## Building a Cellular Automaton Model Using BioFVM

**Note:** This is part of a series of “how-to” blog posts to help new users and developers of BioFVM. See below for guides to setting up a C++ compiler in Windows or OSX.

### What you’ll need

- A working C++ development environment with support for OpenMP. See these prior tutorials if you need help.
- A download of BioFVM, available at http://BioFVM.MathCancer.org and http://BioFVM.sf.net. Use Version 1.1.4 or later.
- The source code for this project (see below).

Matlab or Octave for visualization. Matlab might be available for free at your university. Octave is open source and available from a variety of sources.

### Our modeling task

We will implement a basic 3-D cellular automaton model of tumor growth in a well-mixed fluid, containing oxygen pO_{2} (mmHg) and a drug *c* (e.g., doxorubicin, μM), inspired by modeling by Alexander Anderson, Heiko Enderling, Jan Poleszczuk, Gibin Powathil, and others. (I highly suggest seeking out the sophisticated cellular automaton models at Moffitt’s Integrated Mathematical Oncology program!) This example shows you how to extend BioFVM into a new cellular automaton model. I’ll write a similar post on how to add BioFVM into an existing cellular automaton model, which you may already have available.

Tumor growth will be driven by oxygen availability. Tumor cells can be live, apoptotic (going through energy-dependent cell death, or necrotic (undergoing death from energy collapse). Drug exposure can both trigger apoptosis and inhibit cell cycling. We will model this as growth into a well-mixed fluid, with pO_{2} = 38 mmHg (about 5% oxygen: a physioxic value) and *c* = 5 μM.

### Mathematical model

As a cellular automaton model, we will divide 3-D space into a regular lattice of voxels, with length, width, and height of 15 μm. (A typical breast cancer cell has radius around 9-10 μm, giving a typical volume around 3.6×10^{3} μm^{3}. If we make each lattice site have the volume of one cell, this gives an edge length around 15 μm.)

In voxels unoccupied by cells, we approximate a well-mixed fluid with Dirichlet nodes, setting pO_{2} = 38 mmHg, and initially setting *c *= 0. Whenever a cell dies, we replace it with an empty automaton, with no Dirichlet node. Oxygen and drug follow the typical diffusion-reaction equations:

\[ \frac{ \partial \textrm{pO}_2 }{\partial t} = D_\textrm{oxy} \nabla^2 \textrm{pO}_2 – \lambda_\textrm{oxy} \textrm{pO}_2 – \sum_{ \textrm{cells} i} U_{i,\textrm{oxy}} \textrm{pO}_2 \]

\[ \frac{ \partial c}{ \partial t } = D_c \nabla^2 c – \lambda_c c – \sum_{\textrm{cells }i} U_{i,c} c \]

where each uptake rate is applied across the cell’s volume. We start the treatment by setting *c = *5 μM on all Dirichlet nodes at *t *= 504 hours (21 days). For simplicity, we do not model drug degradation (pharmacokinetics), to approximate the *in vitro *conditions.

In any time interval [*t*,*t*+Δ*t*], each live tumor cell *i* has a probability *p _{i,D}* of attempting division, probability

*p*of apoptotic death, and probability

_{i,A}*p*of necrotic death. (For simplicity, we ignore motility in this version.) We relate these to the birth rate

_{i,N}*b*, apoptotic death rate

_{i}*d*, and necrotic death rate

_{i,A}*d*by the linearized equations (from Macklin et al. 2012):

_{i,N}\[ \textrm{Prob} \Bigl( \textrm{cell } i \textrm{ becomes apoptotic in } [t,t+\Delta t] \Bigr) = 1 – \textrm{exp}\Bigl( -d_{i,A}(t) \Delta t\Bigr) \approx d_{i,A}\Delta t \]

\[ \textrm{Prob} \Bigl( \textrm{cell } i \textrm{ attempts division in } [t,t+\Delta t] \Bigr) = 1 – \textrm{exp}\Bigl( -b_i(t) \Delta t\Bigr) \approx b_{i}\Delta t \]

\[ \textrm{Prob} \Bigl( \textrm{cell } i \textrm{ becomes necrotic in } [t,t+\Delta t] \Bigr) = 1 – \textrm{exp}\Bigl( -d_{i,N}(t) \Delta t\Bigr) \approx d_{i,N}\Delta t \]

