Revise README for project overview and details#5
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Updated project title and expanded README content to provide a comprehensive overview of the simulation project, including research objectives, computational framework, and implementation details.
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Pull request overview
This PR substantially expands README.md to provide a full project overview of the CancerInvasion CompuCell3D simulation, including biological motivation, modeling framework, parameterization, and getting-started guidance.
Changes:
- Replaces the minimal README with a detailed, structured project description (objectives, CPM/GGH background, results narrative, references).
- Adds “Getting Started” instructions (prerequisites, repo structure, run steps) and multiple parameter/field tables.
- Introduces internal reference anchors and a long bibliography-style references section.
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| | **Cancer1 — epithelial-like** | High cell–cell adhesion and low cell–ECM adhesion; forms cohesive spheroids and tends to invade collectively [[1]](#ref-1) [[2]](#ref-2). | | ||
| | **Cancer2 — mesenchymal-like** | Low cell–cell adhesion and high cell–ECM adhesion; displays dispersed, motile behavior associated with advanced invasion [[1]](#ref-1) [[2]](#ref-2). | | ||
| | **CD8+ T cells** | Generated at the model boundary, chemotax toward the tumor, and eliminate tumor cells according to a configurable killing probability [[1]](#ref-1) [[2]](#ref-2) [[7]](#ref-7). | |
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| Cancer cells secrete MMPs and TIMPs after contact with laminin. ECM degradation occurs only when the local ratio satisfies: | ||
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| $$ | ||
| \frac{\text{MMP}}{\text{TIMP}} > 2.0 | ||
| $$ |
| | MMP diffusion constant | `D_mmp` | 0.005–0.05 | | ||
| | MMP decay constant | `delta_mmp` | 0.005 | | ||
| | Secretion rate | `lambda_sec` | 0.01–0.1 s⁻¹ | | ||
| | Degradation threshold | `MMP/TIMP` ratio | > 2.0 | |
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| | File | Purpose | | ||
| |---|---| | ||
| | `Simulation.py` | Initializes the simulation and registers steppables. | | ||
| | `Steppables.py` | Implements MMP/TIMP secretion, ECM degradation, immune-cell recruitment, tumor-cell proliferation, and mitosis [[1]](#ref-1) [[18]](#ref-18). | | ||
| | `Simulation.xml` | Defines lattice dimensions, Potts parameters, cell types, diffusion fields, and initial conditions [[13]](#ref-13) [[18]](#ref-18). | | ||
| | `<project-name>.cc3d` | CompuCell3D project definition used by Player or Twedit++. | |
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| - MMP `DiffusionConstant` in `Simulation.xml` | ||
| - `killing_probability` in `Steppables.py` | ||
| - Tumor density and cell-type proportions | ||
| - MMP and TIMP secretion rates |
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| project-root/ | ||
| ├── Simulation.py | ||
| ├── Steppables.py | ||
| ├── Simulation.xml | ||
| └── <project-name>.cc3d |
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Updated project title and expanded README content to provide a comprehensive overview of the simulation project, including research objectives, computational framework, and implementation details.
@kagekageyamayama and @urswc Your due diligence is required for documentation purposes.