This project contains code for PhysiCell (based on version 1.6.0), with edits to begin incorporating MaBoSS boolean networks into each cell.
The edits include (or, will include) a new /subcellular directory where we will compile the MaBoSS files (and perhaps build a MaBoSS library):
~/git/PhysiCell_MaBoSS/subcellular/MaBoSS/engine/src$
- additions to
class Molecularin/core/PhysiCell_phenotype.hwith the MaBoSS/boolean network model for a cell. - additions
/core/PhysiCell_cell_container.cppwhere the subcellular model is solved. - additions
/custom_modules/<custom_code>.cppwhere the subcellular model is referenced by each cell.
If you plan to develop code for this repo: fork it, make edits in the dev branch, and submit pull requests to dev.
On macOS, I build using a brew-install g++ (which is OpenMP-enabled, which PhysiCell requires) as follows:
~/git/PhysiCell_MaBoSS/subcellular/MaBoSS/engine/src$ make -f Makefile.maboss
g++-9 -O2 -Wall -DMAXNODES=64 -std=c++11 -c MaBoSS.cc -o MaBoSS.o
MaBoSS.cc: In function 'int main(int, char**)':
MaBoSS.cc:302:23: warning: 'start_time' may be used uninitialized in this function [-Wmaybe-uninitialized]
302 | runconfig->display(network, start_time, end_time, mabest, *output_run);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MaBoSS.cc:302:23: warning: 'end_time' may be used uninitialized in this function [-Wmaybe-uninitialized]
g++-9 -O2 -Wall -DMAXNODES=64 -std=c++11 -c MaBEstEngine.cc -o MaBEstEngine.o
g++-9 -O2 -Wall -DMAXNODES=64 -std=c++11 -c Cumulator.cc -o Cumulator.o
g++-9 -O2 -Wall -DMAXNODES=64 -std=c++11 -c ProbaDist.cc -o ProbaDist.o
g++-9 -O2 -Wall -DMAXNODES=64 -std=c++11 -c BooleanNetwork.cc -o BooleanNetwork.o
flex -t BooleanGrammar.l | sed -e 's/yy/CTBNDL/g' -e 's/register //g' > lex.CTBNDL.cc
bison -v BooleanGrammar.y
sed -e 's/yy/CTBNDL/g' -e 's/register //g' BooleanGrammar.tab.c > BooleanGrammar.cc
g++-9 -O2 -Wall -DMAXNODES=64 -std=c++11 -c BooleanGrammar.cc -o BooleanGrammar.o
flex -t RunConfigGrammar.l | sed -e 's/yy/RC/g' -e 's/register //g' > lex.RC.cc
bison -v RunConfigGrammar.y
sed -e 's/yy/RC/g' -e 's/register //g' RunConfigGrammar.tab.c > RunConfigGrammar.cc
g++-9 -O2 -Wall -DMAXNODES=64 -std=c++11 -c RunConfigGrammar.cc -o RunConfigGrammar.o
g++-9 -O2 -Wall -DMAXNODES=64 -std=c++11 -c RunConfig.cc -o RunConfig.o
g++-9 -O2 -Wall -DMAXNODES=64 -std=c++11 -c LogicalExprGen.cc -o LogicalExprGen.o
g++-9 -o MaBoSS MaBoSS.o MaBEstEngine.o Cumulator.o ProbaDist.o BooleanNetwork.o BooleanGrammar.o RunConfigGrammar.o RunConfig.o LogicalExprGen.o -lpthread
~/git/PhysiCell_MaBoSS/subcellular/MaBoSS/engine/src$
On Windows/MinGW, I build MaBoSS in a Command Prompt shell:
C:\Users\heiland\git\PhysiCell_MaBoSS\subcellular\MaBoSS\engine\src>make
make -f Makefile.maboss init
make[1]: Entering directory `/c/Users/heiland/git/PhysiCell_MaBoSS/subcellular/MaBoSS/engine/src'
make[1]: Leaving directory `/c/Users/heiland/git/PhysiCell_MaBoSS/subcellular/MaBoSS/engine/src'
make -f Makefile.maboss depend
make[1]: Entering directory `/c/Users/heiland/git/PhysiCell_MaBoSS/subcellular/MaBoSS/engine/src'
make[1]: Leaving directory `/c/Users/heiland/git/PhysiCell_MaBoSS/subcellular/MaBoSS/engine/src'
make -f Makefile.maboss all
make[1]: Entering directory `/c/Users/heiland/git/PhysiCell_MaBoSS/subcellular/MaBoSS/engine/src'
g++ -O2 -Wall -DMAXNODES=64 -std=c++11 -c MaBoSS.cc -o MaBoSS.o
MaBoSS.cc: In function 'int main(int, char**)':
MaBoSS.cc:302:23: warning: 'start_time' may be used uninitialized in this function [-Wmaybe-uninitialized]
runconfig->display(network, start_time, end_time, mabest, *output_run);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MaBoSS.cc:302:23: warning: 'end_time' may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -O2 -Wall -DMAXNODES=64 -std=c++11 -c MaBEstEngine.cc -o MaBEstEngine.o
g++ -O2 -Wall -DMAXNODES=64 -std=c++11 -c Cumulator.cc -o Cumulator.o
g++ -O2 -Wall -DMAXNODES=64 -std=c++11 -c ProbaDist.cc -o ProbaDist.o
g++ -O2 -Wall -DMAXNODES=64 -std=c++11 -c BooleanNetwork.cc -o BooleanNetwork.o
g++ -O2 -Wall -DMAXNODES=64 -std=c++11 -c BooleanGrammar.cc -o BooleanGrammar.o
g++ -O2 -Wall -DMAXNODES=64 -std=c++11 -c RunConfigGrammar.cc -o RunConfigGrammar.o
g++ -O2 -Wall -DMAXNODES=64 -std=c++11 -c RunConfig.cc -o RunConfig.o
g++ -O2 -Wall -DMAXNODES=64 -std=c++11 -c LogicalExprGen.cc -o LogicalExprGen.o
g++ -o MaBoSS MaBoSS.o MaBEstEngine.o Cumulator.o ProbaDist.o BooleanNetwork.o BooleanGrammar.o RunConfigGrammar.o RunConfig.o LogicalExprGen.o -lpthread
make[1]: Leaving directory `/c/Users/heiland/git/PhysiCell_MaBoSS/subcellular/MaBoSS/engine/src'
C:\Users\heiland\git\PhysiCell_MaBoSS\subcellular\MaBoSS\engine\src>
We have not yet added the functionality of MaBoSS into PhysiCell, only commented out "hooks" (rf. bullets at the top of this README).
The basic PhysiCell "model" defined in /custom_modules/custom_bn* is a simple functional test case of just 3 cells that are motile and travel horizontally. It is what we used for an earlier SBML (of ODEs) subcellular model.
~/git/PhysiCell_MaBoSS$ make
...
~/git/PhysiCell_MaBoSS$ bn
...
~/git/PhysiCell_MaBoSS$ cd output
~/git/PhysiCell_MaBoSS/output$ python anim_svg.py