Rogue Scholar Beiträge

language
Veröffentlicht in chem-bla-ics

About two weeks ago, the ChemConnector blog reported an InChIKey collosion detected by Prof. Goodman. Unlike the previous collision, this one was based solely on the graph and not on stereochemistry. The two molecules both have the InChIKey OCPAUTFLLNMYSX-UHFFFAOYSA-N: The compounds are really different, the molecular formulas are C 50 H 102 O and C 57 H 114 O respectively.

Veröffentlicht in chem-bla-ics

The Bioclipse Workshop has ended and, for just three days, turned out quite productive. We have first bits of scripting support for JavaScript using Rhino. At this moment the scripting plugin needs to explicit depend on plugins to be able to access their classpath, but we plan to solve that. An example script: // to have short identifiers Array = Packages.java.lang.reflect.Array; String = Packages.java.lang.String;

Veröffentlicht in chem-bla-ics

Chemical Archeology (see Christoph’s comment) is the process of extracting chemical information from old journal articles. Some time ago, Peter Corbett from the group of Peter Murray-Rust visited the CUBIC to talk to us about Oscar3 which can do just that. That day, we already hooked OPSIN into Bioclipse . Oscar3, however, is capable of more then the name2structure of OPSIN (see also 10.1039/b411033a;

Veröffentlicht in chem-bla-ics

I hacked in a new extension point for Bioclipse yesterday, based on a proposal I made earlier. The new extension point (EP) is called ChildResourceCreator and allows creating child resources for a given IBioResource. One application where this is very useful is the CMLRSS application (earlier blog), or any RSS or Atom enriched with any other XML language.

Veröffentlicht in chem-bla-ics

The Eclipse Rich Client Platform (RCP) is very powerfull, and takes a lot of architectural things of your hand when developing a bio- and chemoinformatics GUIs. Bioclipse is based on it. One thing the RCP offers is a Help View which works with plain (X)HTML files, and one neat feature is the context help. It is help shown in the Help View when one focused on a specific GUI element.

Veröffentlicht in chem-bla-ics

With chemometrics in mind (QSAR, data mining, …), I have started working on matrix support in Bioclipse, because the matrix is the important step between (bio-)molecular content and statistical analysis. I implemented this such that the actual matrix implementation can be freely chosen, that is, bc_statistical provides a IMatrixImplementation extension point.