kcat_flux_relationship

Table of Contents

1. About The Project
2. Getting Started
   • Packages
   • First use
3. Raw data

About The Project

Source code of the bachelor thesis "Analyzing the Relationship Between Enzyme Turnover Numbers and Metabolic Fluxes Predicted by Flux Balance Analyses".

Getting Started

To set up this project locally follow these steps. Python version 3.8 was used for this project.

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Packages

Used packages:

• pandas==1.14
• cobra==0.22.1
• bio==1.3.4
• ete3==3.1.2
• matplotlib==3.1.1
• scipy==1.4.1
• requests==2.25.1

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First use

1. Clone the repo

   git clone https://github.com/Nina181/kcat_flux_relationship

2. Install packages

   pip install <package_name>

3. Update NCBI Database (only necessary for first use)

   uncomment line 93 in method add_lineage() of the class kcat_flux_mapping.mapping

4. Enter your email address necessary for accessing the NCBI Database

   in method add_lineage() line 94 of the class kcat_flux_mapping.mapping

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Raw data

generated minimal environments and predicted fluxes were saved in pickle files. These files were to large to upload and are provided upon request.

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