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Modify model's medium #74

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TolisChal opened this issue Sep 6, 2023 · 1 comment
Closed

Modify model's medium #74

TolisChal opened this issue Sep 6, 2023 · 1 comment
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@TolisChal
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Modify both MetabolicNetwork and PolytopeSampler classes to change the bounds of the medium reactions
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hariszaf commented Sep 6, 2023 •
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use a dictionary as in cobra

 'EX_glc__D_e': 10.0,
 'EX_h_e': 1000.0,
 'EX_h2o_e': 1000.0,
 'EX_nh4_e': 1000.0,
 'EX_o2_e': 1000.0,
 'EX_pi_e': 1000.0}

and an internal one with the reactions' indexes

@hariszaf hariszaf self-assigned this Sep 6, 2023
hariszaf added a commit to hariszaf/dingo that referenced this issue Sep 9, 2023
@hariszaf
address issues GeomScale#74 and GeomScale#75
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@hariszaf hariszaf mentioned this issue Sep 9, 2023
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TolisChal pushed a commit that referenced this issue Jan 25, 2024
@hariszaf
support of medium modification and cobra model loading (#76)
e7a96d9 
* remove commented line

* address issues #74 and #75

* import Dict type

* test for boundary change and decreasing of fba when glc goes down

* edit test for media indices

* edit test for modify_medium()
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