systemic-immune-response

Integrate immune response (ODE) with PhysiCell

• to test without the SBML model, compile with make and run COVID19 to see the dummy lymphatic_main_model being invoked. Files of interest are custom_modules/lymphatic_submodel.{h,cpp} and main.cpp.

• to test with the SBML model, compile with make -f Make-sbml, have your relevant env var pointing to the Roadrunner libs you installed, and run COVID19_sbml config_with_sbml.xml. Note that Make-sbml defines the compiler macro -D LIBROADRUNNER which allows for conditional compilation of #ifdef LIBROADRUNNER code (rf. intracellular/PhysiCell_intracellular.h). However, we still need to make meaningful mappings between the SBML species and PhysiCell cells' custom data and, of course, do something meaningful in the custom code.

Changes from original 3.2 code (and latest immune-response model)

• added custom_modules/lymphatic_submodel.{h,cpp}

Not yet using, but also:

• added beta/setup_libroadrunner.py
• added intracellular/PhysiCell_intracellular.h
• added std::string sbml_filename; into class Cell_Definition (in core/PhysiCell_cell.h)
• parse <molecular> XML in core/PhysiCell_cell.cpp
• incorporate intracellular (SBML, libRoadrunner) info into custom.{h,cpp}
  • see assign_SBML_model( Cell* pC ) in custom.cpp
  • see extra code in create_cell_types( void ) where we obtain the desired SBML species' indices.
• added Make-sbml

Immune response ODE model

Tarun provided a Tellurium version (tellurium_ODE_model) of the immune response ODE model. We converted it to an Antimony file (ode_model.ant), loaded it into Tellurium, and generated a SBML model (immune_response.xml).

In [1]: import tellurium as te

In [2]: r = te.loadAntimonyModel('ode_model.ant')
Warning: species 'D' has neither initial amount nor concentration set.  Setting initial concentration to 0.0
Warning: species 'Ev' has neither initial amount nor concentration set.  Setting initial concentration to 0.0
Warning: species 'Tc' has neither initial amount nor concentration set.  Setting initial concentration to 0.0
Warning: species 'Da' has neither initial amount nor concentration set.  Setting initial concentration to 0.0
Warning: species 'Dm' has neither initial amount nor concentration set.  Setting initial concentration to 0.0
Warning: species 'B' has neither initial amount nor concentration set.  Setting initial concentration to 0.0
Warning: species 'Pss' has neither initial amount nor concentration set.  Setting initial concentration to 0.0
Warning: species 'Psn' has neither initial amount nor concentration set.  Setting initial concentration to 0.0
Warning: species 'Pls' has neither initial amount nor concentration set.  Setting initial concentration to 0.0
Warning: species 'Pln' has neither initial amount nor concentration set.  Setting initial concentration to 0.0
Warning: species 'sIgM' has neither initial amount nor concentration set.  Setting initial concentration to 0.0
Warning: species 'nIgM' has neither initial amount nor concentration set.  Setting initial concentration to 0.0
Warning: species 'sIgG' has neither initial amount nor concentration set.  Setting initial concentration to 0.0
Warning: species 'nIgG' has neither initial amount nor concentration set.  Setting initial concentration to 0.0


In [3]: print(r.getCurrentSBML())
# --> outputs SBML which we copy/paste into immune_response.xml

COPASI

Using COPASI, one can File -> Import SBML the model and examine it in various ways.