What is CLEML?
CLEML is short for Carbon Labeling Experiment Markup Language, a SBML dialect
format for representation and exchange of 13C metabolic flux analysis models.
CLEML extends SBML through the annotation tag, so it not only completely
compatible with SBML Level 1 and SBML Level 2,
but also fully supports carbon labeling experiment based metabolic flux analysis(13C MFA).
CLEML allows for describing a carbon labeling experiment(CLE) by defining the structure and stationary states of a metabolic system,
e.g. metabolites, reactions, carbon atom transition, flux constraints and measurement data.
As far as we know, 13C MFA is the only existing metabolic flux estimation method that is not tied
to a particular metabolic topology. In recent years, 13C MFA has become an important tool
in metabolic engineering, it allows the accurate, detailed quantification of all intracellular
fluxes in the central metabolism of a microorganism.
The description of structure and stationary states of a metabolic system possibly consists of five conponents
(In real-world model definition, some compoments may be omitted):
- Compartment: A container of finite volume for well-stirred substances in which reactions take place.
- Species: A chemical substance or entity that takes part in a reaction.
The information about species' carbon atoms (e.g., number of carbon atoms, input isotopomer fractions et al)
is stored as an annotation.
- Reaction: A statement describing some transformation, transport or binding process that can change
one or more species. Every reactant and product in reaction is annotated to specify the carbon atom transition
taking place during the biochemical reaction process.
- Constraint: A dependency assumption imposed to metabolic fluxes.
Constraint can be linear equality or inequality relationships between fluxes.
- Measurement: A partial revelation of metabolic system's stationary states by using various measurement
techniques such as nuclear magnetic resonance (NMR) and mass spectrometry (MS).
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