Finally all the paper work is in place for me to visit the EBI in May to run a hands-on workshop on doing cheminformatics in R. This is part of a two day program. On May 17th I will be discussing the use of the rcdk and rpubchem packages, considering a variety of use cases […]
Simple XML Parsing with Clojure
A while back I had started playing with Clojure. It’s always been a spare-time hobby and not having had much spare time I haven’t really gotten as far ahead with it as I’d have liked. I’m still not sure why I like Clojure, but it is fun to code in. My interest was revitalized when […]
ChEMBL in RDF and Other Musings
Earlier today, Egon announced the release of an RDF version of ChEMBL, hosted at Uppsala. A nice feature of this setup is that one can play around with the data via SPARQL queries as well as explore the classes and properties that the Uppsala folks have implemented. Having fiddled with SPARQL on and off, it […]
Molecules & MongoDB – Numbers and Thoughts
In my previous post I had mentioned that key/value or non-relational data stores could be useful in certain cheminformatics applications. I had started playing around with MongoDB and following Rich’s example, I thought I’d put it through its paces using data from PubChem. Installing MongoDB was pretty trivial. I downloaded the 64 bit version for […]
Cheminformatics and Non-Relational Datastores
Over the past year or so I’ve been seeing a variety of non-relational data stores coming up. They also go by terms such as document databases or key/value stores (or even NoSQL databases). These systems are alternatives to traditional RDBMS’s in that they do not require explicit schema defined a priori. While they do not […]