viral-replication-model

Integrate virus replication model (BioNetGen/SBML/ODEs) with PhysiCell.

Overview

• if you plan to use libRoadrunner as your SBML solver, you should run the script setup_libroadrunner.py in the /beta directory and follow instructions there. You may then need to edit Make-sbml (in the root, /PhysiCell directory) to have LIBRR* paths be valid.

• PhysiCell/config_with_sbml.xml is a PhysiCell configuration file that contains the basic "linkage" to the SBML model (search for "sbml" or "SBML" in it).

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

additional notes

• 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