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Shadrin


Posts: 6
Registered:
May 2010
Re: Definition of units 30 Jun '10 03:39 Go to previous messageGo to previous message

I have one more technical question. It is not actually about definition of units, but it seems unreasonable to create separate topic for it. Let's consider xml description of test case 182, level 1 version 2:
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level1" level="1" version="2">
<model name="case00182">
<listOfCompartments>
<compartment name="AssignedName"/>
</listOfCompartments>
<listOfParameters>
<parameter name="S1" value="0.5"/>
<parameter name="S2" value="0.5"/>
<parameter name="k1" value="1"/>
<parameter name="k2" value="0.8"/>
</listOfParameters>
<listOfRules>
<algebraicRule formula="-1 * k1 + S1 + S2"/>
<parameterRule formula="k2 * S2" type="rate" name="S1"/>
</listOfRules>
</model>
</sbml>

From the file 00182-model.m it is seen that parameter k1 is constant and S2 parameter is variable, but it is not clear from xml. Doing automatic simulation we should relay, as I understand, only on xml file. The question is: how can we distinguish this parameters using only xml description? (Because, without knowing it we have here system of 2 equations with 3 variables....) Or may be this description is incorrect?

P.S. To make correct representation of this model we can rewrite listOfRules block:
<listOfRules>
<parameterRule formula="-1* S2 + k1" type="scalar" name="S2"/>
<parameterRule formula="k2 * S2" type="rate" name="S1"/>
</ ListOfRules>

      

SubjectPosterDate
Read Message   Definition of units Shadrin24 May '10 03:03
Read Message   Re: Definition of units Sarah Keating24 May '10 11:03
Read Message   Re: Definition of units  Shadrin30 Jun '10 03:39
Read Message   Re: Definition of units myers30 Jun '10 10:57
Read Message   Re: Definition of units Andreas Dräger24 Aug '10 06:49
Read Message   Re: Definition of units Sarah Keating26 Aug '10 01:41
Read Message   Re: Definition of units Andreas Dräger26 Aug '10 04:45
Read Message   Re: Definition of units Sarah Keating26 Aug '10 08:08
Read Message   Re: Definition of units Sven Sahle26 Aug '10 08:18
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