Taverna runs with Classpath 0.91

Classpath 0.91 is released with 1.45 million lines of code and with 98.96% coverage of Java 1.4.2, and 99.82% of java.swing. Or, as Dave calls it: 0.91 rocks! JChemPaint runs again (they fixed the XML parsing problem), and Jmol still runs, but slow. I also tested Taverna which now also starts up, but has an XML parsing error too:

less than 1 minute read

New open access journal Source Code for Biology and Medicine

BioMed Central is setting up a new peer-reviewed, open access journal Source Code for Biology and Medicine. It will “encompass all aspects of workflow for information systems, decision support systems, client user networks, database management, and data mining”. Basically, anything that fits into chem-bla-ics. (Thanx to Werner, for pointing me to the website!)

2 minute read

Open Text Mining Interface and Bioclipse

Timo Hannay blogged in Nature’s Nascent blog about the Open Text Mining Interface (OTMI), which is “a suggestion from Nature about how we might achieve text-mining and indexing purposes”. The idea is that each article has a link pointing to a machine readable file containing raw data about (and from?) the article. The standing example uses Atom 1.0 as a container, allowing raw data to be included using foreign namespaces, such as Dublic Core (for metadata) and Prism (for bibliographic data), and the OTMI text mining statistics uses a namespace too.

1 minute read

Four graph mining methods integrated in ParMol

Joerg Wegner mentioned in his blog the graph mining program ParMol which integrates four mining algorithms: MoSS (aka MoFa) and Gaston, which I mentioned in November last year , and FFSM and gSpan, which I did not know about yet. ParMol provides a common interface to the four different algorithms and is, like the four mining modules, licensed GPL. An interesting aspect is that Gaston was originally written in C++.

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Nightly CDK builds now available

Rajarshi Guha has set a nightly build service for the Chemistry Development Kit (CDK). The output is pretty, but information rich: it includes results for the JUnit test, DocCheck, and PMD. The compiled jar and the corresponding JavaDoc can be downloaded, offering a cutting edge distribution for users.

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Protein support in Bioclipse using Jmol and the CDK

I have not blogged for about a week now, and been too busy with other things, like finishing my PhD articles/manuscript, my new job at the CUBIC where I continued the work on proper protein support in Bioclipse using the CDK and Jmol:

1 minute read

Download statistics for chemblaics components

Here are some quick download statistics for some of the chemblaics components. First Jmol. The new stable Jmol 10.2 was release just over a week ago, and this obviously boosted downloads, breaking the monthly download total of two earlier this year (source):

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