Digitized version of the Roche Applied Science "Biochemical Pathways" wall chart. The map, linked to relevant ENZYME database entries, can be browsed online, and keyword searches are available.
The efmtool computes elementary flux modes (EFMs) of metabolic networks. It is implemented in Java and has been integrated into MATLAB (see http://www.mathworks.com).
EFM computation is a special case of extreme ray enumeration of polyhedral cones.
ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.
MetaNetX.org allows to access, analyse and manipulate genome-scale metabolic networks as well as biochemical pathways. It consistently integrates data from various public resources and makes the data accessible in a standardized format using a common namespace. Models can be interactively compared, analysed (e.g. detection of dead-end metabolites/reactions, flux balance analysis or simulation of reaction/gene knockouts), manipulated and exported. Users can upload their own metabolic models.
Rhea is a comprehensive and non-redundant resource of expert curated biochemical reactions described using species from ChEBI (Chemical Entities of Biological Interest). Rhea has been designed for the functional annotation of enzymes and the description, analysis and reconciliation of genome-scale metabolic networks.
Rhea reactions are extensively curated with links to source literature and are mapped to other resources such as SwissLipids, MetaNetX, Reactome, BioCyc, KEGG and UniPathway.
SwissLipids is a comprehensive reference database that links mass spectrometry-based lipid identifications to curated knowledge of lipid structures, metabolic reactions, enzymes and interacting proteins. It features approximately 500,000 lipid structures from more than 115 lipid classes and over 3,000 enzymatic reactions and 800 proteins.
An easy-to-use open source software package and API for systems biologists. It performs multiple analyses on stoichiometric reaction networks and other biological networks, and can be easily extended via a number of plugins.
UniPathway is a curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase.