On Thursay I joined Antony Williams as a guest lecturer in Jean Claude-Bradleys‘ class on chemical information retrieval at Drexel University. Using a combination of WebEx and Skype, we were able to give our presentations – seamlessly joining three different locations. Technology is great! Tony gave an excellent talk on citizen science and ChemSpider and […]
Are Bioinformatics Results Too Good To Be True?
I came across an interesting paper by Ann Boulesteix where she discusses the problem of false positive results being reported in the bioinformatics literature. She highlights two underlying phenomena that lead to this issue – “fishing for significance” and “publication bias”. The former phenomenon is characterized by researchers identifying datasets on which their method works better […]
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 […]