PhysiBoSS-Tutorial

This repository contains three examples of multiscale models: a modified version of a previously published model of cell fate decision processes in response to death receptor engagement and the effect of a tumor necrosis factor (TNF) treatment on these decisions, a cell cycle model for investigating the consequences of genetic perturbations in signaling, and a simplified model of immune cell differentiation.

Manuscript

The manuscript of the paper is available here, and the supplementary materials (containing the detailed instructions to build the model) is available here

Model XML settings

We provide several XML files in the config folders, for the different models.

Cell fate model

• config/simple_tnf/0_Initial.xml : Initial step of the model, with a growing tumour
• config/simple_tnf/1_Long_TNF.xml : Simulation of a long TNF treatment
• config/simple_tnf/1_Long_TNF_stochastic_time.xml : Simulation of a long TNF treatment, with cell desynchronisation
• config/simple_tnf/2_Short_TNF.xml : Simulation of pulsatile TNF treatment
• config/simple_tnf/3_Necrotic_core.xml : Simulation of a necrotic core in the tumour
• config/simple_tnf/4_Mutants.xml : Simulation of an heterogenous tumour, with a population resistant to the TNF treatment

Cell cycle model

• config/cell_cycle/PhysiCell_settings.xml : Default simulation of the cell cycle
• config/cell_cycle/PhysiCell_settings_plk1_knockout.xml : Simulation of the cell cycle with a PLK1 inhibition
• config/cell_cycle/PhysiCell_settings_foxo3_knockout.xml : Simulation of the cell cycle with a FOXO3 inhibition
• config/cell_cycle/PhysiCell_settings_p110_knockin.xml : Simulation of the cell cycle with a p110 activation

Differentiation model

• config/differentiation/PhysiCell_settings.xml : Default simulation of the T Cell differentiation model
• config/differentiation/PhysiCell_settings_FOXP3_2_mutant.xml : Simulation of the T Cell differentiation model with FOXP3_2 knockout in naive T cells
• config/differentiation/PhysiCell_settings_NFKB_mutant.xml : Simulation of the T Cell differentiation model with NFKB knockout in naive T cells
• config/differentiation/PhysiCell_settings_FOXP3_2_lower.xml : Simulation of the T Cell differentiation model with lower activation rate for FOXP3_2 in naive T cells
• config/differentiation/PhysiCell_settings_NFKB_lower.xml : Simulation of the T Cell differentiation model with lower activation rate for NFKB in naive T cells