*T*, which will vary by the type of cell death. Each dead cell automaton has a probability

_{i,D}*p*of lysis (rupture and removal) in any time span [

_{i,L}*t*,

*t+*Δ

*t*]. The duration

*T*is converted to a probability of cell lysis by

_{D}\[ \textrm{Prob} \Bigl( \textrm{dead cell } i \textrm{ lyses in } [t,t+\Delta t] \Bigr) = 1 – \textrm{exp}\Bigl( -\frac{1}{T_{i,D}} \Delta t\Bigr) \approx \frac{ \Delta t}{T_{i,D}} \]

##### (Illustrative) parameter values

We use *D*_{oxy} = 10^{5} μm^{2}/min (Ghaffarizadeh et al. 2016), and we set *U*_{i,oxy} = 20 min^{-1} (to give an oxygen diffusion length scale of about 70 μm, with steeper gradients than our typical 100 μm length scale). We set *λ*_{oxy} = 0.01 min^{-1} for a 1 mm diffusion length scale in fluid.

We set *D _{c}* = 300 μm

^{2}/min, and

*U*

_{c}= 7.2×10

^{-3}min

^{-1}(

*D*from Weinberg et al. (2007), and

_{c}*U*twice as large as the reference value in Weinberg et al. (2007) to get a smaller diffusion length scale of about 204 μm). We set

_{i,c}*λ*= 3.6×10

_{c}^{-5}min

^{-1}to give a drug diffusion length scale of about 2.9 mm in fluid.

We use *T _{D}* = 8.6 hours for apoptotic cells, and

*T*= 60 days for necrotic cells (Macklin et al., 2013). However, note that necrotic and apoptotic cells lose volume quickly, so one may want to revise those time scales to match the point where a cell loses 90% of its volume.

_{D}#### Functional forms for the birth and death rates

We model pharmacodynamics with an area-under-the-curve (AUC) type formulation. If *c*(*t*) is the drug concentration at any cell *i*‘s location at time *t*, then let its integrated exposure *E _{i}*(

*t*) be

\[ E_i(t) = \int_0^t c(s) \: ds \]

and we model its response with a Hill function

\[ R_i(t) = \frac{ E_i^h(t) }{ \alpha_i^h + E_i^h(t) }, \]

where *h *is the drug’s Hill exponent for the cell line, and *α *is the exposure for a half-maximum effect.

We model the microenvironment-dependent birth rate by:

\[ b_i(t) = \left\{ \begin{array}{lr} b_{i,P} \left( 1 – \eta_i R_i(t) \right) & \textrm{ if } \textrm{pO}_{2,P} < \textrm{pO}_2 \\ \\ b_{i,P} \left( \frac{\textrm{pO}_{2}-\textrm{pO}_{2,N}}{\textrm{pO}_{2,P}-\textrm{pO}_{2,N}}\right) \Bigl( 1 – \eta_i R_i(t) \Bigr) & \textrm{ if } \textrm{pO}_{2,N} < \textrm{pO}_2 \le \textrm{pO}_{2,P} \\ \\ 0 & \textrm{ if } \textrm{pO}_2 \le \textrm{pO}_{2,N}\end{array} \right. \]

where pO_{2,P} is the physioxic oxygen value (38 mmHg), and pO_{2,N} is a necrotic threshold (we use 5 mmHg), and 0 < *η* < 1 the drug’s birth inhibition. (A fully cytostatic drug has *η* = 1.)

We model the microenvironment-dependent apoptosis rate by:

\[ d_{i,A}(t) = d_{i,A}^* + \Bigl( d_{i,A}^\textrm{max} – d_{i,A}^* \Bigr) R_i(t) \]

*d*

_{i,A}^{max}is the maximum apoptotic death rate. We model the microenvironment-dependent necrosis rate by:

\[ d_{i,N}(t) = \left\{ \begin{array}{lr} 0 & \textrm{ if } \textrm{pO}_{2,N} < \textrm{pO}_{2} \\ \\ d_{i,N}^* & \textrm{ if } \textrm{pO}_{2} \le \textrm{pO}_{2,N} \end{array}\right. \]

*d*

_{i,N}^{*}.

