Tuesday, 12 August 2008

ANN: cinfony 0.8 - "the one with documentation"

I've just released a new version of cinfony. This one comes with full documentation of the API as well as a description of how the API is used. It should be ready for use on both Windows and Linux.

The website is at http://cinfony.googlecode.com and here's the front page:


Cinfony presents a common API to several cheminformatics toolkits. It uses the Python programming language, and builds on top of OpenBabel, RDKit and the CDK.


PubChemSR makes it to top 10

In the 3 months since publication in Chemistry Central Journal, Junguk Hur and David Wild's paper on PubChemSR has shot up the Chemistry Central rankings and has now entered the top 10 most highly accessed papers of all time (that is, since Jan 2007). I should know, as I've watched it overtake my Pybel paper and squeeze me out of that same top 10, but not for long I hope. :-)

Here's the abstract:
Recent years have seen an explosion in the amount of publicly available chemical and related biological information. A significant step has been the emergence of PubChem, which contains property information for millions of chemical structures, and acts as a repository of compounds and bioassay screening data for the NIH Roadmap. There is a strong need for tools designed for scientists that permit easy download and use of these data. We present one such tool, PubChemSR.

PubChemSR (Search and Retrieve) is a freely available desktop application written for Windows using Microsoft .NET that is designed to assist scientists in search, retrieval and organization of chemical and biological data from the PubChem database. It employs SOAP web services made available by NCBI for extraction of information from PubChem.

Results and Discussion
The program supports a wide range of searching techniques, including queries based on assay or compound keywords and chemical substructures. Results can be examined individually or downloaded and exported in batch for use in other programs such as Microsoft Excel. We believe that PubChemSR makes it straightforward for researchers to utilize the chemical, biological and screening data available in PubChem. We present several examples of how it can be used.