KIMBLE: A versatile visual NMR metabolomics workbench in KNIME

Highlights: • KIMBLE is a novel KNIME-based NMR metabolomics workflow platform. • KIMBLE supports both targeted and untargeted NMR metabolomics. • KIMBLE can be extended and adapted to specific projects and biofluids. • KIMBLE is self-documenting and combines data, algorithms and software in one file. The problem of reproducibility of scientific research is a serious issue in biomedical sciences. In addition to experimental repeatability, limiting the (pre-) analytical variance is also essential. To address this problem in the field of metabolomics, we have designed KIMBLE, the KNIME-based Integrated MetaBoLomics Environment, a novel platform for the processing and analysis of NMR metabolomics data. It consists of an elaborate NMR metabolomics workflow in the KNIME workflow management system that handles both targeted and untargeted metabolomics. The workflow provides a self-documenting way of transforming raw time-domain NMR data into metabolic insights. Parameters for the quantification of a number of interesting metabolites in urine are included in the workflow, and several useful statistical analysis and visualization tools are incorporated as well. The workflow comes with an interesting sports-induced ketosis dataset so that new users can easily get acquainted with the platform. The user is free to adapt and extend the workflow to his or her personal needs. The KIMBLE workflow, the KNIME software and all the required libraries are installed in a VirtualBox virtual machine that allows for facile installation and use by non-experts.