cobra-fseof

cobra-fseof is a COBRApy implementation of the FSEOF (Flux Scanning based on Enforced Objective Flux) algorithm (Choi et al., 2010). The image above is taken from Figure 1 of their paper. This library supports one core function:

def fseof(
    model: cobra.Model,
    num_steps: int,
    enforced: ReactionLike,
    objective: ReactionLike,
    enforced_direction: Literal["min", "max"] = "max",
    enforced_frac_opt: float = 0.9,
    reactions: Optional[List[ReactionLike]] = None,
    optimizer: Optional[Callable[[cobra.Model], cobra.Solution]] = None,
) -> FSEOFResults:

which can be used as follows:

import cobra_fseof

results = cobra_fseof.fseof(...)

Please refer to the source code for further documentation.

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Installation

Pip from source:

git clone https://github.com/igem-toronto/cobra-fseof
 
cd cobra-fseof
pip install -e .   

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Usage

Lycopene Production

In the examples/lycopene folder, we try to reproduce the results from Choi et al. (2010), where they use FSEOF to find gene amplification targets to enhance lycopene production in E. coli.

iGEM Toronto 2023

This repository was created as a part of iGEM Toronto 2023 project. For further details, we refer readers to the iGEM homepage and our team wiki.