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klamt-lab
iMM904 Production Envelopes plot_flux_space
Hi, I got the following problem running plot_flux_space function on the iMM904 model (no modification from the BiGG). Am I missing any argument? Thank you in advance and beautiful module!
import cobra
import straindesign as sd
model = cobra.io.read_sbml_model("iMM904.xml")
product_id = "EX_etoh_e"
biomass_id = "BIOMASS_SC5_notrace"
sd.plot_flux_space(model, (biomass_id, product_id))
Empty plot and several warnings:
WARNING:root:Computing matrix rank or Delaunay simplices failed.
Hi Emanuel,
This error is produced when straindesign attempts to plot the flux space and then fails because it cannot connect the calculated outlines of the flux space projection into a shape. This either happens if there are no solutions to the model or if some number of calculated solutions are invalid. The latter is the case here. This is definitely a bug since both fluxes, ethanol exchange and growth, have upper and lower bounds and the flux space within these boundaries is convex.
I was able to reproduce your problem when using python 3.12. I tried it with python 3.10 instead, and all four solvers managed to produce a valid plot.
Can you test your code with python 3.10 and different solvers (at least glpk and scip) and/or with different solvers in 3.12 and tell me if the problem persists? I should try to resolve the issue and if not possible, pin the python version for strain design to 3.10 (or 3.11) and below.
Hi Philipp,
Many thanks for your very prompt help!
I'm actually using Python 3.10.12 and the Optlang GLPK solver. Could it be the version of the packages? I leave bellow the details of my environment.
# packages in environment at /opt/miniconda3/envs/cobrapy:
#
# Name Version Build Channel
annotated-types 0.6.0 pypi_0 pypi
anyio 3.7.1 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
appnope 0.1.4 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
bzip2 1.0.8 h80987f9_5
ca-certificates 2024.2.2 hf0a4a13_0 conda-forge
certifi 2024.2.2 pypi_0 pypi
click 8.1.7 pypi_0 pypi
cobra 0.26.2 pypi_0 pypi
comm 0.2.2 pyhd8ed1ab_0 conda-forge
cycler 0.12.1 pypi_0 pypi
debugpy 1.6.7 py310h313beb8_0
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
depinfo 1.7.0 pypi_0 pypi
diskcache 5.6.3 pypi_0 pypi
exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge
executing 2.0.1 pyhd8ed1ab_0 conda-forge
fonttools 4.50.0 pypi_0 pypi
future 1.0.0 pypi_0 pypi
h11 0.12.0 pypi_0 pypi
httpcore 0.15.0 pypi_0 pypi
httpx 0.23.0 pypi_0 pypi
idna 3.6 pypi_0 pypi
importlib-metadata 7.1.0 pyha770c72_0 conda-forge
importlib-resources 6.4.0 pypi_0 pypi
importlib_metadata 7.1.0 hd8ed1ab_0 conda-forge
inspyred 1.0.2 pypi_0 pypi
ipykernel 6.29.3 pyh3cd1d5f_0 conda-forge
ipython 8.23.0 pypi_0 pypi
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jmetalpy 1.5.5 pypi_0 pypi
joblib 1.3.2 pypi_0 pypi
jpype1 1.5.0 pypi_0 pypi
jupyter_client 8.6.1 pyhd8ed1ab_0 conda-forge
jupyter_core 5.5.0 py310hca03da5_0
kiwisolver 1.4.5 pypi_0 pypi
libcxx 16.0.6 h4653b0c_0 conda-forge
libffi 3.4.4 hca03da5_0
libsodium 1.0.18 h27ca646_1 conda-forge
markdown-it-py 3.0.0 pypi_0 pypi
matplotlib 3.5.0 pypi_0 pypi
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mdurl 0.1.2 pypi_0 pypi
mewpy 0.1.34 pypi_0 pypi
mpmath 1.3.0 pypi_0 pypi
ncurses 6.4 h313beb8_0
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
networkx 3.2.1 pypi_0 pypi
numpy 1.23.5 pypi_0 pypi
openssl 3.2.1 h0d3ecfb_1 conda-forge
optlang 1.8.1 pypi_0 pypi
packaging 24.0 pyhd8ed1ab_0 conda-forge
pandas 1.5.3 pypi_0 pypi
parso 0.8.3 pyhd8ed1ab_0 conda-forge
patsy 0.5.6 pypi_0 pypi
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.3.0 pypi_0 pypi
pip 23.3.1 py310hca03da5_0
platformdirs 4.2.0 pyhd8ed1ab_0 conda-forge
plotly 5.20.0 pypi_0 pypi
prompt-toolkit 3.0.43 pypi_0 pypi
psutil 5.9.0 py310h1a28f6b_0
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pydantic 1.10.14 pypi_0 pypi
