Molecular indexing on the KDE and OS/X desktops

Geoff Hutchinson blogged about his OS/X ChemSpotLight, an indexing tool for chemistry documents. It’s like, but more advanced than, the kfile_chemical and Kat I have been working on (with others) for the KDE desktop (see earlier blog items).

1 minute read

XML validation on Eclipse with Web Tools Platform

Yesterday I installed the Eclipse Web Tools Platform again, and now succesfully, using the Eclipse update mechanism, on my Kubuntu dapper eclipse install. Because it has a validating XML editor, the one last thing I still needed jEdit for. (I do miss the vertical selection feature of jEdit, though.) It signals me of errors, and allows autocompletion.

1 minute read

A live life-sciences CD

November last year, I reported my plans to develop a live CD with all our favorite chemo- and bioinformatics software. Bioclipse requires Java5 and sort of still depends on the Sun JVM (I will experiment with classpath-generics later), but is now distributable with operating systems. So, I made a Kubuntu derived operating system with OpenBabel, Jmol, PyMOL, Bioclipse, and, on systems level, the chemical MIMEs and kfile_chemical, wich extends the desktop with chemistry awareness. In addition, I added the Blue Obelisk Data Repository, all CDK News issues, and the full NMRShiftDB data in CML format.

less than 1 minute read

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++.

less than 1 minute read