biology

BiologPlate()

This class assembles media from lists of compounds and HTML representations of the well media:

from modelseedpy.core import BiologPlate
bioplate = BiologPlate(plate_id, rows, cols)

  • plate_id str: The ID of the plate that will be parsed to develop a simulation media.

  • rows & cols list: The rows and columns of the experimental system, respectively.

add_base()

A list of compounds are ascribed a value to construct a media:

bioplate.add_base(compounds, value)

  • compounds list: The compounds that will constitute a media.

  • value float: The value that will be assigned to each compound.

get_media()

The generate a media from a defined well ID in the set of all wells:

bioplate.get_media(well_id)

  • well_id dict: The collection of compounds and values that supplant default entries from the add_base function, where compounds and values are provided as the values of the “compounds” and value” keys, respectively.

returns media dict: The media that is created from the parameterized list of compounds and the respective value.

_repr_html_()

An HTML table is constructed for the plate ID, for all of the experimental wells:

bioplate._repr_html_()

Accessible content

The BilevelPkg class contains a couple of accessible content that may be useful for subsequent post-processing or troubleshooting:

  • id str: The plate ID that will be assessed.

  • rows & cols list: The rows and columns of the experimental system, respectively.

  • wells & base dict: Dictionaries of the experimental wells and added solution that will be constructed into media, respectively.

Biolog()

This class applies plates to the model medium:

from modelseedpy.fbapkg import Biolog
biol = Biolog()

add_plate()

The parameterized plate is added to the collection of plates:

biol.add_plate(plate)

  • plate Plate object: A plate object of the experimental content.

run_plates()

Each well of each plate is defined as the model media, and the simulation results from that media are stored will the respective plate and well:

biol.run_plates(model, biomass=None, cmp='e')

  • model cobra.core.model.Model: The model whose medium will be updated with the composed media.

  • cmp str: The compartment of the exchange metabolite.

Accessible content

The BilevelPkg class contains a couple of accessible content that may be useful for subsequent post-processing or troubleshooting:

  • plates dict: The collection of plates (values) for all plate IDs (keys), will is updated with simulation results from each well media.