BEES

Biochemical Engine for Enzymatic kinetic modelS

Overview

BEES is a tool for generating biochemical reaction networks from enzyme and substrate inputs. It automatically creates reaction networks by combining enzyme-substrate pairs, retrieves kinetic parameters from a database when available and take envriomantal factors into consideration.

Purpose

BEES will helps researchers and engineering to model biochemical systems by:

• Generating reaction networks from enzyme and substrate specifications
• Retrieving kinetic parameters from a database
• Creating structured reaction summaries with stoichiometry and rate laws

Current Capabilities

This version of BEES provides two main capabilities:

1. Network Generation: Automatically generates biochemical reaction networks from enzyme-substrate pairs. Given a set of enzymes and substrates, BEES creates all possible reactions, determines products, and establishes stoichiometry based on enzyme EC numbers.

2. Kinetic Parameter Retrieval: Queries a kinetic database to find kinetic parameters (Km, kcat, Vmax, ΔG) for enzyme-substrate reactions. When parameters are found, they are included in the reaction model. When not found, the system falls back to template-based generation without kinetic parameters.

Installation

Prerequisites

• Python 3.12 or higher
• Conda (for environment management)

Setup

1. Clone the repository:

git clone <repository-url>
cd BEES

2. Create the conda environment:

conda env create -f environment.yaml

3. Activate the environment:

conda activate bees_env

4. Verify installation:

python BEES.py --help

Quick Start

1. Create an input YAML file. You can start with the minimal example:

cp examples/minimal/input.yml my_input.yml

2. Edit my_input.yml to specify your species and enzymes. At minimum, you need:

   • A project name
   • At least one species (substrate)
   • At least one enzyme with an EC number
   • Environment settings (temperature, pH)
   • Database settings
   • Settings (end_time, time_step)

3. Run BEES:

python BEES.py --input_file my_input.yml

4. Check the output. BEES will create a project directory in projects/ containing:
   • reactions_summary.txt - Summary of all generated reactions
   • <ProjectName>.log - Execution log
   • <ProjectName>_errors.log - Error log (if any)

Running Examples

BEES includes several example configurations that demonstrate different capabilities. you will find all the explantion in the example file in " Test_project_summeary.md"

Database

BEES uses a CSV database located at db/db.csv. The database contains kinetic parameters for various enzyme-substrate reactions. See docs/kinetic_database_schema.md for database structure details.

Documentation

• examples/TEST_PROJECTS_SUMMARY.md - Complete guide to all example projects
• docs/kinetic_database_schema.md - Database schema documentation
• examples/example_output/ - Example output files showing expected format

Development

To run tests:

pytest tests/

To run a specific test:

pytest tests/test_comprehensive_demo.py -v

License

See LICENSE file for details.