PyCoMo Maximum Growth-Rate
This tutorial show-cases how to find the maximum growth-rate of a community - across all possible abundance profiles.
The expected runtime for this notebook is less than 10 minutes.
[1]:
from pathlib import Path
import sys
import os
import cobra
import math
import time
import warnings
[2]:
path_root = "../src" # Change path according to your PyCoMo location
sys.path.append(str(path_root))
import pycomo
pycomo.configure_logger(level="info")
2025-02-11 16:57:51,049 - pycomo - INFO - Logger initialized.
2025-02-11 16:57:51,051 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:57:51,051 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:57:51,053 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:57:51,054 - pycomo - INFO - Log level set to info
Load the Toy Models
These are simple toy models of 2 organisms. In a community, they are expexted to grow at a maximum of 10/h, however one organism alone can grow as fast as 15/h. Both cases can be calculated.
[3]:
# create two cobra models from sbml (change the path according to where the models are located)
toy1 = cobra.io.read_sbml_model("../data/use_case/toy_models/toy_1.xml")
toy2 = cobra.io.read_sbml_model("../data/use_case/toy_models/toy_2_2.xml")
# create Single Organism Models from cobra models
Toy1 = pycomo.SingleOrganismModel(toy1, "toy1")
Toy2 = pycomo.SingleOrganismModel(toy2, "toy2")
# create Community Model from Single Organism Models
C = pycomo.CommunityModel([Toy1, Toy2], name = "Toy_community")
# instantiate the model and set cplex as a solver (if available)
#C.model.solver = "cplex"
Compute maximum community growth rate
The method max_growth_rate calculates the overall maximum growth rate of the community, regardless of its composition.
[4]:
C.max_growth_rate()
2025-02-11 16:57:51,118 - pycomo - INFO - No community model generated yet. Generating now:
2025-02-11 16:57:51,126 - pycomo - INFO - Identified biomass reaction from objective: R4
2025-02-11 16:57:51,146 - pycomo - INFO - Identified biomass reaction from objective: R4
2025-02-11 16:57:51,207 - pycomo - WARNING - Not all reactions in the model are mass and charge balanced. To check which reactions are imbalanced, please run the get_unbalanced_reactions method of this CommunityModel object
2025-02-11 16:57:51,209 - pycomo - INFO - Generated community model.
2025-02-11 16:57:51,212 - pycomo - INFO - New round: lb: 0.0, ub: 1000.0, x: 2e-06
2025-02-11 16:57:52,205 - pycomo - INFO - Logger initialized.
2025-02-11 16:57:52,206 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:57:52,206 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:57:52,208 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:57:52,217 - pycomo - INFO - Logger initialized.
2025-02-11 16:57:52,217 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:57:52,218 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:57:52,219 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:57:52,237 - pycomo - INFO - Log level set to 20
2025-02-11 16:57:52,242 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:57:52,261 - pycomo - INFO - New round: lb: 10.0, ub: 1000.0, x: 10.000002
2025-02-11 16:57:53,214 - pycomo - INFO - Logger initialized.
2025-02-11 16:57:53,214 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:57:53,214 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:57:53,214 - pycomo - INFO - Logger initialized.
2025-02-11 16:57:53,215 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:57:53,215 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:57:53,216 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:57:53,217 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:57:53,246 - pycomo - INFO - Log level set to 20
2025-02-11 16:57:53,247 - pycomo - INFO - Log level set to 20
2025-02-11 16:57:53,248 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:57:53,267 - pycomo - INFO - New round: lb: 15.000000000000002, ub: 1000.0, x: 15.000002000000002
2025-02-11 16:57:54,245 - pycomo - INFO - Logger initialized.
2025-02-11 16:57:54,246 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:57:54,246 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:57:54,248 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:57:54,253 - pycomo - INFO - Logger initialized.
2025-02-11 16:57:54,254 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:57:54,255 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:57:54,256 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:57:54,277 - pycomo - INFO - Log level set to 20
2025-02-11 16:57:54,281 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:57:54,301 - pycomo - WARNING - Upper and lower bounds do not allow abundances to sum up to 1: toy1_fraction_reaction 0.0
toy2_fraction_reaction 0.0
Name: max_flux, dtype: float64, toy1_fraction_reaction 0
toy2_fraction_reaction 0
Name: min_flux, dtype: int64
2025-02-11 16:57:54,302 - pycomo - INFO - New round: lb: 15.000000000000002, ub: 15.000002000000002, x: 15.000001000000001
2025-02-11 16:57:55,252 - pycomo - INFO - Logger initialized.
