Location: Metabolic Component Library @ 51fdf06899b4 / components.vm

Author:
Matthias K?nig <matthias.koenig@charite.de>
Date:
2013-05-17 15:08:43+02:00
Desc:
HTML Documentation updated.
Permanent Source URI:
http://models.cellml.org/w/matthiaskoenig/MetabolicComponentLibrary/rawfile/51fdf06899b48001d9c282b8c32eeace8e8ea6a0/components.vm

Metabolic Component Library for CellML

Matthias Koenig [1] & Randall Britten [2]
[1] Charite Berlin, matthias.koenig@charite.de
[2] Auckland Bioengineering Institute

Implementation of standardized reaction kinetics in CellML for reuse in metabolic models. The library covers the metabolic function definitions for processes from COPASI 4.8 (Bulid 35).

Naming Conventions

Substrate is named S (S1, S2, ... in case of multiple substrates)
Products is named P (P1, P2, ... in case of multiple productes)
Inhibitor is named I (I1, I2, ...)
Activator is named A (A1, A2, ...)
Modifier is named M (M1, M2, ...)
Km values are subscripted with the respective substrates or products (P -> Km_P, S -> Km_S, P1 -> Km_P1, ...)
Analog convention for inhibition constants Ki and activation constants Ka.

Units

Time: second
Volume Unit: liter
Quantity Unit: mmol
#* 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. *#

Components

#foreach( $c in $cSet )

$c.getName()

#foreach ( $var in $c.getVariablesFromKineticsComponent() ) $var
#end Validation Errors: $c.getNValidationErrors()
CellML
$c.getName()
#foreach( $m in $c.getSBGNSet()) $m ${m}  #end

#end