carrascomj / mmodes

MMODES (Metabolic Models based Ordinary Differential Equations Simulation)

What is MMODES?

MMODES (Metabolic Models based Ordinary Differential Equations Simulation) provides an straight-forward framework to run dynamic simulations of metabolic models communities using COBRApy and Scipy.

It implements a version of dFBA. The scipy ODE implementation of the script was inspired by DAPHNE, although this code was built for a general case. It also provides I/O utilities to generate and parse COMETS-like files and to manage "languages" of GEM models.

Documentation

User documentation can be found on https://mmodes.readthedocs.io/.

Installation

Working on a virtualenv is highly recommended since the package uses the latest python3 versions of the modules required. More information about Python virtualenv's here.

MMODES is on PyPi, therefore, given that pip in installed:

pip upgrade pip --user
pip3 install mmodes --user

Another option is building from source. Clone this repository and install it via setup.py:

git clone https://github.com/carrascomj/mmodes.git # or ssh
cd path_to_mmodes/mmodes
sudo python3 setup.py install

On both cases, uninstalling can be accomplished via pip:

pip3 uninstall mmodes --user # if user install
sudo pip3 uninstall mmodes # if superuser install (from source)

Docker

A Docker container is under development.

Example script simulation

An example with one strain can be found on "example.py".

mmodes's Issues

MMODES is not able to recognise metabolites to plot in my GEM

I have been trying to use MMODES to do a simulation using my GEM tracking the acetate and propionate production over time. However when I try to run the model I get this error:
"Metabolite ac_e won't be plotted. Check your spelling of this metabolite.

Metabolite ppa_e won't be plotted. Check your spelling of this metabolite.
Metabolites weren't properly supplied in 'mets_to_plot' parameter. Plot won't be generated!"

I have used the exact same metabolite names as in the SBML file and I have used all different variations of the name as well already. The rest of my code looks like this:
"from mmodes import Consortium, dMetabolite
cons = Consortium(mets_to_plot = ['ac_e', 'ppa_e'])
glc = dMetabolite(id = 'glc__D_e', Km = 14.8, Vmax = 0.13)
path_to_model = "C:/Users/Sam/Jupyter notebooks/prevotella_ruminicola_1_v7_biomass.xml"
cons.add_model(path_to_model, 0.03, dMets = {glc.id: glc})
medium = {'ala__L_e': 0.938846598,
'arab__L_e': 0.666427627,
'arg__L_e': 0.133660701,
'asn__L_e': 0.400330802,
'ca2_e': 1000,
'cl_e': 1000,
'cobalt2_e': 1000,
'cu2_e': 1000,
'cys__L_e': 0.114920408,
'fe2_e': 1000,
'fe3_e': 1000,
'gal_e': 0.075513967,
'glc__D_e': 2.725243655,
'gln__L_e': 0.080568485,
'glu__L_e': 1.597816364,
'glucan4_e': 0.320930655,
'gly_e': 0.268595078,
'h2_e': 1000,
'h2o_e': 1000,
'h2s_e': 1000,
'h_e': 1000,
'his__L_e': 0.124559013,
'ile__L_e': 0.211165444,
'k_e': 1000,
'leu__L_e': 1.148366562,
'lys__L_e': 0.098373937,
'met__L_e': 0.233929798,
'mg2_e': 1000,
'mn2_e': 1000,
'nh4_e': 1000,
'no2_e': 1000,
'no3_e': 1000,
'phe__L_e': 0.310015056,
'pi_e': 0.005244478,
's_e': 1000,
'ser__D_e': 0.317276246,
'so3_e': 1000,
'so4_e': 0.004273279,
'thr__L_e': 0.261179221,
'tyr__L_e': 0.218417727,
'urea_e': 0.629166662,
'val__L_e': 0.385856944,
'xyl__D_e': 0.877945961,
'zn2_e': 1000,
'sucr_e': 0.834726132,
'lnlc_e': 0.610370885,
'gtp_e': 0.007734655,
'man_e': 0.021731242,
'ctp_e': 0.00730785,
'atp_e': 0.006289719,
'utp_e': 0.005932755,
'datp_e': 0.001147315,
'dttp_e': 0.001147552,
'dgtp_e': 0.001012678,
'dctp_e': 0.001016235, 'ac_e' : 0, 'ppa_e':0}
cons.media = cons.set_media(medium)
cons.run(maxT = 10, stepChoiceLevel = (0, 1, 10), outf = "output_test2.tsv", outp = "plot_test2.png", verbose=True)"

How can I fix this? Thank you in advance!