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Hello,
Learning from cobrapy tutorials, I have noticed a characteristic way of defining the biomass growth objective function, written as:
1.0Biomass_Ecoli_core - 1.0Biomass_Ecoli_core_reverse_2cdba
(see: https://cobrapy.readthedocs.io/en/latest/getting_started.html)
I do not yet understand the convention of naming these two reactions (i.e. the forward one and the reverse one). In cobrapy, I can print out the details of the forward reaction, obtaining:
1.496 3pg_c + 3.7478 accoa_c + 59.81 atp_c + 0.361 e4p_c + 0.0709 f6p_c + 0.129 g3p_c + 0.205 g6p_c + 0.2557 gln__L_c + 4.9414 glu__L_c + 59.81 h2o_c + 3.547 nad_c + 13.0279 nadph_c + 1.7867 oaa_c + 0.5191 pep_c + 2.8328 pyr_c + 0.8977 r5p_c
-->
59.81 adp_c + 4.1182 akg_c + 3.7478 coa_c + 59.81 h_c + 3.547 nadh_c + 13.0279 nadp_c + 59.81 pi_c
However, I cannot print out the reverse reaction; well, logically, it should just have a reverse direction (i.e. <-- instead of -->), and it such a case storing it separately would not be necessary. But how should I interpret the letters and numbers ending the name string ("2cdba")? Interestingly, when my colleague sent me a raw GEM of another taxon, generated with CarveMe defaults, I listed the default objective and got this:
"Maximize 1.0Growth - 1.0Growth_reverse_699ae"
with some other combination of numbers and letters.
Can someone shed some light on this?
Regards
Marek Augustyniak
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Hello,
Learning from cobrapy tutorials, I have noticed a characteristic way of defining the biomass growth objective function, written as:
1.0Biomass_Ecoli_core - 1.0Biomass_Ecoli_core_reverse_2cdba
(see: https://cobrapy.readthedocs.io/en/latest/getting_started.html)
I do not yet understand the convention of naming these two reactions (i.e. the forward one and the reverse one). In cobrapy, I can print out the details of the forward reaction, obtaining:
1.496 3pg_c + 3.7478 accoa_c + 59.81 atp_c + 0.361 e4p_c + 0.0709 f6p_c + 0.129 g3p_c + 0.205 g6p_c + 0.2557 gln__L_c + 4.9414 glu__L_c + 59.81 h2o_c + 3.547 nad_c + 13.0279 nadph_c + 1.7867 oaa_c + 0.5191 pep_c + 2.8328 pyr_c + 0.8977 r5p_c
-->
59.81 adp_c + 4.1182 akg_c + 3.7478 coa_c + 59.81 h_c + 3.547 nadh_c + 13.0279 nadp_c + 59.81 pi_c
However, I cannot print out the reverse reaction; well, logically, it should just have a reverse direction (i.e. <-- instead of -->), and it such a case storing it separately would not be necessary. But how should I interpret the letters and numbers ending the name string ("2cdba")? Interestingly, when my colleague sent me a raw GEM of another taxon, generated with CarveMe defaults, I listed the default objective and got this:
"Maximize 1.0Growth - 1.0Growth_reverse_699ae"
with some other combination of numbers and letters.
Can someone shed some light on this?
Regards
Marek Augustyniak
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