2025-02-11 16:57:55,253 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:57:55,253 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:57:55,256 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:57:55,284 - pycomo - INFO - Log level set to 20
2025-02-11 16:57:55,289 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:57:55,305 - pycomo - WARNING - Upper and lower bounds do not allow abundances to sum up to 1: toy1_fraction_reaction 0.0
toy2_fraction_reaction 0.0
Name: max_flux, dtype: float64, toy1_fraction_reaction 0
toy2_fraction_reaction 0
Name: min_flux, dtype: int64
2025-02-11 16:57:55,308 - pycomo - INFO - Maximum growth-rate is 15.0
[4]:
np.float64(15.0)
max_growth_rate has the following parameters:
minimal_abundance(default = 0)return_abundances(default = False)sensitivity(default = 6)gurobi(default = False)
Return Abundances
By setting the parameter return_abundances to True, additional information about the feasible community compositions at the maximum growth rate is returned in the form of a pandas dataframe.
The minimal flux of x_fraction_reaction corresponds to the minimal abundance of member x in the community. Likewise, the maximal flux corresponds to the maximal abundance of member x.
[5]:
C.max_growth_rate(return_abundances=True)
2025-02-11 16:57:55,317 - pycomo - INFO - New round: lb: 0.0, ub: 1000.0, x: 2e-06
2025-02-11 16:57:56,280 - pycomo - INFO - Logger initialized.
2025-02-11 16:57:56,280 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:57:56,280 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:57:56,282 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:57:56,297 - pycomo - INFO - Logger initialized.
2025-02-11 16:57:56,298 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:57:56,298 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:57:56,299 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:57:56,312 - pycomo - INFO - Log level set to 20
2025-02-11 16:57:56,315 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:57:56,333 - pycomo - INFO - New round: lb: 10.0, ub: 1000.0, x: 10.000002
2025-02-11 16:57:57,234 - pycomo - INFO - Logger initialized.
2025-02-11 16:57:57,234 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:57:57,234 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:57:57,236 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:57:57,267 - pycomo - INFO - Log level set to 20
2025-02-11 16:57:57,273 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:57:57,291 - pycomo - INFO - New round: lb: 15.000000000000002, ub: 1000.0, x: 15.000002000000002
2025-02-11 16:57:58,167 - pycomo - INFO - Logger initialized.
2025-02-11 16:57:58,167 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:57:58,168 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:57:58,169 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:57:58,198 - pycomo - INFO - Log level set to 20
2025-02-11 16:57:58,203 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:57:58,219 - pycomo - WARNING - Upper and lower bounds do not allow abundances to sum up to 1: toy1_fraction_reaction 0.0
toy2_fraction_reaction 0.0
Name: max_flux, dtype: float64, toy1_fraction_reaction 0
toy2_fraction_reaction 0
Name: min_flux, dtype: int64
2025-02-11 16:57:58,220 - pycomo - INFO - New round: lb: 15.000000000000002, ub: 15.000002000000002, x: 15.000001000000001
2025-02-11 16:57:59,219 - pycomo - INFO - Logger initialized.
2025-02-11 16:57:59,219 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:57:59,220 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:57:59,222 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:57:59,225 - pycomo - INFO - Logger initialized.
2025-02-11 16:57:59,226 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:57:59,226 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:57:59,228 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:57:59,250 - pycomo - INFO - Log level set to 20
2025-02-11 16:57:59,255 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:57:59,271 - pycomo - WARNING - Upper and lower bounds do not allow abundances to sum up to 1: toy1_fraction_reaction 0.0
toy2_fraction_reaction 0.0
Name: max_flux, dtype: float64, toy1_fraction_reaction 0
toy2_fraction_reaction 0
Name: min_flux, dtype: int64
2025-02-11 16:58:00,294 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:00,295 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:00,295 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:00,296 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:00,325 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:00,325 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:00,325 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:00,327 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:00,328 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:00,332 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:58:00,346 - pycomo - INFO - Maximum growth-rate is reaction_id min_flux max_flux
0 toy1_fraction_reaction 0.0 0.0
1 toy2_fraction_reaction 1.0 1.0
2 community_biomass 15.0 15.0
[5]:
| reaction_id | min_flux | max_flux | |
|---|---|---|---|
| 0 | toy1_fraction_reaction | 0.0 | 0.0 |
| 1 | toy2_fraction_reaction | 1.0 | 1.0 |
| 2 | community_biomass | 15.0 | 15.0 |
Minimal abundance
Edge cases exist in which the highest growth rate of a community is not achieved by a combination of all the members. Instead, one member with an abundance of 100% may achieve the maximum growth rate.
