While trying to update rcdk on CRAN it was pointed out to me that usage of the library resulted in modifications to the users home directory. Specifically, this occurred when generating InChI‘s. The CDK makes use of jni-inchi, which in turn depends on JNATI which enables Java code to work with native libraries in a platform […]
HTS and Message Queues
In my previous post I discussed how we’d like to automate some of our screens – starting from the primary screen, going through data processing and compound selection and completing the secondary (follow up) screen. A key feature of such a workflow is the asynchronous nature of the individual steps. Messaging and Message queues (MQ) provide […]
Automating the Screening Pipeline
A key feature of high throughput screening (HTS) efforts is automation. The NCGC is no stranger to automation, with two Kalypsys robots and a variety of automated components such as liquid handlers and so on. But while the screen itself is automated, the transitions between subsequent steps are not. Thus, after a screen is complete, […]
Faster Maximum Common Substructures
Recently Syed Asad Rahman of the EBI sent around a message regarding some new code that he has been developing to perform maximum common substructure detection. It employs the CDK but also includes some alternative methods, which allow it to handle some cases for which the CDK takes forever. An example is determining the MCSS […]
Consolidating Services
Over the last few months I’ve been writing about REST services that I’ve made available. While useful they’ve been a hassle to maintain. The main reason is that many of the Python services (such as the depiction and descriptor services) are actually front-ends to SOAP services written in Java using the CDK. Thus, I have […]