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#115 Models can be underdetermined and unsimulatable
closed
1
2014-06-10
2008-02-13
No
The L2 specs never mention that having a model be undetermined or unsimulatable is permitted. This should be mentioned somewhere. The spec currently only talks about how overdetermined models are disallowed, but never says anything about the other direction (i.e., incomplete models).
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I agree with the proposed change and that it should be done.
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I think this is so basic that we overlooked to state it. After all the following is said to be legal SBML
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
<model id="My Model">
</model>
</sbml>
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Stefan, I think this is not an underdetermined model. The following is:
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2"
version="3">
<model id="My Model">
<listOfCompartments>
<compartment id="X" />
</listOfCompartments>
<listOfSpecies>
<species id="A" compartment="X"/>
</listOfSpecies>
<listOfReactions>
<reaction>
<listOfProducts>
<speciesReference species="A" />
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> k </ci>
</math>
<listOfParameters>
<parameter id="k" />
</listOfParameters>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
And this should be allowed. It is not MIRIAM compliant, but it is correct SBML.
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I am accepting this issue as valid.
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I agree with the proposed change and that it should be done.
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I agree with the proposed change and that it should be done.
I'm reducing the priority of this because it's not a critical change.
I agree with the proposed change and that it should be done.
We should perhaps state that there are different kinds of underdetermined models. One kind is explicitly missing parts (like in Nicolas´ exmample), like missing numbers or a missing kinetic law. The other kind would be missing structural information, e.g. if you have an algebraic rule A+B=1 and nothing in the model tells you wether A should be calculated from B or the other way round (if they both have const=false and boundaryCondition=true).
I agree with the proposed change and that it should be done.
We should perhaps state that there are different kinds of underdetermined models. One kind is explicitly missing parts (like in Nicolas´ exmample), like missing numbers or a missing kinetic law. The other kind would be missing structural information, e.g. if you have an algebraic rule A+B=1 and nothing in the model tells you wether A should be calculated from B or the other way round (if they both have const=false and boundaryCondition=true).
We should perhaps state that there are different kinds of underdetermined models. One kind is explicitly missing parts (like in Nicolas´ exmample), like missing numbers or a missing kinetic law. The other kind would be missing structural information, e.g. if you have an algebraic rule A+B=1 and nothing in the model tells you wether A should be calculated from B or the other way round (if they both have const=false and boundaryCondition=true).
I agree with the proposed change and that it should be done.
We should perhaps state that there are different kinds of underdetermined models. One kind is explicitly missing parts (like in Nicolas´ exmample), like missing numbers or a missing kinetic law. The other kind would be missing structural information, e.g. if you have an algebraic rule A+B=1 and nothing in the model tells you wether A should be calculated from B or the other way round (if they both have const=false and boundaryCondition=true).
I agree with the proposed change and that it should be done.