In order to exclude these cases, the parameter minimal_abundance must be set to a float greater than 0. This sets the minimal abundance of all members to the set float. Take care that the sum of the minimal abundances is not greater than 1, as this will result in an error.
[6]:
C.max_growth_rate(minimal_abundance=0.1)
2025-02-11 16:58:00,355 - pycomo - INFO - New round: lb: 0.0, ub: 1000.0, x: 2e-06
2025-02-11 16:58:01,304 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:01,305 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:01,305 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:01,307 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:01,312 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:01,312 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:01,313 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:01,314 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:01,335 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:01,340 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:58:01,357 - pycomo - INFO - New round: lb: 10.0, ub: 1000.0, x: 10.000002
2025-02-11 16:58:02,281 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:02,281 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:02,281 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:02,283 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:02,313 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:02,317 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:58:02,335 - pycomo - WARNING - Not all upper bounds are bigger than the set minimal abundance:
toy1_fraction_reaction 0.0
toy2_fraction_reaction 1.0
Name: max_flux, dtype: float64
2025-02-11 16:58:02,335 - pycomo - INFO - New round: lb: 10.0, ub: 10.000002, x: 10.000001000000001
2025-02-11 16:58:03,265 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:03,265 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:03,265 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:03,267 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:03,276 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:03,277 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:03,277 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:03,279 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:03,295 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:03,298 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:58:03,313 - pycomo - WARNING - Not all upper bounds are bigger than the set minimal abundance:
toy1_fraction_reaction 0.0
toy2_fraction_reaction 1.0
Name: max_flux, dtype: float64
2025-02-11 16:58:03,314 - pycomo - INFO - New round: lb: 10.0, ub: 10.000001000000001, x: 10.0000005
2025-02-11 16:58:04,201 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:04,201 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:04,201 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:04,203 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:04,206 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:04,206 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:04,206 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:04,208 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:04,228 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:04,232 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:58:04,251 - pycomo - INFO - Maximum growth-rate is 10.0
[6]:
np.float64(10.0)
[7]:
# too large minimal_abundance value leads to an error
try:
C.max_growth_rate(minimal_abundance=0.6)
except ValueError:
print("Error thrown!")
# The community has two members:
# 2 * 0.6 = 1.2
# 1.2 > 1
Error thrown!
Example: Biogas producing community
The example for this part will be a three member community published by Koch et al. 2019 (https://doi.org/10.1371/journal.pcbi.1006759). The three member organisms are representatives of functional guilds in a biogas community.
[8]:
# create cobra models from sbml
dv = cobra.io.read_sbml_model("../data/use_case/koch/dv.xml")
mh = cobra.io.read_sbml_model("../data/use_case/koch/mh.xml")
mb = cobra.io.read_sbml_model("../data/use_case/koch/mb.xml")
# change infinite upper bounds to 1000
for model in [dv,mh,mb]:
for reaction in model.reactions:
if reaction.upper_bound == math.inf:
reaction.upper_bound = 1000.
if reaction.lower_bound == -math.inf:
reaction.lower_bound = -1000.
# create Single Organism Models from cobra models
DV = pycomo.SingleOrganismModel(dv, "dv")
MH = pycomo.SingleOrganismModel(mh, "mh")
MB = pycomo.SingleOrganismModel(mb, "mb")
# create Community Model from Single Organism Models
C2 = pycomo.CommunityModel([DV, MH, MB], name = "dv_mh_mb_community")
# set solver to cplex (if available)
#C2.model.solver = "cplex"
# apply the same medium as in the paper by Koch et al.
medium = {
'EX_CO2_EX_medium': 1000.0,
'EX_Eth_EX_medium': 1000.0,
'EX_BM_tot_medium': 1000.0
}
C2.medium = medium
C2.apply_medium()
# Formate and Hydrogen are not allowed to accumulate in the medium.
C2.model.reactions.get_by_id("EX_Form_EX_medium").upper_bound = 0.
