bug: two unnecessary boundary metabolites - Githubissues

SysBioChalmers / Sco-GEM

The consensus GEM for Streptomyces coelicolor -

https://sysbiochalmers.github.io/Sco-GEM/

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bug: two unnecessary boundary metabolites #136

Closed sulheim closed 3 years ago

sulheim commented 3 years ago

Description of the issue:

Two exchange reactions included from iAA1259 contains so-called boundary metabolites, i.e.:

cellul_e_boundary
xylan_e_boundary Remove these metabolites

Expected feature/value/output:

(from yaml-file)

id: EX_cellul_e
- name: Cellulose exchange reaction
- metabolites: !!omap
  - cellul_e: -1.0
- lower_bound: 0.0 ....
id: EX_xylan_e
- name: Xylan exchange reaction
- metabolites: !!omap
  - xylan_e: -1.0
- lower_bound: 0.0 .....

Current feature/value/output:

id: EX_cellul_e
- name: Cellulose exchange reaction
- metabolites: !!omap
  - cellul_e: -1.0
  - cellul_e_boundary: 1.0
- lower_bound: 0.0 ....
id: EX_xylan_e
- name: Xylan exchange reaction
- metabolites: !!omap
  - xylan_e: -1.0
  - xylan_e_boundary: 1.0
- lower_bound: 0.0 .....

Reproducing these results:

Check model file

To do:

[ ] E.g. generate script for performing curation

I hereby confirm that:

[x] This problem persists in the master branch of the repository
[x] A similar issue does not already exist
[x] I've considered asking this first in the Gitter chat room