SOMA--workflow for small molecule property calculations on a multiplatform computing grid.

ABSTRACT

We present the concept of the SOMA workflow developed at the Finnish IT Center for Science CSC. The SOMA workflow unites multiplatform UNIX/LINUX computing resources and third-party software for calculating molecular structure and properties. The presented workflow components consist of the computing program XML descriptions, the core workflow program Grape, the toolkit for parsing program input and output, and the extranet interface. The program Grape and the developed XML descriptions of scientific programs allow researchers to link molecular modeling software into highly sophisticated computational workflows. SOMA collects the calculated data produced by the workflow and stores the computed information in the Chemical Markup Language (CML) format. The extranet interface is used for user authentication, building of the program interfaces and the workflows, and for sorting, filtering, and visualizing the results.