Model : curve_types_model

Creator
Matthias, Koenig, Humboldt-University Berlin, Institute for Theoretical Biology, koenigmx@hu-berlin.de
Created: 1900-01-01 00:00
Modified: 1900-01-01 00:00

id	curve_types_model `meta_curve_types_model`
name	curve_types_model
time	min
substance	mmole
extent	mmole
volume	litre
area
length	metre

L3V1 comp-V1

Koenig sbmlutils example

Description

Single reaction.

The content of this model has been carefully created in a manual research effort.

This file has been created by Matthias Koenig.

Terms of use

Redistribution and use of any part of this model, with or without modification, are permitted provided that the following conditions are met:

Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
Redistributions in a different form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

type	Ports [5]	name	referenced element	unit ref	sbo
Port	min_port `min_port` min_port <comp:port metaid="min_port" sboTerm="SBO:0000599" comp:unitRef="min" comp:id="min_port" comp:name="min_port"/>	min_port	`UnitDefinition: min`	min	SBO:0000599
Port	mmole_port `mmole_port` mmole_port <comp:port metaid="mmole_port" sboTerm="SBO:0000599" comp:unitRef="mmole" comp:id="mmole_port" comp:name="mmole_port"/>	mmole_port	`UnitDefinition: mmole`	mmole	SBO:0000599
Port	mM_port `mM_port` mM_port <comp:port metaid="mM_port" sboTerm="SBO:0000599" comp:unitRef="mM" comp:id="mM_port" comp:name="mM_port"/>	mM_port	`UnitDefinition: mM`	mM	SBO:0000599
Port	mmole_per_min_port `mmole_per_min_port` mmole_per_min_port <comp:port metaid="mmole_per_min_port" sboTerm="SBO:0000599" comp:unitRef="mmole_per_min" comp:id="mmole_per_min_port" comp:name="mmole_per_min_port"/>	mmole_per_min_port	`UnitDefinition: mmole_per_min`	mmole_per_min	SBO:0000599
Port	litre_per_min_port `litre_per_min_port` litre_per_min_port <comp:port metaid="litre_per_min_port" sboTerm="SBO:0000599" comp:unitRef="litre_per_min" comp:id="litre_per_min_port" comp:name="litre_per_min_port"/>	litre_per_min_port	`UnitDefinition: litre_per_min`	litre_per_min	SBO:0000599

type	UnitDefinitions [5]	units
UnitDefinition	min min <unitDefinition id="min"> <listOfUnits> <unit kind="second" exponent="1" scale="0" multiplier="60"/> </listOfUnits> </unitDefinition>	$60 s$
UnitDefinition	mmole mmole <unitDefinition id="mmole"> <listOfUnits> <unit kind="mole" exponent="1" scale="-3" multiplier="1"/> </listOfUnits> </unitDefinition>	$103 mole$
UnitDefinition	mM mM <unitDefinition id="mM"> <listOfUnits> <unit kind="mole" exponent="1" scale="-3" multiplier="1"/> <unit kind="litre" exponent="-1" scale="0" multiplier="1"/> </listOfUnits> </unitDefinition>	$103 mole litre$
UnitDefinition	mmole_per_min mmole_per_min <unitDefinition id="mmole_per_min"> <listOfUnits> <unit kind="mole" exponent="1" scale="-3" multiplier="1"/> <unit kind="second" exponent="-1" scale="0" multiplier="60"/> </listOfUnits> </unitDefinition>	$103 mole 60 s$
UnitDefinition	litre_per_min litre_per_min <unitDefinition id="litre_per_min"> <listOfUnits> <unit kind="litre" exponent="1" scale="0" multiplier="1"/> <unit kind="second" exponent="-1" scale="0" multiplier="60"/> </listOfUnits> </unitDefinition>	$litre 60 s$

type	Compartments [1]	name	size	constant	spatial dimensions	units	derived units	sbo	cvterm
Compartment	cell cell <compartment id="cell" name="cell" spatialDimensions="3" size="1" units="litre" constant="true"/>	cell	1.0	T	3	litre	$litre$

type	Species [3]	compartment	hasOnlySubstanceUnits	boundaryCondition	constant	initialConcentration	units	substanceUnits	derivedUnits	sbo
Species	S1 S1 <species sboTerm="SBO:0000247" id="S1" compartment="cell" initialConcentration="10" substanceUnits="mmole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>	cell	F	F	F	10.0	mmole	mmole	$103 mole litre$	SBO:0000247
Species	S2 S2 <species sboTerm="SBO:0000247" id="S2" compartment="cell" initialConcentration="5" substanceUnits="mmole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>	cell	F	F	F	5.0	mmole	mmole	$103 mole litre$	SBO:0000247
Species	S3 S3 <species sboTerm="SBO:0000247" id="S3" compartment="cell" initialConcentration="0" substanceUnits="mmole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>	cell	F	F	F	0.0	mmole	mmole	$103 mole litre$	SBO:0000247

type	Parameters [1]	name	constant	value	unit	derived unit	sbo	cvterm	uncertainties
Parameter	k k <parameter id="k" value="0.3" units="litre_per_min" constant="true"/>		T	0.3	litre_per_min	$litre 60 s$

type	Reactions [2]	name		equation	modifiers	kinetic law	derived units	sbo	cvterm
Reaction	_J0 _J0 <reaction id="_J0" reversible="false" fast="false" compartment="cell"> <listOfReactants> <speciesReference species="S1" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="S2" stoichiometry="1" constant="true"/> </listOfProducts> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> k </ci> <ci> S1 </ci> </apply> </math> </kineticLaw> </reaction>		➞	S1 ➞ S2		$k S1$	$103 mole 60 s$
Reaction	_J1 _J1 <reaction id="_J1" reversible="false" fast="false" compartment="cell"> <listOfReactants> <speciesReference species="S2" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="S3" stoichiometry="1" constant="true"/> </listOfProducts> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> k </ci> <ci> S2 </ci> </apply> </math> </kineticLaw> </reaction>		➞	S2 ➞ S3		$k S2$	$103 mole 60 s$