vivarium-collective / vivarium-notebooks Goto Github PK

from bioscrape_cobra.bioscrape_cobra_deterministic import BioscrapeCOBRAdeterministic
from bioscrape_cobra.simulate import get_bioscrape_cobra_config, simulate_bioscrape_cobra, plot_variables_list_deterministic
from bioscrape_cobra.plot import plot_single, config_single_cell_bioscrape_cobra_topology
from vivarium.plots.topology import plot_topology

# Show full topology here
#TODO wrap this so I can get the Composite before simulating
#bsc_composite_det = BioscrapeCOBRAdeterministic(get_bioscrape_cobra_config())

biocobra_data_det, comp0_det = simulate_bioscrape_cobra(
    initial_glucose=10, #mM
    initial_lactose=200, #mM
    total_time = 360, 
    output_type='timeseries')

biocobra_data_det, comp0_det = simulate_bioscrape_cobra(
    initial_glucose=10, #mM
    initial_lactose=200, #mM
    total_time = 361, 
    output_type='timeseries')

Using license file /Users/zuck016/gurobi.lic
Set parameter TokenServer to value leghorn.emsl.pnl.gov
Initializing experiment deterministic_20210706.184055
/Users/zuck016/.pyenv/versions/anaconda3-2020.11/lib/python3.8/site-packages/cobra/util/solver.py:508: UserWarning: Solver status is 'infeasible'.
  warn(f"Solver status is '{status}'.", UserWarning)
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-1-5f835dc253a1> in <module>
      8 #bsc_composite_det = BioscrapeCOBRAdeterministic(get_bioscrape_cobra_config())
      9 
---> 10 biocobra_data_det, comp0_det = simulate_bioscrape_cobra(
     11     initial_glucose=10, #mM
     12     initial_lactose=200, #mM

~/Projects/AgileBio/WholeCell/vivarium-notebooks/bioscrape_cobra/simulate.py in simulate_bioscrape_cobra(division, stochastic, spatial, initial_glucose, initial_lactose, initial_agent_states, bounds, n_bins, depth, diffusion_rate, jitter_force, divide_threshold, external_volume, n_agents, halt_threshold, total_time, sbml_file, emitter, output_type, parallel)
    599                 biocobra_experiment.update(sim_step)
    600     else:
--> 601         biocobra_experiment.update(total_time)
    602 
    603     # print runtime and finalize

~/.pyenv/versions/anaconda3-2020.11/lib/python3.8/site-packages/vivarium/core/engine.py in update(self, interval)
    644                     # TODO(chris): Is there any reason to generate a process's
    645                     #  schema dynamically like this?
--> 646                     update = self._process_update(
    647                         path, process, store, states, process_timestep)
    648 

~/.pyenv/versions/anaconda3-2020.11/lib/python3.8/site-packages/vivarium/core/engine.py in _process_update(self, path, process, store, states, interval)
    432         """
    433 
--> 434         update = self.invoke_process(
    435             process,
    436             path,

~/.pyenv/versions/anaconda3-2020.11/lib/python3.8/site-packages/vivarium/core/engine.py in invoke_process(self, process, path, interval, states)
    401             return self.parallel[path]
    402         # if not parallel, perform a normal invocation
--> 403         return self.invoke(process, interval, states)
    404 
    405     def _process_update(

~/.pyenv/versions/anaconda3-2020.11/lib/python3.8/site-packages/vivarium/core/engine.py in __init__(self, process, interval, states)
    188         self.interval = interval
    189         self.states = states
--> 190         self.update = invoke_process(
    191             self.process,
    192             self.interval,

~/.pyenv/versions/anaconda3-2020.11/lib/python3.8/site-packages/vivarium/core/engine.py in invoke_process(process, interval, states)
    124     """
    125     if process.update_condition(interval, states):
--> 126         return process.next_update(interval, states)
    127     return {}
    128 

~/.pyenv/versions/anaconda3-2020.11/lib/python3.8/site-packages/vivarium_cobra/processes/cobra_fba.py in next_update(self, timestep, states)
    270 
    271         # solve the fba problem
--> 272         objective_exchange = self.fba.optimize() * timestep  # mmol/L/s
    273         exchange_reactions = self.fba.read_exchange_reactions()
    274         exchange_fluxes = self.fba.read_exchange_fluxes()  # mmol/L/s

~/.pyenv/versions/anaconda3-2020.11/lib/python3.8/site-packages/vivarium_cobra/library/cobra_wrapper.py in optimize(self)
    339             self.solution = self.model.optimize()
    340 
--> 341         return self.objective_value()
    342 
    343     def external_reactions(self):

~/.pyenv/versions/anaconda3-2020.11/lib/python3.8/site-packages/vivarium_cobra/library/cobra_wrapper.py in objective_value(self)
    327     def objective_value(self):
    328         if self.solution:
--> 329             objective_value = self.solution.objective_value * self.flux_scaling
    330             return objective_value
    331         else:

TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'