A generalized numerical model for clonal growth in scleractinian coral colonies
Data files
Jul 20, 2024 version files 56.50 KB
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colony_measurements.txt
54.38 KB
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README.md
2.12 KB
Jul 20, 2024 version files 56.46 KB
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colony_measurements.txt
54.38 KB
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README.md
2.08 KB
Abstract
Coral reefs, vital ecosystems supporting diverse marine life, are primarily shaped by the clonal expansion of coral colonies. Although the principles of coral clonal growth, involving polyp division for spatial extension, are well-understood, numerical modeling efforts are notably scarce in the literature. In this article, we present a parsimonious numerical model based on the cloning of polyps, utilizing five key parameters to simulate a range of coral shapes. The model is agent-based, where each polyp represents an individual. The colony's surface expansion is dictated by the growth mode parameter (s), guiding the preferred growth direction. Varying s facilitates the emulation of diverse coral shapes, including massive, branching, cauliflower, columnar, and tabular colonies. Additionally, we introduce a novel approach for self-regulatory branching, inspired by the intricate mesh-like canal system and internode regularity observed in Acropora species.
Through a comprehensive sensitivity analysis, we demonstrate the robustness of our model, paving the way for future applications that incorporate environmental factors, such as light and water flow. Coral colonies are known for their high plasticity, and understanding how individual polyps interact with each other and their surroundings to create the reef structure has been a longstanding question in the field. This model offers a powerful framework for studying these interactions, enabling a future implementation of environmental factors, and the possibility of identifying the key mechanisms influencing coral colonies’ morphogenesis.
Authors: Eva Llabrés, Eleonora Re, Naira Pluma, Tomàs Sintes, and Carlos M. Duarte
Contents:
1. Code
- File:
code.zip
- Description: This archive contains Python notebooks that can be run to reproduce the figures included in the article.
- Languages: Python, with dependencies on C++ and MATLAB libraries
- Instructions:
- Extract the contents of
code.zip
. - Follow the instructions to set up the environment, dependencies and libraries.
- Run the Jupyter notebooks to reproduce the results.
- Extract the contents of
2. Data
- File:
data_measurements.txt
- Description: This file contains the magnitudes measured in coral colonies (such as volume, surface, number of polyps, etc.) for every colony type. These measurements are extracted from
LLABRES_objects_ESM.zip
. Units included in the .txt file. - Format:
- Columns:
- Volume
- Surface Area
- Number of Polyps
- Additional measured parameters
- Note: Each row represents a different time step of the various colony types.
- Columns:
3. Supplementary Materials
- File:
LLABRES_objects_ESM.zip
- Description: Contains the 3D objects used for the analysis and visualization of the coral colonies.
- File:
LLABRES_figures_ESM.pdf
- Description: Includes all figures referenced in the article, illustrating the results of the numerical model.
- File:
LLABRES_movies_ESM.zip
- Description: Contains video files that demonstrate the dynamic growth processes of the coral colonies as simulated by the model.
4. Additional Information
- The code is written in Python and utilizes libraries based in C++ and MATLAB for certain computational tasks and visualizations.
- For more detailed information on the code and its implementation, please refer to the documentation included in
code.zip
. - The supplementary materials (LLABRES_objects_ESM.zip, LLABRES_figures_ESM.pdf, and LLABRES_movies_ESM.zip) are also included in the article.