Comments (3)
Hi @vfisikop
The medium is being used by the user as you can see here.
Though, we were missing a setter, I fixed that already.
I also added an example of how to use this in the README
.
Similarly, the shut_down_reaction
is supposed not to allow a reaction to occur if the user goes for it.
These functions alter the model, thus the polytope that will be returned later on from the get_polytope
.
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Thanks for the clarification. Regarding medium
method if it is only used to update the dictionary then why not simply add a method update_medium
instead. Then the update will be done in one line of code and (more important) you will not copy the entire dictionary just to update a few entries.
from dingo.
Apologies, I am not sure I am following.
Once the medium is changed we need to change certain things in the model.
That's what we do in the setter
I tried to follow the scheme of cobrapy
for that as it's tricky.
I need to still work a little bit on it because now if someone tries this:
for k,v in model.medium.items():
model.medium[k] = 0
model.medium
will get
{'EX_co2_e': 0, 'EX_glc__D_e': 0, 'EX_h_e': 0, 'EX_h2o_e': 0, 'EX_nh4_e': 0, 'EX_o2_e': 0, 'EX_pi_e': 0}
but if they run model.fba()
they still get the initial solution.
Meaning the model.medium
looks like it changes but the constraints did not.
If you have any ideas let me know! :)
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Related Issues (20)
- include volume approximation HOT 1
- segmentation fault when ESS low
- Error importing MetabolicNetwork class from dingo package in Google Colab (GSoC 2023) HOT 1
- Add volume computation support and motivation
- sample asking for a min/max value of the objective function HOT 3
- non-uniqueness issue in dynamic FBA HOT 1
- Sampling on the flux space of multiple metabolic networks HOT 2
- rounding.py is excluded from github actions HOT 5
- Modify model's medium HOT 1
- alternative suffix for sbml models
- Error in installation (incompatible versions of Python and numpy) HOT 17
- Consider a docker image HOT 1
- Consider renaming `biomass_function` routine HOT 3
- `generate_steady_states` fails when you edit a model's optimal percentage twice
- Modernize LP solver interface HOT 1
- loopless sampling HOT 1
- Update README installation instructions to be more user friendly HOT 5
- Refactor mmcs algorithm
- Error using fva after sampling HOT 6
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