Location: Metabolic Component Library @ e0e2c28e2dfd / CellML-source / CellMLTools / template / components.vm

Author:
Tommy Yu <tommy.yu@auckland.ac.nz>
Date:
2015-02-12 19:28:32+13:00
Desc:
Merging to remove the extra head - Since the title is changed and in the interest of maintaining the current structure we keep it as is.
Permanent Source URI:
https://models.cellml.org/w/matthiaskoenig/MetabolicComponentLibrary/rawfile/e0e2c28e2dfdfe37ea2cae3390a6ae26c28a3393/CellML-source/CellMLTools/template/components.vm
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Metabolic Component Library(MCL)

Two of the great challenges in the mathematical modelling of biological systems are
  • the reuse of model components, thereby allowing the combination of model parts and models, and
  • the annotation of model components to ontologiesproviding additional level of information.
    • We present the Metabolic Component Library (MCL), the first library of reusable and annotated model components for the modelling of metabolic metabolic networks. MCL is implemented in CellML, an XML based markup language to store and exchange mathematical models.
    The library covers among others the full set of function definitions for processes from COPASI 4.8 (Bulid 35) as well as standard simplified kinetics like mass action kinetics.
Key features are
  • Large set of standard reaction components for metabolic modelling
  • Annotation of components to multiple ontologies
  • Usage examples and re-implemented published models
MCL was developed by Matthias König at the Charité Berlin with support from Randall Britten from the Auckland Bioengineering Institute and Maxwell Neal from the University of Washington. Charite Logo       Biomedical Health Informatics Washington Logo
Auckland Bioengineering Institute Logo
The project was funded by the Virtual Liver Network (VLN).
Please try and report any questions or problems to matthias.koenigcharite.de

Thanks and have fun
The MCL team. 		VLN Logo

Examples

Usage examples of the MCL: TODO

Annotations

All components in the SBML are annotated to the Systems Biology Ontology (SBO) and the The Ontology of Physics for Biology (OPB). The example models are furthermore annotated to biological databased like the Gene Ontology, KEGG and ChEBI.
Annotation of the metabolic components to biological ontologies was performed with SemGen developed by Dr. Maxwell Neal at the University of Washington.
The annotations are distributed in OWL format with the MCL and the MCL examples and can be read with SemGen. 		SemGen Logo

Components

Substrate(s) : S (S1, S2, ...)
Product(s) : P (P1, P2, ... )
Inhibitor(s) : I (I1, I2, ...)
Activator(s) : A (A1, A2, ...)
Modifier(s) : M (M1, M2, ...)
#* Render the HTML overview dynamically based on the defined components. Changes in the underlying definitions of the components will be directly reflected in the documentation. *# #foreach( $c in $cSet )

$c.getName()

(Validation Errors: $c.getNValidationErrors())

#foreach ( $var in $c.getVariablesFromKineticsComponent() ) $var
#end
          $c.getName()
Mechanisms
#foreach( $m in $c.getSBGNSet()) $m
#end 		#foreach( $m in $c.getSBGNSet()) ${m}    #end
#end