def start(self): num_cells = len(self.cellList) cancer_cell_created = False if simulate_flag and template_flag: genomes.update( load_genomes_into_dict(file_name=TEMPLATES['genome_file'])) pass for cell in self.cellList: divisions_left[cell.id] = 0 divide_times[cell.id] = 0 cell.targetVolume = GLOBAL['targetVolume'] cell.lambdaVolume = 1.5 if simulate_flag and not template_flag: genomes[cell.id] = Genome(mutation_rate=1, name=cell.id, ploidy_probability=0.0, ploidy=2) # create a cancer cell in the middle if not cancer_cell_created and ( cell.xCOM <= LATTICE['center_x_max'] and cell.xCOM >= LATTICE['center_x_min']) and ( cell.yCOM <= LATTICE['center_y_max'] and cell.yCOM >= LATTICE['center_y_min']): cell.type = self.CANCER2 cancer_cell_created = True if cell.type == self.CANCER2: if simulate_flag and not template_flag: genomes[cell.id] = Genome(mutation_rate=10, name=cell.id, ploidy_probability=0.0, ploidy=2) else: # this is template flag, therefore we must just update this genomes' attribute. genomes[cell.id].mutation_rate = 10 genomes[cell.id].ploidy_probability = 0.0 divisions_left[cell.id] = -1 # unlimited cell divisions if save_flag: trackers['start_tracker'].stash( [cell.id, cell.type, genomes[cell.id].mutation_rate]) # holder[cell.id] = { 'g': Genome( mutation_rate = 20 , genome_order = 10 ) } ## check if we successfully initiated a cancer cell. count = 0 for cell in self.cellList: if cell.type == self.CANCER2: count += 1 if count != 1: print 'FAILED TO INITIALZE A CANCER CELL.' sys.exit(0)
def start(self): num_cells = len(self.cellList) # r = np.random.randint(0,num_cells) if simulate_flag and template_flag: genomes.update( load_genomes_into_dict( file_name = TEMPLATES['genome_file'] ) ) pass for cell in self.cellList: divide_times[cell.id] = 0 cell.targetVolume=GLOBAL['targetVolume'] cell.lambdaVolume=1.5 if simulate_flag and not template_flag: genomes[cell.id] = Genome( mutation_rate = 1 , name = cell.id, ploidy_probability=0.0 , ploidy=2 ) if cell.type == self.CANCER1: if simulate_flag and not template_flag: genomes[cell.id] = Genome( mutation_rate = 10 , name = cell.id, ploidy_probability=0.0 , ploidy=2 ) if save_flag: trackers['start_tracker'].stash( [ cell.id, cell.type , genomes[cell.id].mutation_rate ] ) # holder[cell.id] = { 'g': Genome( mutation_rate = 20 , genome_order = 10 ) } ## check if we successfully initiated a cancer cell. count = 0 for cell in self.cellList: if cell.type == self.CANCER1: count += 1
def start(self): num_cells = len(self.cellList) r = np.random.randint(0, num_cells) for cell in self.cellList: divide_times[cell.id] = 0 cell.targetVolume = GLOBAL['targetVolume'] cell.lambdaVolume = 1.5 if simulate_flag: genomes[cell.id] = Genome(mutation_rate=50, name=cell.id, ploidy_probability=0.0001, ploidy=2) # phenotypes[cell.id] = Phenotype( phenotype_template ) divisions_left[cell.id] = GLOBAL['init_num_divisions'] if cell.id == r: cell.type = self.CANCER2 if simulate_flag: genomes[cell.id] = Genome(mutation_rate=120, name=cell.id, ploidy_probability=0.002, ploidy=2) divisions_left[cell.id] = -1 if save_flag: self.start_tracker.stash( [cell.id, cell.type, genomes[cell.id].mutation_rate]) # holder[cell.id] = { 'g': Genome( mutation_rate = 20 , genome_order = 10 ) } ## check if we successfully initiated a cancer cell. count = 0 for cell in self.cellList: if cell.type == self.CANCER2: count += 1 if count != 1: print 'FAILED TO INITIALZE A CANCER CELL.' sys.exit(0)
def start(self): num_cells = len(self.cellList) r = np.random.randint(0, num_cells) for cell in self.cellList: divide_times[cell.id] = 0 cell.targetVolume = GLOBAL['targetVolume'] cell.lambdaVolume = 1.5 if simulate_flag: genomes[cell.id] = Genome(mutation_rate=50, name=cell.id) if cell.id == r: cell.type = self.CANCER1 if simulate_flag: genomes[cell.id] = Genome(mutation_rate=120, name=cell.id) if save_flag: self.start_tracker.stash( [cell.id, cell.type, genomes[cell.id].mutation_rate]) # holder[cell.id] = { 'g': Genome( mutation_rate = 20 , genome_order = 10 ) } ## check if we successfully initiated a cancer cell. count = 0 for cell in self.cellList: if cell.type == self.CANCER1: count += 1 if count != 1: print 'FAILED TO INITIALZE A CANCER CELL.' sys.exit(0)
def start(self): num_cells = len(self.cellList) for cell in self.cellList: divide_times[cell.id] = 0 cell.targetVolume = GLOBAL['targetVolume'] cell.lambdaVolume = 1.5 if simulate_flag: genomes[cell.id] = Genome(mutation_rate=50, name=cell.id, ploidy_probability=0.0001, ploidy=2) if save_flag: self.start_tracker.stash( [cell.id, cell.type, genomes[cell.id].mutation_rate])