##### (Illustrative) parameter values

We use *b _{i,P}* = 0.05 hour

^{-1}(for a 20 hour cell cycle in physioxic conditions),

*d*

_{i,A}^{*}= 0.01

*b*, and

_{i,P}*d*

_{i,N}^{*}= 0.04 hour

^{-1}(so necrotic cells survive around 25 hours in low oxygen conditions).

We set *α* = 30 μM*hour (so that cells reach half max response after 6 hours’ exposure at a maximum concentration *c* = 5 μM), *h* = 2 (for a smooth effect), *η* = 0.25 (so that the drug is partly cytostatic), and *d _{i,A}*

^{max}= 0.1 hour^-1 (so that cells survive about 10 hours after reaching maximum response).

### Building the Cellular Automaton Model in BioFVM

BioFVM already includes Basic_Agents for cell-based substrate sources and sinks. We can extend these basic agents into full-fledged automata, and then arrange them in a lattice to create a full cellular automata model. Let’s sketch that out now.

#### Extending Basic_Agents to Automata

The main idea here is to define an Automaton class which extends (and therefore includes) the Basic_Agent class. This will give each Automaton full access to the microenvironment defined in BioFVM, including the ability to secrete and uptake substrates. We also make sure each Automaton “knows” which microenvironment it lives in (contains a pointer pMicroenvironment), and “knows” where it lives in the cellular automaton lattice. (More on that in the following paragraphs.)

So, as a schematic (just sketching out the most important members of the class):

class Standard_Data; // define per-cell biological data, such as phenotype, // cell cycle status, etc.. class Custom_Data; // user-defined custom data, specific to a model. class Automaton : public Basic_Agent { private: Microenvironment* pMicroenvironment; CA_Mesh* pCA_mesh; int voxel_index; protected: public: // neighbor connectivity information std::vector<Automaton*> neighbors; std::vector<double> neighbor_weights; Standard_Data standard_data; void (*current_state_rule)( Automaton& A , double ); Automaton(); void copy_parameters( Standard_Data& SD ); void overwrite_from_automaton( Automaton& A ); void set_cellular_automaton_mesh( CA_Mesh* pMesh ); CA_Mesh* get_cellular_automaton_mesh( void ) const; void set_voxel_index( int ); int get_voxel_index( void ) const; void set_microenvironment( Microenvironment* pME ); Microenvironment* get_microenvironment( void ); // standard state changes bool attempt_division( void ); void become_apoptotic( void ); void become_necrotic( void ); void perform_lysis( void ); // things the user needs to define Custom_Data custom_data; // use this rule to add custom logic void (*custom_rule)( Automaton& A , double); };

So, the Automaton class includes everything in the Basic_Agent class, some Standard_Data (things like the cell state and phenotype, and per-cell settings), (user-defined) Custom_Data, basic cell behaviors like attempting division into an empty neighbor lattice site, and user-defined custom logic that can be applied to any automaton. To avoid lots of switch/case and if/then logic, each Automaton has a function pointer for its current activity (current_state_rule), which can be overwritten any time.

Each Automaton also has a list of neighbor Automata (their memory addresses), and weights for each of these neighbors. Thus, you can distance-weight the neighbors (so that corner elements are farther away), and very generalized neighbor models are possible (e.g., all lattice sites within a certain distance). When updating a cellular automaton model, such as to kill a cell, divide it, or move it, you leave the neighbor information alone, and copy/edit the information (standard_data, custom_data, current_state_rule, custom_rule). In many ways, an Automaton is just a bucket with a cell’s information in it.

Note that each Automaton also “knows” where it lives (pMicroenvironment and voxel_index), and knows what CA_Mesh it is attached to (more below).

#### Connecting Automata into a Lattice

An automaton by itself is lost in the world–it needs to link up into a lattice organization. Here’s where we define a CA_Mesh class, to hold the entire collection of Automata, setup functions (to match to the microenvironment), and two fundamental operations at the mesh level: copying automata (for cell division), and swapping them (for motility). We have provided two functions to accomplish these tasks, while automatically keeping the indexing and BioFVM functions correctly in sync. Here’s what it looks like:

class CA_Mesh{ private: Microenvironment* pMicroenvironment; Cartesian_Mesh* pMesh; std::vector<Automaton> automata; std::vector<int> iteration_order; protected: public: CA_Mesh(); // setup to match a supplied microenvironment void setup( Microenvironment& M ); // setup to match the default microenvironment void setup( void ); int number_of_automata( void ) const; void randomize_iteration_order( void ); void swap_automata( int i, int j ); void overwrite_automaton( int source_i, int destination_i ); // return the automaton sitting in the ith lattice site Automaton& operator[]( int i ); // go through all nodes according to random shuffled order void update_automata( double dt ); };

