DOI: 10.5061/dryad.fxpnvx11t
title: A generalized numerical model for clonal growth in scleractinian coral colonies

description: 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.
description: # A generalized numerical model for clonal growth in scleractinian coral
 colonies ### 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. ### 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. ### 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.