pydantic-core 2.16.3 pypi_0 pypi
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pyparsing 3.1.2 pypi_0 pypi
python 3.10.12 hb885b13_0
python-dateutil 2.9.0.post0 pypi_0 pypi
python-libsbml 5.20.2 pypi_0 pypi
pytz 2024.1 pypi_0 pypi
pyzmq 25.1.2 py310h313beb8_0
readline 8.2 h1a28f6b_0
reframed 1.5.1 pypi_0 pypi
rfc3986 1.5.0 pypi_0 pypi
rich 13.7.1 pypi_0 pypi
ruamel-yaml 0.18.6 pypi_0 pypi
ruamel-yaml-clib 0.2.8 pypi_0 pypi
scipy 1.12.0 pypi_0 pypi
setuptools 68.2.2 py310hca03da5_0
setuptools-scm 8.0.4 pypi_0 pypi
six 1.16.0 pyh6c4a22f_0 conda-forge
sniffio 1.3.1 pypi_0 pypi
sqlite 3.41.2 h80987f9_0
stack-data 0.6.3 pypi_0 pypi
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
statsmodels 0.14.1 pypi_0 pypi
straindesign 1.11 pypi_0 pypi
swiglpk 5.0.10 pypi_0 pypi
sympy 1.12 pypi_0 pypi
tdqm 0.0.1 pypi_0 pypi
tenacity 8.2.3 pypi_0 pypi
tk 8.6.12 hb8d0fd4_0
tomli 2.0.1 pypi_0 pypi
tornado 6.3.3 py310h80987f9_0
tqdm 4.66.2 pypi_0 pypi
traitlets 5.14.2 pyhd8ed1ab_0 conda-forge
typing_extensions 4.10.0 pyha770c72_0 conda-forge
tzdata 2024.1 pypi_0 pypi
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
wheel 0.41.2 py310hca03da5_0
xz 5.4.6 h80987f9_0
zeromq 4.3.5 hebf3989_1 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h5a0b063_0
Hi,
I was digging a bit more on this I found that:
- I had
cobrapy 0.26.2, I created a new environment andpip installed straindesignwith bringscobrapy 0.29.0. I still get the warnings:
sd.plot_flux_space(model, (rxnBiomass, rxnTarget))
WARNING:root:Computing matrix rank or Delaunay simplices failed.
WARNING:root:Computing matrix rank or Delaunay simplices failed.
WARNING:root:Computing matrix rank or Delaunay simplices failed.
(...)
and generates this plot:
- I tried the production envelope function from cobrapy and get a different result, which to me makes more sense.
prod_env = production_envelope(model, [rxnTarget], objective=rxnBiomass)
prod_env.plot(kind="line", x="flux_maximum", y=rxnTarget)
Whole script:
import cobra
import straindesign as sd
import matplotlib.pyplot as plt
from cobra.flux_analysis import production_envelope
from cobra.flux_analysis import flux_variability_analysis
rxnBiomass = "BIOMASS_SC5_notrace"
rxnTarget = "EX_etoh_e"
rxnGlucose = "EX_glc__D_e"
rxnOxygen = "EX_o2_e"
model = cobra.io.read_sbml_model("iMM904.xml")
medium_changed = model.medium.copy()
medium_changed[rxnGlucose] = 10.0
medium_changed[rxnOxygen] = 1.0
model.medium = medium_changed
# Strain desgin
sd.plot_flux_space(model, (rxnBiomass, rxnTarget))
# Cobrapy
prod_env = production_envelope(model, [rxnTarget], objective=rxnBiomass)
prod_env.plot(kind="line", x="flux_maximum", y=rxnTarget)
plt.show()
Thank you!
Hi again. I just wanted to tell you that I'm working on a solution for this. There seem to be two problems, both with GLPK at their root. Problem one is that the solver selection for computing the production envelope is inconsistent and would pick GLPK for some things, even though a different solver was selected by the user. After fixing this, I would produce the right production envelope for gurobi, scip and cplex, but not yet for GLPK, so that's where I'm at.
For the meantime, you might want to install gurobi or cplex and make it your model solver https://anaconda.org/conda-forge/pyscipopt until I have fixed the GLPK issue.
This was fixed with my last commit, by simply increasing the bounding tolerance for GLPK. Hope that doesn't worsen other aspects of straindesign that involve GLPK. I will close this issue for now, fix the other issue, bump the version and make a new release. Please test and reopen this issue if the problem persists.
I'm reopening this. Loosening the tolerance for GLPK breaks other parts of the package. Consider using SCIP, instead, for the time being. I will try to find a solution without changing GLPK tolerances.
Thank you again for raising the issue. This really helps to improve StrainDesign :)