So, the CA_Mesh has a vector of Automata (which are never themselves moved), pointers to the microenvironment and its mesh, and a vector of automata indices that gives the iteration order (so that we can sample the automata in a random order). You can easily access an automaton with operator[], and copy the data from one Automaton to another with overwrite_automaton() (e.g, for cell division), and swap two Automata’s data (e.g., for cell migration) with swap_automata(). Finally, calling update_automata(dt) iterates through all the automata according to iteration_order, calls their current_state_rules and custom_rules, and advances the automata by dt.

#### Interfacing Automata with the BioFVM Microenvironment

The setup function ensures that the CA_Mesh is the same size as the Microenvironment.mesh, with same indexing, and that all automata have the correct volume, and dimension of uptake/secretion rates and parameters. If you declare and set up the Microenvironment first, all this is take care of just by declaring a CA_Mesh, as it seeks out the default microenvironment and sizes itself accordingly:

// declare a microenvironment Microenvironment M; // do things to set it up -- see prior tutorials // declare a Cellular_Automaton_Mesh CA_Mesh CA_model; // it's already good to go, initialized to empty automata: CA_model.display();

If you for some reason declare the CA_Mesh fist, you can set it up against the microenvironment:

// declare a CA_Mesh CA_Mesh CA_model; // declare a microenvironment Microenvironment M; // do things to set it up -- see prior tutorials // initialize the CA_Mesh to match the microenvironment CA_model.setup( M ); // it's already good to go, initialized to empty automata: CA_model.display();

Because each Automaton is in the microenvironment and inherits functions from Basic_Agent, it can secrete or uptake. For example, we can use functions like this one:

void set_uptake( Automaton& A, std::vector<double>& uptake_rates ) { extern double BioFVM_CA_diffusion_dt; // update the uptake_rates in the standard_data A.standard_data.uptake_rates = uptake_rates; // now, transfer them to the underlying Basic_Agent *(A.uptake_rates) = A.standard_data.uptake_rates; // and make sure the internal constants are self-consistent A.set_internal_uptake_constants( BioFVM_CA_diffusion_dt ); }

A function acting on an automaton can sample the microenvironment to change parameters and state. For example:

void do_nothing( Automaton& A, double dt ) { return; } void microenvironment_based_rule( Automaton& A, double dt ) { // sample the microenvironment std::vector<double> MS = (*A.get_microenvironment())( A.get_voxel_index() ); // if pO2 < 5 mmHg, set the cell to a necrotic state if( MS[0] < 5.0 ) { A.become_necrotic(); } // if drug > 5 uM, set the birth rate to zero if( MS[1] > 5 ) { A.standard_data.birth_rate = 0.0; } // set the custom rule to something else A.custom_rule = do_nothing; return; }

#### Implementing the mathematical model in this framework

We give each tumor cell a tumor_cell_rule (using this for custom_rule):

void viable_tumor_rule( Automaton& A, double dt ) { // If there's no cell here, don't bother. if( A.standard_data.state_code == BioFVM_CA_empty ) { return; } // sample the microenvironment std::vector<double> MS = (*A.get_microenvironment())( A.get_voxel_index() ); // integrate drug exposure A.standard_data.integrated_drug_exposure += ( MS[1]*dt ); A.standard_data.drug_response_function_value = pow( A.standard_data.integrated_drug_exposure, A.standard_data.drug_hill_exponent ); double temp = pow( A.standard_data.drug_half_max_drug_exposure, A.standard_data.drug_hill_exponent ); temp += A.standard_data.drug_response_function_value; A.standard_data.drug_response_function_value /= temp; // update birth rates (which themselves update probabilities) update_birth_rate( A, MS, dt ); update_apoptotic_death_rate( A, MS, dt ); update_necrotic_death_rate( A, MS, dt ); return; }

