+
+
+
+
+
+
+In [1]:
+
+
+
+
+
+import itertools
+from process_bigraph import Composite
+from spatio_flux import core
+from spatio_flux.viz.plot import plot_time_series, plot_species_distributions_to_gif, plot_species_distributions_with_particles_to_gif
+from spatio_flux.processes.dfba import DynamicFBA, get_single_dfba_spec, get_spatial_dfba_state
+from spatio_flux.processes.diffusion_advection import DiffusionAdvection, get_diffusion_advection_spec, get_diffusion_advection_state
+from spatio_flux.processes.particles import Particles, get_particles_spec, get_particles_state
+from spatio_flux.processes.particle_comets import get_particle_comets_state
+
+
+
+
+
+
+
+
+In [2]:
+
+
+
+
+
+core.process_registry.list()
+
+
+
+
+
+
+
+
+Out[2]:
+
+
+['Particles', + 'DynamicFBA', + 'console-emitter', + 'bounds', + 'ram-emitter', + 'DiffusionAdvection', + 'composite']+
+
+
+
+
+
+
+
+
+
+Processes¶
+
+
+
+
+
+
+
+
+
+dFBA process¶
+
+
+
+
+
+
+
+In [3]:
+
+
+
+
+
+total_time = 60.0
+
+# get dfba config
+single_dfba_config = {
+ 'dfba': get_single_dfba_spec(path=['fields']),
+ 'fields': {
+ 'glucose': 10,
+ 'acetate': 0,
+ 'biomass': 0.1
+ }
+}
+
+# make the simulation
+sim = Composite({
+ 'state': single_dfba_config,
+ 'emitter': {'mode': 'all'}
+}, core=core)
+
+# save the document
+sim.save(filename='single_dfba.json', outdir='out')
+
+# simulate
+print('Simulating...')
+sim.update({}, total_time)
+
+# gather results
+dfba_results = sim.gather_results()
+
+
+
+
+
+
+
+
+
+
+
+Created new file: out/single_dfba.json +Simulating... ++
+
+
+
+
+
+
+
+In [4]:
+
+
+
+
+
+print('Plotting results...')
+# plot timeseries
+plot_time_series(
+ dfba_results,
+ out_dir='out',
+ filename='dfba_single_timeseries.png',
+)
+
+
+
+
+
+
+
+
+
+
+
+Plotting results... +saving out/dfba_single_timeseries.png ++
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Diffusion advection process¶
+
+
+
+
+
+
+
+In [5]:
+
+
+
+
+
+total_time = 50
+bounds = (10.0, 20.0)
+n_bins = (10, 20)
+
+# get the config
+composite_state = get_diffusion_advection_state(
+ bounds=bounds,
+ n_bins=n_bins,
+ mol_ids=['glucose', 'acetate', 'biomass'],
+ advection_coeffs={
+ 'biomass': (0, -0.1)
+ }
+)
+
+# make the composite
+print('Making the composite...')
+sim = Composite({
+ 'state': composite_state,
+ 'emitter': {'mode': 'all'},
+}, core=core)
+
+# save the document
+sim.save(filename='diffadv.json', outdir='out')
+
+# # save a viz figure of the initial state
+
+# simulate
+print('Simulating...')
+sim.update({}, total_time)
+
+# gather results
+diffadv_results = sim.gather_results()
+
+
+
+
+
+
+
+
+
+
+
+Making the composite... +Created new file: out/diffadv.json +Simulating... ++
+
+
+
+
+
+
+
+In [6]:
+
+
+
+
+
+print('Plotting results...')
+# plot 2d video
+plot_species_distributions_to_gif(
+ diffadv_results,
+ out_dir='out',
+ filename='diffadv_results.gif',
+ title='',
+ skip_frames=1
+)
+
+
+
+
+
+
+
+
+
+
+
+Plotting results... +saving out/diffadv_results.gif ++
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Particles process¶
+
+
+
+
+
+
+
+In [7]:
+
+
+
+
+
+total_time=100
+bounds=(10.0, 20.0) # Bounds of the environment
+n_bins=(20, 40) # Number of bins in the x and y directions
+n_particles=20
+diffusion_rate=0.1
+advection_rate=(0, -0.1)
+add_probability=0.4
+field_interactions=None
+initial_min_max=None
+
+composite_state = get_particles_state(
+ bounds=bounds,
+ n_bins=n_bins,
+ n_particles=n_particles,
+ diffusion_rate=diffusion_rate,
+ advection_rate=advection_rate,
+ add_probability=add_probability,
+ field_interactions=field_interactions,
+ initial_min_max=initial_min_max,
+)
+
+# make the composite
+print('Making the composite...')
