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)
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:
divide_times[cell.id] = 0
cell.targetVolume=GLOBAL['targetVolume']
cell.lambdaVolume=1.5
phenotypes[cell.id] = Phenotype( phenotype_template ) # simulate phenotypes
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.CANCER1
cancer_cell_created = True
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 )
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
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
if count != 1:
print 'FAILED TO INITIALZE A CANCER CELL.'
sys.exit(0)