The functional tumor birth and death rates are implemented as:

void update_birth_rate( Automaton& A, std::vector<double>& MS, double dt ) { static double O2_denominator = BioFVM_CA_physioxic_O2 - BioFVM_CA_necrotic_O2; A.standard_data.birth_rate = A.standard_data.drug_response_function_value; // response A.standard_data.birth_rate *= A.standard_data.drug_max_birth_inhibition; // inhibition*response; A.standard_data.birth_rate *= -1.0; // - inhibition*response A.standard_data.birth_rate += 1.0; // 1 - inhibition*response A.standard_data.birth_rate *= viable_tumor_cell.birth_rate; // birth_rate0*(1 - inhibition*response) double temp1 = MS[0] ; // O2 temp1 -= BioFVM_CA_necrotic_O2; temp1 /= O2_denominator; A.standard_data.birth_rate *= temp1; if( A.standard_data.birth_rate < 0 ) { A.standard_data.birth_rate = 0.0; } A.standard_data.probability_of_division = A.standard_data.birth_rate; A.standard_data.probability_of_division *= dt; // dt*birth_rate*(1 - inhibition*repsonse) // linearized probability return; } void update_apoptotic_death_rate( Automaton& A, std::vector<double>& MS, double dt ) { A.standard_data.apoptotic_death_rate = A.standard_data.drug_max_death_rate; // max_rate A.standard_data.apoptotic_death_rate -= viable_tumor_cell.apoptotic_death_rate; // max_rate - background_rate A.standard_data.apoptotic_death_rate *= A.standard_data.drug_response_function_value; // (max_rate-background_rate)*response A.standard_data.apoptotic_death_rate += viable_tumor_cell.apoptotic_death_rate; // background_rate + (max_rate-background_rate)*response A.standard_data.probability_of_apoptotic_death = A.standard_data.apoptotic_death_rate; A.standard_data.probability_of_apoptotic_death *= dt; // dt*( background_rate + (max_rate-background_rate)*response ) // linearized probability return; } void update_necrotic_death_rate( Automaton& A, std::vector<double>& MS, double dt ) { A.standard_data.necrotic_death_rate = 0.0; A.standard_data.probability_of_necrotic_death = 0.0; if( MS[0] > BioFVM_CA_necrotic_O2 ) { return; } A.standard_data.necrotic_death_rate = perinecrotic_tumor_cell.necrotic_death_rate; A.standard_data.probability_of_necrotic_death = A.standard_data.necrotic_death_rate; A.standard_data.probability_of_necrotic_death *= dt; // dt*necrotic_death_rate return; }

And each fluid voxel (Dirichlet nodes) is implemented as the following (to turn on therapy at 21 days):

void fluid_rule( Automaton& A, double dt ) { static double activation_time = 504; static double activation_dose = 5.0; static std::vector<double> activated_dirichlet( 2 , BioFVM_CA_physioxic_O2 ); static bool initialized = false; if( !initialized ) { activated_dirichlet[1] = activation_dose; initialized = true; } if( fabs( BioFVM_CA_elapsed_time - activation_time ) < 0.01 ) { int ind = A.get_voxel_index(); if( A.get_microenvironment()->mesh.voxels[ind].is_Dirichlet ) { A.get_microenvironment()->update_dirichlet_node( ind, activated_dirichlet ); } } }

At the start of the simulation, each non-cell automaton has its custom_rule set to fluid_rule, and each tumor cell Automaton has its custom_rule set to viable_tumor_rule. Here’s how:

void setup_cellular_automata_model( Microenvironment& M, CA_Mesh& CAM ) { // Fill in this environment double tumor_radius = 150; double tumor_radius_squared = tumor_radius * tumor_radius; std::vector<double> tumor_center( 3, 0.0 ); std::vector<double> dirichlet_value( 2 , 1.0 ); dirichlet_value[0] = 38; //physioxia dirichlet_value[1] = 0; // drug for( int i=0 ; i < M.number_of_voxels() ;i++ ) { std::vector<double> displacement( 3, 0.0 ); displacement = M.mesh.voxels[i].center; displacement -= tumor_center; double r2 = norm_squared( displacement ); if( r2 > tumor_radius_squared ) // well_mixed_fluid { M.add_dirichlet_node( i, dirichlet_value ); CAM[i].copy_parameters( well_mixed_fluid ); CAM[i].custom_rule = fluid_rule; CAM[i].current_state_rule = do_nothing; } else // tumor { CAM[i].copy_parameters( viable_tumor_cell ); CAM[i].custom_rule = viable_tumor_rule; CAM[i].current_state_rule = advance_live_state; } } }