C2.model.reactions.get_by_id("EX_H2_EX_medium").upper_bound = 0.
'3PG' is not a valid SBML 'SId'.
'2PG' is not a valid SBML 'SId'.
'2PG__PEP' is not a valid SBML 'SId'.
'3PG__2PG' is not a valid SBML 'SId'.
'0Pyr__AcCoA' is not a valid SBML 'SId'.
'5CHOMPT' is not a valid SBML 'SId'.
'3PG' is not a valid SBML 'SId'.
'2PG' is not a valid SBML 'SId'.
'2PG__3PG' is not a valid SBML 'SId'.
'3PG__DPG' is not a valid SBML 'SId'.
'5CHOMPT__CHH4MPT' is not a valid SBML 'SId'.
'3PG' is not a valid SBML 'SId'.
'2PG' is not a valid SBML 'SId'.
'5CHOMPT' is not a valid SBML 'SId'.
'3PG__2PG__3PG' is not a valid SBML 'SId'.
'5CHOMPT__CHH4MPT' is not a valid SBML 'SId'.
2025-02-11 16:58:04,460 - pycomo - INFO - No community model generated yet. Generating now:
2025-02-11 16:58:04,473 - pycomo - INFO - Identified biomass reaction from objective: r_BMDV2BMc
2025-02-11 16:58:04,607 - pycomo - INFO - Identified biomass reaction from objective: BM_Synth
2025-02-11 16:58:04,798 - pycomo - INFO - Identified biomass reaction from objective: BM_Synth
2025-02-11 16:58:05,046 - pycomo - WARNING - No annotation overlap found for matching several metabolites (8). Please make sure that the matched metabolites are indeed representing the same substance in all models! The list of metaboliteswithout annotation overlap can be accessed via 'model.no_annotation_overlap'
2025-02-11 16:58:05,117 - pycomo - INFO - Generated community model.
[9]:
# calculate max growth rate of community
C2.max_growth_rate()
2025-02-11 16:58:05,131 - pycomo - INFO - New round: lb: 0.0, ub: 1000.0, x: 2e-06
2025-02-11 16:58:06,131 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:06,131 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:06,131 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:06,133 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:06,234 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:06,999 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:07,000 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:07,000 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:07,001 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:07,100 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:08,108 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:08,109 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:08,109 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:08,111 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:08,153 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:58:08,214 - pycomo - INFO - New round: lb: 0.05212885425733065, ub: 1000.0, x: 0.052130854257330654
2025-02-11 16:58:08,290 - pycomo - INFO - New round: lb: 0.05212885425733065, ub: 0.052130854257330654, x: 0.05212985425733065
2025-02-11 16:58:08,346 - pycomo - INFO - New round: lb: 0.05212885425733065, ub: 0.05212985425733065, x: 0.05212935425733065
2025-02-11 16:58:09,356 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:09,357 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:09,357 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:09,359 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:09,481 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:10,201 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:10,201 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:10,201 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:10,203 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:10,319 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:10,974 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:10,975 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:10,975 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:10,976 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:11,034 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:58:11,048 - pycomo - WARNING - Upper and lower bounds do not allow abundances to sum up to 1: dv_fraction_reaction 0.0
mh_fraction_reaction 0.0
mb_fraction_reaction 0.0
Name: max_flux, dtype: float64, dv_fraction_reaction 0
mh_fraction_reaction 0
mb_fraction_reaction 0
Name: min_flux, dtype: int64
2025-02-11 16:58:11,077 - pycomo - INFO - Maximum growth-rate is 0.052128
[9]:
np.float64(0.052128)
[10]:
# calculate abundance profile as well
C2.max_growth_rate(return_abundances=True)
2025-02-11 16:58:11,085 - pycomo - INFO - New round: lb: 0.0, ub: 1000.0, x: 2e-06
2025-02-11 16:58:12,016 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:12,016 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:12,016 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:12,018 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:12,156 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:12,937 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:12,938 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:12,938 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:12,940 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:13,042 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:13,815 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:13,816 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:13,816 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:13,818 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:13,859 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:58:13,910 - pycomo - INFO - New round: lb: 0.05212885425733052, ub: 1000.0, x: 0.05213085425733052
2025-02-11 16:58:13,982 - pycomo - INFO - New round: lb: 0.05212885425733052, ub: 0.05213085425733052, x: 0.05212985425733052
2025-02-11 16:58:14,020 - pycomo - INFO - New round: lb: 0.05212885425733052, ub: 0.05212985425733052, x: 0.05212935425733052
