Monodomain example cellml file

[ssat335]

I was trying to validate the n98.xml file at ~/examples/Bioelectrics/Monodomain/PythonChasteModel/n98.xml using https://chaste.cs.ox.ac.uk/cellml/ web-based cellml validator

The validator showed the following errors:

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• /var/www/cellml/%3Cfdopen%3E:515:0:ERROR:RELAXNGV:RELAXNG_ERR_INVALIDATTR: Invalid attribute id for element math
• :0:0:ERROR:RELAXNGV:RELAXNG_ERR_INTEREXTRA: Extra element math in interleave
• /var/www/cellml/%3Cfdopen%3E:515:0:ERROR:RELAXNGV:RELAXNG_ERR_CONTENTVALID: Element component failed to validate content
• :0:0:ERROR:RELAXNGV:RELAXNG_ERR_INTEREXTRA: Extra element component in interleave
• /var/www/cellml/%3Cfdopen%3E:446:0:ERROR:RELAXNGV:RELAXNG_ERR_CONTENTVALID: Element model failed to validate content

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I also tried to remove the comments from the equations and then rerun the validator and it showed the following unit mismatch errors:

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• Error checking units: Operator exp requires operands to be dimensionless; operand 1 has units mV
• Context: 2nd expression in the 1st math element in component fast_sodium_current_m_gate
• XPath: /[1]/[45]/[6]/[2]/[3]/[2]/[1]/[3]/*[3]
• Error checking units: Operator exp requires operands to be dimensionless; operand 1 has units mV
• Context: 3rd expression in the 1st math element in component fast_sodium_current_m_gate
• XPath: /[1]/[45]/[6]/[3]/[3]/[3]
• Error checking units: Operator exp requires operands to be dimensionless; operand 1 has units mV
• Context: 1st expression in the 1st math element in component fast_sodium_current_h_gate
• XPath: /[1]/[46]/[4]/[1]/[3]/[2]/*[3]
• Error checking units: Operator exp requires operands to be dimensionless; operand 1 has units 'K nC per kelvin per pJ'
• Context: 1st expression in the 1st math element in component L_type_Ca_channel
• XPath: /[1]/[49]/[30]/[1]/[3]/[3]/[2]/[3]
• Error checking units: Operator exp requires operands to be dimensionless; operand 1 has units 'K nC per kelvin per pJ'
• Context: 2nd expression in the 1st math element in component L_type_Ca_channel
• XPath: /[1]/[49]/[30]/[2]/[3]/[8]/[2]/[3]
• Error checking units: Operator exp requires operands to be dimensionless; operand 1 has units 'K nC per kelvin per pJ'
• Context: 3rd expression in the 1st math element in component L_type_Ca_channel
• XPath: /[1]/[49]/[30]/[3]/[3]/[8]/[2]/[3]
• Error checking units: Operator exp requires operands to be dimensionless; operand 1 has units 'K nC per kelvin per pJ'
• Context: 4th expression in the 1st math element in component L_type_Ca_channel
• XPath: /[1]/[49]/[30]/[4]/[3]/[3]/[2]/[3]
• ...... _

[nickerso]

I'd suggest using OpenCOR to validate CellML models as the pyCML that Chaste uses is not (yet) going to handle CellML 1.1 models and some of the extra features that are generally found in models on PMR (such as id attributes on math in this case, which is actually valid).

Units checking is currently not easy and not always accurate. OpenCOR will do some checking, but results always need to be treated sceptically :)