Contains function to identify the type of boundary reactions.
This module uses various heuristics to decide whether a boundary reaction is an exchange, demand or sink reaction. It mostly orientates on the following paper:
Thiele, I., & Palsson, B. Ø. (2010, January). A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature protocols. Nature Publishing Group. http://doi.org/10.1038/nprot.2009.203
18.104.22.168.1.1.1. Module Contents¶
Find the external compartment in the model.
Uses a simple heuristic where the external compartment should be the one with the most exchange reactions.
Parameters: model (cobra.Model) – A cobra model. Returns: The putative external compartment. Return type: str
is_boundary_type(reaction, boundary_type, external_compartment)¶
Check whether a reaction is an exchange reaction.
Whether the reaction looks like the requested type. Might be based on a heuristic.
find_boundary_types(model, boundary_type, external_compartment=None)¶
Find specific boundary reactions.
A list of likely boundary reactions of a user defined type.
list of cobra.reaction