2025-02-11 16:58:14,905 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:14,905 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:14,905 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:14,907 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:15,012 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:15,730 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:15,731 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:15,731 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:15,733 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:15,847 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:16,571 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:16,572 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:16,572 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:16,574 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:16,651 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:58:16,669 - pycomo - WARNING - Upper and lower bounds do not allow abundances to sum up to 1: dv_fraction_reaction 0.0
mh_fraction_reaction 0.0
mb_fraction_reaction 0.0
Name: max_flux, dtype: float64, dv_fraction_reaction 0
mh_fraction_reaction 0
mb_fraction_reaction 0
Name: min_flux, dtype: int64
2025-02-11 16:58:17,561 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:17,562 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:17,563 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:17,565 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:17,677 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:18,445 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:18,446 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:18,446 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:18,448 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:18,548 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:19,277 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:19,278 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:19,278 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:19,280 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:19,316 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:58:19,332 - pycomo - INFO - Maximum growth-rate is reaction_id min_flux max_flux
0 dv_fraction_reaction 0.074553 0.393590
1 mh_fraction_reaction 0.000000 0.681848
2 mb_fraction_reaction 0.000000 0.925447
3 community_biomass 0.052128 0.052128
[10]:
| reaction_id | min_flux | max_flux | |
|---|---|---|---|
| 0 | dv_fraction_reaction | 0.074553 | 0.393590 |
| 1 | mh_fraction_reaction | 0.000000 | 0.681848 |
| 2 | mb_fraction_reaction | 0.000000 | 0.925447 |
| 3 | community_biomass | 0.052128 | 0.052128 |
Sensitivity
The sensitivity parameter describes the amount of decimal places that should be calculated. The default is set to 6, as the cplex solver may return inaccurate results at a higher value.
[11]:
# sensitivity = 4
C2.max_growth_rate(sensitivity=4)
2025-02-11 16:58:19,340 - pycomo - INFO - New round: lb: 0.0, ub: 1000.0, x: 0.0002
2025-02-11 16:58:20,217 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:20,218 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:20,218 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:20,219 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:20,319 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:21,085 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:21,086 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:21,086 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:21,088 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:21,193 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:21,990 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:21,991 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:21,991 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:21,993 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:22,031 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:58:22,084 - pycomo - INFO - New round: lb: 0.0521288542573306, ub: 1000.0, x: 0.052328854257330595
2025-02-11 16:58:22,151 - pycomo - INFO - New round: lb: 0.0521288542573306, ub: 0.052328854257330595, x: 0.05222885425733059
2025-02-11 16:58:22,221 - pycomo - INFO - Maximum growth-rate is 0.0521
[11]:
np.float64(0.0521)
[12]:
# sensitivity = 2
C2.max_growth_rate(sensitivity=2)
2025-02-11 16:58:22,229 - pycomo - INFO - New round: lb: 0.0, ub: 1000.0, x: 0.02
2025-02-11 16:58:23,158 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:23,159 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:23,159 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:23,161 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:23,260 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:24,086 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:24,087 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:24,087 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:24,089 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:24,199 - pycomo - INFO - Log level set to 20
2025-02-11 16:58:24,972 - pycomo - INFO - Logger initialized.
2025-02-11 16:58:24,973 - pycomo - INFO - Process Pool Logger initialized.
2025-02-11 16:58:24,973 - pycomo - INFO - Utils Logger initialized.
2025-02-11 16:58:24,975 - pycomo - INFO - Multiprocess Logger initialized.
2025-02-11 16:58:25,014 - pycomo - INFO - Processed 100.0% of fva steps
2025-02-11 16:58:25,068 - pycomo - INFO - New round: lb: 0.052128854257330645, ub: 1000.0, x: 0.07212885425733065
2025-02-11 16:58:25,138 - pycomo - INFO - New round: lb: 0.052128854257330645, ub: 0.07212885425733065, x: 0.06212885425733065
2025-02-11 16:58:25,175 - pycomo - INFO - New round: lb: 0.052128854257330645, ub: 0.06212885425733065, x: 0.05712885425733065
2025-02-11 16:58:25,243 - pycomo - INFO - Maximum growth-rate is 0.05
[12]:
np.float64(0.05)
[ ]: