Closed vladpetyuk closed 1 year ago
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
Working Example can be found at: https://github.com/PNNL-CompBio/ConsortiumModels/blob/main/Notebooks/Binary_Consortium_SE_RT.ipynb
depends on #35