The other day I was reading a paper and as is my habit, while reading I flip to see what papers are being cited. Since this was an ACS journal, the references are listed in the order that they occur in the text. When the authors were discussing a point in the paper, they’d usually […]
Moving to SlideShare
Finally got round to putting a number of my slides onto SlideShare. While I was skeptical initially, I’ve found it quite handy to quickly browse through a presentation without having to download PDF’s or PPT’s and start up the viewers. Also this lets me not have to maintain a webpage listing all the presentations I’ve […]
CDL – A Cheminformatics Toolkit
The Chemical Descriptors Library (CDL) has been around for a while, but hasn’t seemed to get much publicity. A paper describing the design and performance of the library just came out today. While the name suggests a library of descriptors, it’s actually a general C++ library for cheminformatics. The library appears to use the molecular […]
Faster Substructure Search in the CDK
The CDK uses the UniversalIsomorphismTester to perform graph and subgraph isomorphism. However it’s not very efficient and this shows when performing substructure searches over large collections. A quick test where I compared the CDK code to OpenBabel’s obgrep showed that the CDK is nearly forty times slower than OpenBabel. Improvements in this code will enhance […]
Computational Research and Software in Academia
This paper by Prof. Tim Pederson in the Journal of Computational Linguistics highlights the need for authors of computational linguistics papers to release working software that can be used to reproduce results in their papers. While the paper focuses on the field of computational linguistics (CL), the discussion is perfectly applicable to other fields that […]