The sim.sedml of combined models stores parameters by their id + an index referencing the sub-model it belongs to. While this workaround is necessary because the Java Object "Parameter" only allows SBML Sid's, in the FSKX file the entry should be a URI. This would lead to minimal changes for the FSK guidance document and only affect combined models.
we should store the information as:
<model id="defaultSimulation" name="" language="https://iana.org/assignments/mediatypes/text/x-r" source="./model.r"><listOfChanges><changeAttribute newValue="33" target="submodel1/x" /><changeAttribute newValue="3.6" target="submodel2/y" /><changeAttribute newValue="2" target="submodel2/x" />
The changes would be limited to the Writer and Reader.
It needs to be tested if there is anything preventing the use of URI's in the CombineArchive or if there is a hard focus on SBML Sid's as well.
The sim.sedml of combined models stores parameters by their id + an index referencing the sub-model it belongs to. While this workaround is necessary because the Java Object "Parameter" only allows SBML Sid's, in the FSKX file the entry should be a URI. This would lead to minimal changes for the FSK guidance document and only affect combined models.
Instead of
<model id="defaultSimulation" name="" language="https://iana.org/assignments/mediatypes/text/x-r" source="./model.r"><listOfChanges><changeAttribute newValue="33" target="x1" /><changeAttribute newValue="3.6" target="y1" /><changeAttribute newValue="2" target="x2" />we should store the information as:
<model id="defaultSimulation" name="" language="https://iana.org/assignments/mediatypes/text/x-r" source="./model.r"><listOfChanges><changeAttribute newValue="33" target="submodel1/x" /><changeAttribute newValue="3.6" target="submodel2/y" /><changeAttribute newValue="2" target="submodel2/x" />The changes would be limited to the Writer and Reader.
It needs to be tested if there is anything preventing the use of URI's in the CombineArchive or if there is a hard focus on SBML Sid's as well.