#### Overall program loop

There are two inherent time scales in this problem: cell processes like division and death (happen on the scale of hours), and transport (happens on the order of minutes). We take advantage of this by defining two step sizes:

double BioFVM_CA_dt = 3; std::string BioFVM_CA_time_units = "hr"; double BioFVM_CA_save_interval = 12; double BioFVM_CA_max_time = 24*28; double BioFVM_CA_elapsed_time = 0.0; double BioFVM_CA_diffusion_dt = 0.05; std::string BioFVM_CA_transport_time_units = "min"; double BioFVM_CA_diffusion_max_time = 5.0;

Every time the simulation advances by BioFVM_CA_dt (on the order of hours), we run diffusion to quasi-steady state (for BioFVM_CA_diffusion_max_time, on the order of minutes), using time steps of size BioFVM_CA_diffusion time. We performed numerical stability and convergence analyses to determine 0.05 min works pretty well for regular lattice arrangements of cells, but you should always perform your own testing!

Here’s how it all looks, in a main program loop:

BioFVM_CA_elapsed_time = 0.0; double next_output_time = BioFVM_CA_elapsed_time; // next time you save data while( BioFVM_CA_elapsed_time < BioFVM_CA_max_time + 1e-10 ) { // if it's time, save the simulation if( fabs( BioFVM_CA_elapsed_time - next_output_time ) < BioFVM_CA_dt/2.0 ) { std::cout << "simulation time: " << BioFVM_CA_elapsed_time << " " << BioFVM_CA_time_units << " (" << BioFVM_CA_max_time << " " << BioFVM_CA_time_units << " max)" << std::endl; char* filename; filename = new char [1024]; sprintf( filename, "output_%6f" , next_output_time ); save_BioFVM_cellular_automata_to_MultiCellDS_xml_pugi( filename , M , CA_model , BioFVM_CA_elapsed_time ); cell_counts( CA_model ); delete [] filename; next_output_time += BioFVM_CA_save_interval; } // do the cellular automaton step CA_model.update_automata( BioFVM_CA_dt ); BioFVM_CA_elapsed_time += BioFVM_CA_dt; // simulate biotransport to quasi-steady state double t_diffusion = 0.0; while( t_diffusion < BioFVM_CA_diffusion_max_time + 1e-10 ) { M.simulate_diffusion_decay( BioFVM_CA_diffusion_dt ); M.simulate_cell_sources_and_sinks( BioFVM_CA_diffusion_dt ); t_diffusion += BioFVM_CA_diffusion_dt; } }

### Getting and Running the Code

**Start a project:**Create a new directory for your project (I’d recommend “BioFVM_CA_tumor”), and enter the directory. Place a copy of BioFVM (the zip file) into your directory. Unzip BioFVM, and copy BioFVM*.h, BioFVM*.cpp, and pugixml* files into that directory.**Download the demo source code:**Download the source code for this tutorial: BioFVM_CA_Example_1, version 1.0.0 or later. Unzip its contents into your project directory.**Go ahead and overwrite the Makefile**.**Edit the makefile (if needed):**Note that if you are using OSX, you’ll probably need to change from “g++” to your installed compiler. See these tutorials.**Test the code:**Go to a command line (see previous tutorials), and test:make ./BioFVM_CA_Example_1

(If you’re on windows, run BioFVM_CA_Example_1.exe.)

### Simulation Result

If you run the code to completion, you will simulate 3 weeks of *in vitro * growth, followed by a bolus “injection” of drug. The code will simulate one one additional week under the drug. (This should take 5-10 minutes, including full simulation saves every 12 hours.)

