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

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.

Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry.

MS-based proteomics and metabolomics are rapidly evolving research fields driven by the development of novel instruments, experimental approaches, and analysis methods. Monolithic analysis tools perform well on single tasks but lack the flexibility to cope with the constantly changing requirements and experimental setups. Workflow systems, which combine small processing tools into complex analysis pipelines, allow custom-tailored and flexible data-processing workflows that can be published or shared with collaborators.

KNIME-CDK: Workflow-driven cheminformatics.

Background: Cheminformaticians have to routinely process and analyse libraries of small molecules. Among other things, that includes the standardization of molecules, calculation of various descriptors, visualisation of molecular structures, and downstream analysis. For this purpose, scientific workflow platforms such as the Konstanz Information Miner can be used if provided with the right plug-in.

Extending KNIME for next-generation sequencing data analysis.

Summary: KNIME (Konstanz Information Miner) is a user-friendly and comprehensive open-source data integration, processing, analysis and exploration platform. We present here new functionality and workflows that open the door to performing next-generation sequencing analysis using the KNIME framework.

Availability: All sources and compiled code are available via the KNIME update mechanism.