# ---------------------------------------------------------------------- # A model for HumanCyc # # ---------------------------------------------------------------------- pgdb: human # ====================================================================== # Fixed sets. These sets could be empty. # ====================================================================== reactions: metab-all remove-reactions: # The fixed set of biomass metabolites. biomass: THIAMINE-PYROPHOSPHATE # thiamine diphosphate FAD # flavin adenine dinucleotide PYRIDOXAL_PHOSPHATE # pyridoxal 5'-phosphate CO-A # coenzyme A # Lipids PALMITATE # Palmitic # CPD-7836 # Myristic CPD-9245 # Palmitoleic STEARIC_ACID # Stearic # OLEATE-CPD # Oleic CHOLESTEROL # Cholesterol CPD66-34 # Diglycerides CPD66-35 # tripalmitate 1-2-DIPALMITOYLPHOSPHATIDYLCHOLINE CPD-12819 # 1,2-dipalmitoyl-phosphatidyl-ethanolamine CPD66-42 # Sphingomyelin CPD66-46 # (dipalmitoyl-1-phosphatidyl-1D-myo-inositol 4-phosphate) CPD-12817 # 1,2-dipalmitoyl-phosphatidylserine CPD-8260 # 1,2-dipalmitoyl-phosphatidyl-glycerol DAMP DCMP DGMP TMP AMP CMP GMP UMP L-ALPHA-ALANINE # Alanine ARG # Arginine ASN # Asparagine L-ASPARTATE # Aspartate CYS # Cysteine GLT # Glutamate GLN # Glutamine GLY # Glycine HIS # Histidine ILE # Isoleucine LEU # Leucine LYS # Lysine MET # Methionine PHE # Phenylalanine PRO # Proline SER # Serine THR # Threonine TRP # Tryptophan TYR # Tyrosine VAL # Valine ATP # ATP ADP # ADP Pi # |Pi| PROTON # H WATER # H2O # The fixed nutrients (metabolites) to use. nutrients: # Vitamins THIAMINE # thiamine (B1) RIBOFLAVIN # riboflavin (B2) PYRIDOXINE # pyridoxine PANTOTHENATE # (R)-pantothenate GLC :lower-bound 0.1 # beta-D-glucose # Amino acids # ARG GLN :lower-bound 0.1 HIS ILE LEU LYS MET PHE THR :lower-bound 0.1 TRP VAL # The fixed secretions (metabolites) to use. secretions: carbon-dioxide urea 4-methylpentanal # ============================================================================== # Try sets. These sets could be empty. There can be several non-empty try sets. # If at least one try set is not empty, the FBA analysis is a gap filling FBA. # If there are no try sets, it is a standard FBA analysis. # =============================================================================== # # The biomass metabolites to try to add to the model. # try-biomass: TESTOSTERONE # testosterone ESTRONE # estrone CORTISOL # cortisol ALDOSTERONE # aldosterone # The nutrients (metabolites) to try to add to the model. try-nutrients: # BUTYRIC_ACID # CA+2 # HCO3 # CL- # CPD-7836 # OLEATE-CPD OXYGEN-MOLECULE Pi # K+ PYRUVATE # Na+ # STEARIC_ACID # SULFATE WATER NADH NADPH CHOLINE try-reactions: metacyc-metab-all # The secretions (metabolites) to try to add to the model. try-secretions: # Weights for the try sets. # # Note: if no try-sets are given all these weights are not used. # A weight is only meaningful if a corresponding try set # is specified for it. # The weight for adding one nutrient. This value is typically a small negative value (cost). try-nutrients-weight: -1 # The weight for adding one reaction from MetaCyc. This value is typically negative (cost). try-reactions-weight: -120 # The weight for adding the reverse of a irreversible reaction from # the pgdb. This is typically negative (cost). try-reactions-reverse-weight: -40 # The weight for adding the reverse of a irreversible reaction from # the MetaCyc. This is typically negative (cost). try-reactions-reverse-try-weight: -150 # The weight for adding one reaction from MetaCyc in the taxonomic range of # the pgdb. This is typically negative (cost). try-reactions-in-taxa-weight: -80 # The weight for adding one reaction from MetaCyc in the taxonomic range of # the pgdb. This is typically negative (cost). try-reactions-unknown-taxa-weight: -100 # The weight for adding a secretion to the model. try-secretions-weight: 2 # The weight of adding one metabolite to the biomass. # Typically, this is positive and at least ten times larger, # in absolute value, than all the other weights. try-biomass-weight: 10000 # Add, to the try-reactions set, the reverse of irreversible reactions # provided by section reactions? try-add-reverse-rxns: yes # Add, to the try-reactions set, the reverse of irreversible reactions # provided by section try-reactions? try-add-reverse-try-rxns: yes # Other parameters. # The maximum number of seconds to let the solver run. If the solver # has not optimally solved the model after that time, a suboptimal solution # will be reported. max-time-solver: 300 # End of File