Similarity Matrices in Parallel

Today I got an email asking whether it’d be possible to speed up a fingerprint similarity matrix calculation in R. Now, pairwise similarity matrix calculations (whether they’re for molecules or sequences or anything else) are by definition quadratic in nature. So performing these calculations for large collections aren’t always feasible – in many cases, it’s […]

Hadoop and Atom Counting

Over the past few months I’ve been hacking together scripts to distribute data parallel jobs. However, it’s always nice when somebody else has done the work. In this case, Hadoop is an implementation of the map/reduce framework from Google. As Yahoo and others have shown, it’s an extremely scalable framework, and when coupled with Amazons […]

Multi-threaded Database Access with Python

Pub3D contains about 17.3 million 3D structures for PubChem compounds, stored in a Postgres database. One of the things we wanted to do was 3D similarity searching and to achieve that we’ve been employing the Ballester and Graham-Richards method. In this post I’m going to talk about performance – how we went from a single […]