+sim = Composite({
+ 'state': composite_state,
+ 'emitter': {'mode': 'all'},
+}, core=core)
+
+# save the document
+sim.save(filename='particles.json', outdir='out')
+
+# # save a viz figure of the initial state
+
+# simulate
+print('Simulating...')
+sim.update({}, total_time)
+
+# gather results
+particles_results = sim.gather_results()
+emitter_results = particles_results[('emitter',)]
+
+particles_history = [p['particles'] for p in emitter_results]
+
+
+
+
+
+
+
+
+
+
+
+Making the composite... +Created new file: out/particles.json +Simulating... ++
+
+
+
+
+
+
+
+In [8]:
+
+
+
+
+
+print('Plotting...')
+# plot particles
+plot_species_distributions_with_particles_to_gif(
+ particles_results,
+ out_dir='out',
+ filename='particle_with_fields.gif',
+ title='',
+ skip_frames=1,
+ bounds=bounds,
+)
+
+
+
+
+
+
+
+
+
+
+
+Plotting... +saving out/particle_with_fields.gif ++
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Composites¶
+
+
+
+
+
+
+
+
+
+Spatial dFBA¶
+
+
+
+
+
+
+
+In [9]:
+
+
+
+
+
+total_time = 100
+n_bins = (5, 5)
+mol_ids = ['glucose', 'acetate', 'biomass']
+
+composite_state = get_spatial_dfba_state(
+ n_bins=n_bins,
+ mol_ids=mol_ids,
+)
+
+# make the composite
+print('Making the composite...')
+sim = Composite({
+ 'state': composite_state,
+ 'emitter': {'mode': 'all'}
+}, core=core)
+
+# save the document
+sim.save(filename='spatial_dfba.json', outdir='out')
+
+# # save a viz figure of the initial state
+
+# simulate
+print('Simulating...')
+sim.update({}, total_time)
+
+# gather results
+dfba_results = sim.gather_results()
+
+
+
+
+
+
+
+
+
+
+
+Making the composite... +Created new file: out/spatial_dfba.json +Simulating... ++
+
+
+
+
+
+
+In [10]:
+
+
+
+
+
+print('Plotting results...')
+# make video
+plot_species_distributions_to_gif(
+ dfba_results,
+ out_dir='out',
+ filename='spatial_dfba_results.gif',
+ title='',
+ skip_frames=1
+)
+
+
+
+
+
+
+
+
+
+
+
+Plotting results... +saving out/spatial_dfba_results.gif ++
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+In [11]:
+
+
+
+
+
+# plot single traces from spatial dfba
+fixed_x = 0
+coord_combinations = [(fixed_x, y) for y in range(n_bins[1])]
+# coord_combinations = list(itertools.product(range(n_bins[0]), range(n_bins[1]))) # all combinations
+plot_time_series(
+ dfba_results,
+ coordinates=coord_combinations,
+ out_dir='out',
+ filename='spatial_dfba_timeseries.png',
+)
+
+
+
+
+
+
+
+
+
+
+
+saving out/spatial_dfba_timeseries.png ++
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+COMETS¶
+
+
+
+
+
+
+
+In [12]:
+
+
+
+
+
+comets_config = {
+ 'total_time': 10.0,
+ # environment size
+ 'bounds': (10.0, 10.0),
+ 'n_bins': (10, 10),
+ # set fields
+ 'mol_ids': ['glucose', 'acetate', 'biomass'],
+ 'initial_min_max': {
+ 'glucose': (0, 10),
+ 'acetate': (0, 0),
+ 'biomass': (0, 0.1)
+ },
+}
+
+
+
+
+
+
+
+In [13]:
+
+
+
+
+
+# make the composite state
+composite_state = get_spatial_dfba_state(
+ n_bins=comets_config['n_bins'],
+ mol_ids=comets_config['mol_ids'],
+ initial_min_max=comets_config['initial_min_max'],
+)
+composite_state['diffusion'] = get_diffusion_advection_spec(
+ bounds=comets_config['bounds'],
+ n_bins=comets_config['n_bins'],
+ mol_ids=comets_config['mol_ids'],
+ default_diffusion_rate=1e-1,
+ default_advection_rate=(0, 0),
+ diffusion_coeffs=None, # TODO add all these config options
+ advection_coeffs=None,
+)
+
+# make the composite
+print('Making the composite...')
