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HAWRA Project Structure

This document outlines the structure of the HAWRA project, providing an overview of the key directories and their contents.

Root Directory

The root directory contains the following key files and directories:

  • README.md: The main README file for the project.
  • STRUCTURE.md: This file, which describes the project structure.
  • requirements.txt: A list of the Python dependencies for the project.
  • scripts/: A directory containing various scripts for analyzing the simulation results.
  • results/: A directory containing the results of the simulations.

Main Directories

The HAWRA project is organized into the following main directories:

  • 00_docs/: Contains documentation for the project, including papers, notes, and references.
  • 01_genomics/: Contains genomic data, including plasmid maps and raw sequences.
  • 02_arbol_interface/: Contains the source code for the Arbol IDE.
  • 03_unified_simulator/: Contains the source code for the main HAWRA simulator.
  • 05_data/: Contains various data files, including experimental logs and simulation results.
  • arbol/: Contains the source code for the Arbol compiler.
  • bioos/: Contains the source code for the BioOS.

03_unified_simulator Directory

The 03_unified_simulator directory is the heart of the HAWRA project. It contains the source code for the main simulator, as well as the following key files and directories:

  • main.py: The main entry point for the simulator.
  • gene_control.bsim.json: A sample BSIM script for running a gene control simulation.
  • src/: The source code for the simulator, which is organized into the following subdirectories:
    • hawra_simulator/: The main simulator package.
      • engines/: The simulation engines for the biological system, the environment, and the quantum system.
      • simulator.py: The main simulator class.

scripts Directory

The scripts/ directory contains a number of scripts for analyzing the simulation results. Here are a few examples:

  • analyze_gene_control.py: This script analyzes the results of the gene control simulation and generates a plot of the gene expression levels over time.
  • visualize_plasmid.py: This script visualizes a plasmid map from a GenBank file.
  • visualize_results.py: This script visualizes the results of a simulation.

results Directory

The results/ directory contains the results of the simulations. The results are typically saved in JSON format, and can be analyzed using the scripts in the scripts/ directory.