Update and rename build_fba_network.py to build_metabolic_network.py

models/inside-cattle/scripts/build_metabolic_network.py

@@ -0,0 +1,33 @@
+############################################# BUILD METABOLIC NETWORK ###############################################
+# dependencies
+import cobra
+from cobra import *
+import os
+import d3flux as d3f
+from d3flux.core.flux_layouts import render_model
+from jinja2 import Template
+
+curdir = os.getcwd()
+
+# load in SBML file for methanobrevibacter ruminantium M1 - to run, download this from AGORA
+m_ruminantium = cobra.io.read_sbml_model(f"{curdir}/M_Methanobrevibacter_ruminantium_M1__44____32__AGORA__32__version__32__1__46__03.sbml")
+
+optimize = False # set this to run an optimization to minimize biomass
+
+if optimize:
+    # by default, the network is set to optimize biomass production when a flux balance analysis is run. set the objective function to also minimize the methane production and biomass production.
+    # preview objective function
+    print(m_ruminantium.objective)
+
+    # optimize on 'minimum' setting, return the objective value of solution
+    solution = m_ruminantium.optimize(min).objective_value
+
+    # preview solution
+    print(solution)
+
+summary = m_ruminantium.summary()
+print("Flux balance saved to 'assets/m_ruminantium_flux.txt'.")
+
+# with open("../assets/m_ruminantium_flux.txt", "w") as file:
+with open(f"{curdir}/assets/m_ruminantium_flux.txt", "w") as file:
+    file.write(f"{summary}")