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draeger-lab / C_striatum_GEMs

This repository contains all changes made to the strain specific models of Corynebacterium striatum.
MIT License
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changes to the models #1

Closed famosab closed 9 months ago

famosab commented 2 years ago

reference this when the models are changed

famosab commented 2 years 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

famosab commented 2 years ago

The reactions PNCDC_1, NP1_1, NADDPp_1 were duplicates from their counterparts without _1. I found these during map creation.

famosab commented 2 years ago

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).

famosab commented 1 year ago

The refineGEMs.polish module was updated recently. One run of this on each of the models will change identifiers and add parameters (with bounds).