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ReadTheDocs for this project🤯 {WA team name}
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Kindly review if and whenever time permits. |
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Pull request overview
This PR adds project documentation intended to support publishing the research work (MMP/TIMP dynamics + ECM remodeling simulation) via ReadTheDocs and to provide a detailed methodological/implementation overview for the repository.
Changes:
- Added a comprehensive research-focused Markdown README describing the model, parameters, findings, and references.
- Added a text file containing internal “deep research” notes/progress narration.
Reviewed changes
Copilot reviewed 2 out of 4 changed files in this pull request and generated 4 comments.
| File | Description |
|---|---|
MMP-TIMP PHCCO Research README.md |
Adds long-form project/research documentation, including methodology, parameters, and sources. |
DeepResearch into the PJ by Gemz.txt |
Adds internal research notes that are not currently structured as user-facing documentation. |
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| # **Modeling Cell-Type-Specific MMP Dynamics and ECM Remodeling in the Tumor Microenvironment** | ||
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| # **Project Overview** | ||
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| # **Modeling Cell-Type-Specific MMP Dynamics and ECM Remodeling in the Tumor Microenvironment** | |||
| 10. [Formation of motile cell clusters in heterogeneous model tumors: the role of cell-cell alignment \- arXiv](https://arxiv.org/html/2406.14196v2) | ||
| 11. [Cellular Potts Modeling of Tumor Growth, Tumor Invasion, and Tumor Evolution \- Frontiers](https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2013.00087/full) | ||
| 12. [Developing a CompuCell3D (CC3D) Simulation](https://compucell3d.org/BinDoc/cc3d_binaries/Manuals/PASI_compucell3d_quickstartguide_2.0.pdf) | ||
| 13. [CancerInvasion.xml](https://drive.google.com/open?id=11A4YswhcBuN6kZ6SR3Q6Rzk_nBDTdwoz) |
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| Establishing Project Scope | ||
| I am synthesizing the core components of the research on cell-type-specific MMP dynamics and ECM remodeling. I have identified the primary contributors from institutions like IISc and VIT, and I am mapping out the interplay between pro-tumorigenic and anti-tumorigenic factors within the tumor microenvironment. My focus is on how these interactions drive tumor invasion, specifically looking at the roles of epithelial-like and mesenchymal-like cancer cells alongside immune cell populations. | ||
| Resolving Model Technicalities | ||
| I am currently reconciling details regarding the computational framework. While I have confirmed the use of the Cellular Potts Model and identified specific diffusion constants for MMPs, I noticed a gap in the explicit mathematical formulation for the energy calculations used in the simulations. I am cross-referencing available documentation to retrieve the exact Hamiltonian equations and adhesion parameters to ensure the technical section of the documentation is precise and reproducible. | ||
| Structuring the Implementation Guide | ||
| Next, I will be examining project templates and supplementary files to align the documentation with institutional standards. I plan to extract specific installation requirements and execution steps for the simulation environment, ensuring that the transition from Python-based steppables to the final visual results is clearly documented. This includes gathering data on invasion metrics like cell count and volume to provide a comprehensive overview of the study's outcomes. |
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well spotted, a notes folder in the directory structure is required
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ReadTheDocs for this project🤯 {WA team name}