+sim = Composite({
+ 'state': composite_state,
+ 'emitter': {'mode': 'all'},
+}, core=core)
+
+# save the document
+sim.save(filename='comets.json', outdir='out', include_schema=True)
+
+# # save a viz figure of the initial state
+
+# simulate
+print('Simulating...')
+sim.update({}, total_time)
+comets_results = sim.gather_results()
+
+
+
+
+
+
+
+
+
+
+
+Making the composite... +Created new file: out/comets.json +Simulating... ++
+
+
+
+
+
+
+In [14]:
+
+
+
+
+
+print('Plotting results...')
+# plot 2d video
+plot_species_distributions_to_gif(
+ comets_results,
+ out_dir='out',
+ filename='comets_results.gif',
+ title='',
+ skip_frames=1)
+
+
+
+
+
+
+
+
+
+
+
+Plotting results... +saving out/comets_results.gif ++
+
+
+
+
+
+
+
+
+
+
+
+
+
+In [ ]:
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+In [ ]:
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+In [ ]:
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+In [ ]:
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+In [ ]:
+
+
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+
+
+
+
+
+
+In [15]:
+
+
+
+
+
+# plot single traces from comets
+fixed_x = 0
+n_bins = comets_config['n_bins']
+coord_combinations = [(fixed_x, y) for y in range(n_bins[1])]
+# coord_combinations = list(itertools.product(range(n_bins[0]), range(n_bins[1]))) # all combinations
+plot_time_series(
+ comets_results,
+ coordinates=coord_combinations,
+ out_dir='out',
+ filename='comets_timeseries.png',
+)
+
+
+
+
+
+
+
+
+
+
+
+saving out/comets_timeseries.png ++
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Particle-COMETS¶
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+
+
+
+
+
+
+
+
+In [16]:
+
+
+
+
+
+total_time = 20
+particle_comets_config = {
+ # 'total_time': 100.0,
+ # environment size
+ 'bounds': (10.0, 20.0),
+ 'n_bins': (8, 16),
+ # set fields
+ 'mol_ids': ['glucose', 'acetate', 'biomass', 'detritus'],
+ 'field_diffusion_rate': 1e-1,
+ 'field_advection_rate': (0, 0),
+ 'initial_min_max': {
+ 'glucose': (10, 10),
+ 'acetate': (0, 0),
+ 'biomass': (0, 0.1),
+ 'detritus': (0, 0)
+ },
+ # set particles
+ 'n_particles': 10,
+ 'particle_diffusion_rate': 1e-1,
+ 'particle_advection_rate': (0, -0.1),
+ 'particle_add_probability': 0.3,
+ 'particle_boundary_to_add': ['top'],
+ 'field_interactions': {
+ 'biomass': {
+ 'vmax': 0.1,
+ 'Km': 1.0,
+ 'interaction_type': 'uptake'
+ },
+ 'detritus': {
+ 'vmax': -0.1,
+ 'Km': 1.0,
+ 'interaction_type': 'secretion'
+ },
+ },
+}
+
+
+
+
+
+
+
+In [17]:
+
+
+
+
+
+# make the composite state
+composite_state = get_particle_comets_state(**particle_comets_config)
+
+# make the composite
+print('Making the composite...')
+sim = Composite({
+ 'state': composite_state,
+ 'emitter': {'mode': 'all'},
+}, core=core)
+
+# save the document
+sim.save(filename='particle_comets.json', outdir='out', include_schema=True)
+
+# # save a viz figure of the initial state
+
+# simulate
+print('Simulating...')
+sim.update({}, total_time)
+particle_comets_results = sim.gather_results()
+
+
+
+
+
+
+
+
+
+
+
+Making the composite... +Created new file: out/particle_comets.json +Simulating... ++
+
+
+
+
+
+
+
+In [18]:
+
+
+
+
+
+print('Plotting results...')
+# plot
+plot_species_distributions_with_particles_to_gif(
+ particle_comets_results,
+ out_dir='out',
+ filename='particle_comets_with_fields.gif',
+ title='',
+ skip_frames=1,
+ bounds=bounds,
+)
+
+
+
+
+
+
+
+
+
+
+
+Plotting results... +saving out/particle_comets_with_fields.gif ++
+
+
+
+
+
+
+