new format for Raia

[LeonardSchmiester]

No description provided.

[LeonardSchmiester]

sigmas are not included yet

[dweindl]

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'sigma_CD274mRNA' should have a constant value of 'false'.

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'sigma_IL13_cell' should have a constant value of 'false'.

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'sigma_RecSurf' should have a constant value of 'false'.

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'sigma_SOCS3' should have a constant value of 'false'.

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'sigma_SOCS3mRNA' should have a constant value of 'false'.

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'sigma_pIL4Ra' should have a constant value of 'false'.

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'sigma_pJAK2' should have a constant value of 'false'.

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'sigma_pSTAT5' should have a constant value of 'false'.

[dweindl]

Observable scaling_observable_IL13_cell * (IL13_Rec + IL13_DecoyR + p_IL13_Rec + p_IL13_Rec_i) does not have any parameter to override, but has observableParameters = scaling_IL13_cell

[paulstapor]

This model has observable dependent noise Parameters. Has to be fixed in AMICI, see AMICI-dev/AMICI#609

[dweindl]

In the parameter table there are scaling parameters suffixed with '_obs', e.g. scale_pIL4Ra_obs. In the measurement file they are not (e.g. scaling_pIL4Ra)

[LeonardSchmiester]

fixed by commit f2c64bb

[erikadudki]

While adding the visualization table and comparing the visualization to the publication, it occurs that some datasets are missing (in the measurement and simulation files) ? Is this on purpose?
e.g. For

• pIL4Ra, pJAK2, pSTAT5: data1, data4
• RecSurf: data2
• SOCS3: data3
• CD274mRNA: data2, data4

Furthermore, for pIL4Ra the simulation for model1_data2 quite underestimates the data, don't know if we want to have a look into that (but I think in the publication this case is similarly underestimated)