Added SBML models along with the corresponding cellular images and se…

[Medha-B]

Added 300 Spatial SBML models with corresponding cellular images and segmented ground truth images as a part of GSoC 2020 project.

[luciansmith]

Thank you so much!

There are a couple issues: One, I would go ahead and put these models in the 'Sampled Field models' directory, though keeping them in a subdirectory of their own in that directory would probably be good.

Second, I am getting a couple validation errors when spot-checking the models: you use but don't define a 'um' unit, and you define a 'spatial:numSamples3' attribute even though the model is two-dimensional. I also get warnings about units not being defined, but that's much less important. Here are the errors I get from gt1_output.xml:

---

line 10: (spatial-21407 [Error]) The value of the attribute 'spatial:unit' on a <coordinateComponent> must have a taken from the following: the identifier of
 a <unitDefinition> object in the enclosing <model,> or one of the base units in SBML.
Reference: L3V1 Spatial V1 Section
 CoordinateComponent with id 'coordx' uses a unit value of 'um' which is not a built in unit or the identifier of an existing <unitDefinition>.

line 14: (spatial-21407 [Error]) The value of the attribute 'spatial:unit' on a <coordinateComponent> must have a taken from the following: the identifier of
 a <unitDefinition> object in the enclosing <model,> or one of the base units in SBML.
Reference: L3V1 Spatial V1 Section
 CoordinateComponent with id 'coordy' uses a unit value of 'um' which is not a built in unit or the identifier of an existing <unitDefinition>.

line 46: (spatial-21651 [Error]) If the <geometry> of the <model> has exactly two <coordinateComponent> children, a <sampledField> object must define the att
ributes 'spatial:numSamples1' and 'spatial:numSamples2', and must not define the attribute 'spatial:numSamples3'.
Reference: L3V1 Spatial V1 Section
 A SampledField with id 'mySampledField' defines a numSamples3 with a value of '1', but the ListOfCoordinateComponents has exactly two children.

[lkeegan]

Here is a simple fix for the validation errors:

sed -i -e 's/spatial:unit=um/spatial:unit=length/g' gt*_output.xml
sed -i -e 's/ spatial:numSamples3=1//g' gt*_output.xml

A branch with these sed commands applied:
Medha-B/sbml-spatial-models@test_Models...lkeegan:fix_validation_errors_pr3