, publicly perform, or publicly digitally perform the Work with any technological measures that control access or use of the Work in a manner inconsistent with the terms of this License Agreement.CC-BY 3.0 read
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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!
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