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Create a 'main' function #24

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mcnaughtonadm opened this issue Sep 10, 2024 · 0 comments · May be fixed by #28
Open

Create a 'main' function #24

mcnaughtonadm opened this issue Sep 10, 2024 · 0 comments · May be fixed by #28
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enhancement New feature or request

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@mcnaughtonadm
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mcnaughtonadm commented Sep 10, 2024

We would like to make the process of running eflux3 as simple as possible. A standard run of our code should be a simple one-liner:

condition_specific_fluxes = eflux3(cobra_model, transcriptomics)

where the condition_specific_fluxes and transcriptomics are either pandas dataframes or dict, and the cobra_model is a cobrapy compatible model.

We can also have named arguments such as reference_strain, solver, etc.

Note: We should allow for output type to be single valued fluxes versus triangular distribution parameters (lower,center,upper).

@mcnaughtonadm mcnaughtonadm added the enhancement New feature or request label Sep 10, 2024
@mcnaughtonadm mcnaughtonadm linked a pull request Sep 14, 2024 that will close this issue
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@mcnaughtonadm mcnaughtonadm linked a pull request Sep 14, 2024 that will close this issue
5 tasks
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