Chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery.

ABSTRACT:

Background

Analyzing files containing chemical information is at the core of cheminformatics. Each analysis may require a unique workflow. This paper describes the chemalot and chemalot_knime open source packages. Chemalot is a set of command line programs with a wide range of functionalities for cheminformatics. The chemalot_knime package allows command line programs that read and write SD files from stdin and to stdout to be wrapped into KNIME nodes. The combination of chemalot and chemalot_knime not only facilitates the compilation and maintenance of sequences of command line programs but also allows KNIME workflows to take advantage of the compute power of a LINUX cluster.

Results

Use of the command line programs is demonstrated in three different workflow examples: (1)

SUBMITTER: Lee ML 

PROVIDER: S-EPMC5468363 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature