Closed famosab closed 9 months ago
I realised that gly_cys___L
is used in the same way as cgly
. Decided to removegly_cys___L
since it has less reactions, less GPR references and did not occur in the periplasm. All reactions of gly_cys___L
were present with cgly
aswell so that no metabolites should be orphaned / dead-ended by this decision. GLYCYSAP, GLYCYSabc, EX_gly_cys__L_e
are the reactions containing gly_cys___L
and were removed aswell.
Script used: scripts/man_cur_dupmetab.py
The reactions PNCDC_1
, NP1_1
, NADDPp_1
were duplicates from their counterparts without _1. I found these during map creation.
Some automated steps done to the other models were also done on KC-Na-01
to make them a bit more in tune with each other. However KC-Na-01
is still missing the step towards manual refinement in a sense of removing duplicate metabolites and reactions (see README).
The refineGEMs.polish
module was updated recently. One run of this on each of the models will change identifiers and add parameters (with bounds).
reference this when the models are changed