XCMS on Ubuntu Feisty

I just installed XCMS 1.9.2 on my Ubuntu system. XCMS is a GPL-ed R package for metabolomics data analysis. Just for the record, you need to install the Feisty packages for NetCDF: less than 1 minute read

JChemPaint too: PNG embedded connectivity tables

Rich blogged about Firefly embedding MDL molfiles in PNG images , which I found really cool. Rich and Noel later showed how that metadata can be retrieved again , possibly with Python. 1 minute read

Automatic Classification of thousands of Crystal Structures

Clustering and classification of crystal structures is hot. Parkin hit the front cover of CrystEngComm with a story on Comparing entire crystal structures: structural genetic fingerprinting (DOI:10.1039/b704177b). Now, the story itself, while rather interesting and well written, has three major flaws: 2 minute read

Dapagliflozin: the molecular structure

An anonymous reader reported that the American Medical Association published the structure of dapagliflozin. Here are the details. less than 1 minute read

Operator 0.8 released: a new Sechemtic user script

Mike released Operator 0.8, which picks up RDF (RDFa en eRDF) from HTML pages, and adds actions to it. I blogged earlier about the beta and wrote a script for it for chemical RDFa . At this moment, Chemical blogspace and RDF for Molecular Space (see this blog ) are using chemical RDFa to semantically markup molecular information. 1 minute read

Touchgraphing my blog

Via SciFoo Planet (from Partial immortalization ) I learned about TouchGraph Google (Peter brought it into Chemical blogspace). It’s cool, though not open source. Here’s the touch graph for my blog: less than 1 minute read

Centralized or decentralized?

Peter wondered if data should be stored centralized or decentralized, when Deepak blogged about Freebase and Metaweb. Now, I haven’t really looked into these two projects, but the question of centralized versus decentralized is interesting. It’s MySQL versus the world wide web; it’s the PubChem compound ID versus the InChI; it’s http://cb.openmolecules.net/rdf/?InChI=1/CH4/h1H4 versus info:inchi/InChI=1/CH4/h1H4 (see RDF-ing molecular space ). 1 minute read