Over the last few weeks I’ve been getting up to speed on RNAi screening (see Lord et al for a nice overview) and one of the key features in this approach is to reliably select hits for followup. In many ways it is similar to hit selection in small molecule HTS but also employs techniques […]
Nice Article on Open Source Cheminformatics
I met Viven Marx at the BioIT World conference held in Boston earlier this month, in which I spoke on the topic of Open Source cheminformatics. The result of conversations between myself (and Peter Murray Rust) and here were incorporated into an interesting article. (Though the CDK was started at Notre Dame, but is now […]
Cheminformatics with Hadoop and EC2
In the last few posts I’ve described how I’ve gotten up to speed on developing Map/Reduce applications using the Hadoop framework. The nice thing is that I can set it all up and test it out on my laptop and then easily migrate the application to a large production cluster. Over the past few days […]
Substructure Searching with Hadoop
My last two posts have described recent attempts at working with Hadoop, a map/reduce framework. As I noted, Hadoop for cheminformatics is quite trivial when working with SMILES files, which is line oriented but requires a bit more work when dealing with multi-line records such as in SD files. But now that we have a […]
Hadoop and SD Files
In my previous post I had described my initial attempts at working with Hadoop, an implementation of the map/reduce framework. Most Hadoop examples are based on line oriented input files. In the cheminformatics domain, SMILES files are line oriented and so applying Hadoop to a variety of tasks that work with SMILES input is easy. […]