These last few days I’ve been in the UK for an EBI workshop on cheminformatics in R. It was a two day workshop, the first day focusing on general cheminormatics in R using the rcdk and rpubchem packages, and the second day focusing on doing mass spectrometry in R using XCMS and Rdisop, run by […]
2D Depictions in R Plots
In preparation for the upcoming R workshop at the EBI, I’ve been cleaning up the rcdk package and updating some features. One of the new features is the ability to get a 2D depiction as a raster image. Uptil now, 2D depictions were drawn in a Swing window – this allowed you to resize the […]
rcdk On GitHub
I’ve been working on the rcdk and rcdklibs R packages that integrate the CDK into the R environment. For the past year or two it’s been hosted on r-forge.r-project.org which has a nice feature of nightly builds of R packages. Unfortunately their version control system is Subversion. Having used Git for my other projects, this was […]
RNAi in PubChem
While considering ways to disseminate RNAi screening data, I found out that PubChem now contains two RNAi screening datasets – AIDs 1622 and 1904. These screens reuse the PubChem bioaassay formats – which is both good and bad. For example, while there are a few standardized columns (such as PUBCHEM_ACTIVITY_SCORE), the bulk of the user […]
Automating ChemDraw
I’ve been working on a project in which I needed to generate logP values using ChemDraw 12, for thousands of molecules. Since I didn’t have access to the ChemScript module, I needed a way to automate this procedure. After fiddling around with Visual Studio and various debuggers, I came across the Windows Application Testing Using […]