Version 1.4.3 of rpubchem is out on CRAN. There’s some minor code cleanups and also a new function called get.aid.by.cid which allows you to get assay ID’s based on whether they contain a compound (either as an active, inactive, discrepant or just tested). This uses PUG to perform the query, so can be a bit […]
Frequency of a Term via PubMed
A little while back, Egon posted a question on FriendFeed, asking whether there was an easy way, preferably a service, to determine and plot the usage count of a term in PubMed by year. This is simple enough using the Entrez Utilities CGI. A quick Python script to do this (with minimal error checking) is […]
Updated Versions of R Packages
New versions of several of my R packages are now available on CRAN. rcdk 2.9.6 goes along with rcdklibs 1.2.3. The latter now uses the most recent cdk-1.2.x branch from Github. The former fixes a number of bugs relating to descriptor calculations, saving molecules in SD format and setting/getting properties on molecules. Unfortunately, because the […]
Another Conference Done
The CHI RNAi conference is over and will now head back home. Being new to the field of RNAi screening, I’ve been looking for a place (virtual or real) where I can meet other people, especially those working in large scale screening facilities. Reading the literature is certainly useful, but face to face interactions are […]
A New Toolkit on the Block
A few days ago I was pointed to a new cheminformatics toolkit called Indigo, written in C++ with source code available under the GPLv3 license. Rich has previously commented on this. While it’s an initial release, it has a number of interesting components such as an Oracle cartridge, 2D depiction and scaffold detection and R-group […]