In matlab, you can load a saved dataset and check the minimum oxygenation value like this:

MCDS = read_MultiCellDS_xml( 'output_504.000000.xml' ); min(min(min( MCDS.continuum_variables(1).data )))

And then you can start visualizing like this:

contourf( MCDS.mesh.X_coordinates , MCDS.mesh.Y_coordinates , ... MCDS.continuum_variables(1).data(:,:,33)' ) ; axis image; colorbar xlabel('x (\mum)' , 'fontsize' , 12 ); ylabel( 'y (\mum)' , 'fontsize', 12 ); set(gca, 'fontsize', 12 ); title('Oxygenation (mmHg) at z = 0 \mum', 'fontsize', 14 ); print('-dpng', 'Tumor_o2_3_weeks.png' ); plot_cellular_automata( MCDS , 'Tumor spheroid at 3 weeks');

#### Simulation plots

Here are some plots, showing (left from right) pO_{2} concentration, a cross-section of the tumor (red = live cells, green = apoptotic, and blue = necrotic), and the drug concentration (after start of therapy):

##### 1 week:

Oxygen- and space-limited growth are restricted to the outer boundary of the tumor spheroid.

##### 2 weeks:

Oxygenation is dipped below 5 mmHg in the center, leading to necrosis.

##### 3 weeks:

As the tumor grows, the hypoxic gradient increases, and the necrotic core grows. The code turns on a constant 5 micromolar dose of doxorubicin at this point

##### Treatment + 12 hours:

The drug has started to penetrate the tumor, triggering apoptotic death towards the outer periphery where exposure has been greatest.

##### Treatment + 24 hours:

The drug profile hasn’t changed much, but the interior cells have now had greater exposure to drug, and hence greater response. Now apoptosis is observed throughout the non-necrotic tumor. The tumor has decreased in volume somewhat.

##### Treatment + 36 hours:

The non-necrotic tumor is now substantially apoptotic. We would require some pharamcokinetic effects (e.g., drug clearance, inactivation, or removal) to avoid the inevitable, presences of a pre-existing resistant strain, or emergence of resistance.

##### Treatment + 48 hours:

By now, almost all cells are apoptotic.

##### Treatment + 60 hours:

The non-necrotic tumor is nearly completed eliminated, leaving a leftover core of previously-necrotic cells (which did not change state in response to the drug–they were already dead!)

### Source files

You can download completed source for this example here: https://sourceforge.net/projects/biofvm/files/Tutorials/Cellular_Automaton_1/

This file will include the following:

- BioFVM_cellular_automata.h
- BioFVM_cellular_automata.cpp
- BioFVM_CA_example_1.cpp
- read_MultiCellDS_xml.m (updated)
- plot_cellular_automata.m
- Makefile

### What’s next

I plan to update this source code with extra cell motility, and potentially more realistic parameter values. Also, I plan to more formally separate out the example from the generic cell capabilities, so that this source code can work as a *bona fide *cellular automaton framework.

More immediately, my next tutorial will use the reverse strategy: start with an existing cellular automaton model, and integrate BioFVM capabilities.

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Hi,

thank you for this helpful and perfect site.

I’v got a problem in running BioFVM_CA_Example_1.exe. I have run physicell (for 3D and 2D problems) and 2D templates of BioFVM previously on my system. But in this case, after making the BioFVM_CA_Example_1.exe, when I try to run .exe file, I see the following error:

BioFVM_CA_Example_1.exe has stopped working

I don’t think the problem is with the code (because Makefile already creates .exe file!).

I would be grateful if you kindly let me know about the possible solutions.

Hi, I think you also emailed us. (Sorry that I don’t moderate posts here very often.)

I believe I answered in your email, but to restate, the example does not appear to be compatible with the most recent version of BioFVM. We’d need to either re-port the example to newer versions (ideal solution), or for now use the older version of BioFVM indicated in the tutorial.

If updating the example, the work would primarily center on the BioFVM initialization routines.

One last question for you: are you ultimately interested in continuing the example and/or adapting BioFVM to a different cellular automaton model, or are you more generally interested in linking cell behaviors to diffusing substrates? If the latter, you might consider taking a look at PhysiCell, which builds upon BioFVM and is currently much more actively supported.

Thank you!

Hi professor Macklin,

Thank you very much for your response, actually I wrote this post before the email. I am interested in linking diffusing substrates with the automaton. Sure I will work with Physicell in near future.

One more thing for those who read this post… the example works on BioFVM_V.1.1.4 correctly.

Thanks again

Hello.

“This example shows you how to extend BioFVM into a new cellular automaton model. I’ll write a similar post on how to add BioFVM into an existing cellular automaton model, which you may already have available.”

This is my question how I can include BioFVM in an already existing agent-based model or cellular automata model.

Thanks.

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