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Hello ... there were a couple of typo's in the SBML ... for a corrected
version try the one below. Please keep in mind that id's in SBML should
match the regular expression: (_|[a-z]|[A-Z])(_|[a-z]|[A-Z]|[0-9]). In
other words, x1' is not a valid identifier. Other than that, you had a
space missing after the version attribute, before the namespace
declaration ... oh and you are not allowed to define an empty list of
reactants, just leave it out ...

In any case. SBML is not meant to be written by hand ... there are many
tools out there that can help with that ...

Cheers
Frank

<?xml version="1.0" encoding="UTF-8"?>
<sbml level="2" version="1"
xmlns="http://www.sbml.org/sbml/level2"><model name
="SingleCompartmentSystem" >
<listOfCompartments>
<compartment id="one"/>
</listOfCompartments>
<listOfSpecies>
<species compartment="one" id="x1" />
</listOfSpecies>
<listOfReactions>
<reaction id="waterlevel">
<listOfProducts>
<speciesReference species="x1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<apply>
<times/>
<ci> k </ci>
<ci> x1 </ci>
</apply>
</apply>
</math>
<listOfParameters>
<parameter id="k"/>
<parameter id="u"/>
<parameter id="x1"/>
</listOfParameters>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

P.S: the Validator under http://sys-bio.org/Validate will give you a
textbox, so you could fiddle with your xml in there until it passes
validation ...

> -----Original Message-----
> From: sbml-discuss-bounces@caltech.edu [mailto:sbml-discuss-
> bounces@caltech.edu] On Behalf Of Delboy
> Sent: Monday, March 05, 2007 10:00 AM
> To: sbml-discuss@caltech.edu
> Subject: [sbml-discuss] Handwritten sbml model. Please look.
>
>
> Hi, I have a model described below. I've tried writing it out by hand
> in sbml xml. Could you take a look and tell me whats wrong with it?
>
> The model is one of a single water tank(One), with an input(u) and an
> output(k*x1) of water.
>
>
>
> Input: u --> Tank:One --> Output: k*x1
>
>
>
> The equation to measure the level of water in the tank is:
>
>
>
> x1' = u - k * x1.
>
>
>
> Heres the xml i've got so far.
>
>
>
>
>
> <?xml version="1.0" encoding="UTF-8"?>
>
> <sbml level="2"
> version="2"xmlns="http://www.sbml.org/sbml/level2/version2">
>
> <model name="SingleCompartmentSystem">
> <listOfCompartments>
> <compartment id="one"/>
> </listOfCompartments>
> <listOfSpecies>
> <species compartment="one" id="x1'" />
> </listOfSpecies>
> <listOfReactions>
> <reaction id="waterlevel">
> <listOfReactants>
> </listOfReactants>
> <listOfProducts>
> <speciesReference species="x1'"
> </listOfProducts>
> <kineticLaw>
> <math xmls="http://www.w3.org/1998/Math/MathML">
> <apply>
> <minus/>
> <apply>
> <times/>
> <ci> k </ci>
> <ci> x1 </ci>
> </apply>
> </apply>
> </math>
> <listOfParameter>
> <parameter id="k"/>
> <parameter id="u"/>
> <parameter id="x1"/>
> </listOfParameters>
> <kineticLaw>
> </reaction>
> </listOfReactions>
> </model>
> </sbml>
>
>
> Thanks for any help.
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