CellNetAnalyzer - A toolbox for analyzing structure and function of metabolic, signaling, and regulatory networks
CellNetAnalyzer for python (CNApy) - an advanced graphical user interface for exploration and computational analysis of metabolic network models 
circlize - visualization of huge amounts of information
Cloud-based data analysis in metabolomics (PhenomeNal)
e!DAL-PGP - Plant Genomics and Phenomics Research Data Repository
Fusion - a platform for integrative analysis of omics data
Goslin - Tool for lipid shorthand name parsing and normalization
iPath - visualization and analysis of cellular pathways
KNIME - A modern platform for data analytics
LipidCreator - Computing precursor and fragment masses / formulas for lipids for targeted lipidomics
LipidXplorer - Identification and quantification of lipids within MS measurements for shotgun lipidomics
LUX Score - Tool for the comprehensive comparison of lipidomes of different origins
MapMan - Map Gene / Protein / Metabolite Data on biological Pathways
MassBank - repository of mass spectra of small chemical compounds
Mechismo - impact predictions of genetic variants on biomolecular function
MeltDB - framework for the analysis of for raw GC- and LC-MS metabolome data sets
Metabolomics data management and deposition (MetaboLights)
MetFrag - In silico fragmentation for computer assisted identification of metabolite mass spectra
MOFA - versatile and statistically rigorous generalization of PCA to multi-omics data
OpenMS - A C++ library for LC/MS data management and analyses

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