run simulation of the rhodo/syn co-culture under proper media conditions in MICOM

[vladpetyuk]

depends on #35

[mcnaughtonadm]

Initial runs of the binary model under proper media conditions yielded the following result:

compartments	abundance	growth_rate	reactions	metabolites
Rhodosporidium	0.5	2.432312	2398	2051
Synechococcus	0.5	2.0	851	768
medium	NaN	NaN	285	285

Media used for the optimization is as follows:

'EX_co2_m': 1.99, 'EX_h_m': 999999.0, 'EX_h2o_m': 999999.0, 'EX_nh4_m': 999999.0, 'EX_o2_m': 999999.0, 'EX_pi_m': 999999.0, 'EX_so4_m': 999999.0, 'EX_glcD_m': 1.0, 'EX_ca2_m': 999999.0, 'EX_fe2_m': 999999.0, 'EX_fe3_m': 999999.0, 'EX_hco3_m': 1.99, 'EX_k_m': 999999.0, 'EX_leuL_m': 1000.0, 'EX_na1_m': 999999.0, 'EX_no3_m': 1.76, 'EX_mg2_m': 999999.0, 'EX_mn2_m': 999999.0, 'EX_cu2_m': 999999.0, 'EX_zn2_m': 999999.0, 'EX_cobalt2_m': 1.7e-05, 'EX_mobd_m': 0.00016, 'EX_photon410_m': 1000.0, 'EX_photon430_m': 1000.0, 'EX_photon450_m': 1000.0, 'EX_photon470_m': 1000.0, 'EX_photon490_m': 1000.0, 'EX_photon510_m': 1000.0, 'EX_photon530_m': 1000.0, 'EX_photon550_m': 1000.0, 'EX_photon570_m': 1000.0, 'EX_photon590_m': 1000.0, 'EX_photon610_m': 1000.0, 'EX_photon630_m': 1000.0, 'EX_photon650_m': 1000.0, 'EX_photon670_m': 1000.0, 'EX_photon690_m': 1000.0

[mcnaughtonadm]

Working Example can be found at: https://github.com/PNNL-CompBio/ConsortiumModels/blob/main/Notebooks/Binary_Consortium_SE_RT.ipynb