A reproducible implementation of the ICE‑based instability pipeline (Stages 1–5)
- Overview
- Repository Structure
- Installation
- Reproducing Manuscript Figures (Stages 1–5)
- Extensions: Stage 6 & Stage 7
- Citation
- Acknowledgments
- License
This repository contains the full reproducible implementation of the Information‑Coherence Embedding (ICE) pipeline described in the manuscript.
Stages 1–5 constitute the validated, manuscript‑aligned workflow, encompassing:
| Stage | Description |
|---|---|
| 1 | Signal normalization and preprocessing |
| 2 | ICE computation |
| 3 | ΔΦ instability detection |
| 4 | Embedding and manuscript‑grade visualizations |
| 5 | Regime segmentation and final outputs |
The framework is designed for clarity, reproducibility, and scientific transparency. All outputs are deterministic, and validated components are kept strictly separate from conceptual extensions.
Cell-DNA-Dynamics/
├── data/
│ ├── stage1/
│ │ └── stage_i_results.csv
│ ├── stage2/
│ │ └── stage_ii_segmentation.csv
│ ├── stage3/
│ │ └── stage_iii_summary.csv
│ ├── synthetic/
│ ├── null_tests/
│ │ ├── shuffled.csv
│ │ ├── stable_control.csv
│ │ ├── surrogate.csv
│ │ ├── delta_phi.csv
│ │ ├── eic_timeseries.csv
│ │ └── regimes.csv
│ └── README.md
│
├── docs/
│ ├── PAPER.md
│ └── citations.bib
│
├── figures/
│ ├── final/
│ │ └── figure_8_null_comparison.png
│ ├── simulations/
│ │ ├── ice_trajectory.png
│ │ ├── null_tests_comparison.png
│ │ ├── table3_metrics.csv
│ │ └── timeseries_eic_delta_phi.png
│ ├── stage1/
│ │ └── stage_i_figure.png
│ ├── stage2/
│ │ └── stage_ii_regimes.png
│ ├── stage3/
│ │ └── stage_iii_seed0.png
│ ├── stage4_spiral_time/
│ │ ├── phi_chi_curves.png
│ │ └── spiral_embedding.png
│ ├── stage5_regime_transitions/
│ │ ├── delta_phi_thresholds.png
│ │ └── regime_segmentation.png
│ └── extensions/
│ ├── stage6_cellular/
│ │ ├── cellular_mapping.png
│ │ └── cellular_regimes.png
│ └── stage7_dna/
│ ├── dna_mapping.png
│ └── dna_regimes.png
│
├── src/
│ ├── core/
│ │ ├── models.py
│ │ └── utils.py
│ ├── extensions/
│ │ ├── stage6_cellular/
│ │ │ ├── cellular_pipeline.py
│ │ │ ├── map_to_ice.py
│ │ │ └── normalize_cellular.py
│ │ └── stage7_dna/
│ │ ├── chromatin_fret_utils.py
│ │ ├── dna_feature_mapping.py
│ │ └── dna_pipeline.py
│ ├── simulation/
│ │ ├── generate_synthetic.py
│ │ ├── metrics.py
│ │ ├── null_tests.py
│ │ └── table3_utils.py
│ ├── stage1/
│ │ └── stage_i.py
│ ├── stage2/
│ │ └── stage_ii.py
│ ├── stage3/
│ │ └── stage_iii.py
│ ├── stage4_spiral_time/
│ │ ├── compute_chi.py
│ │ ├── compute_phi.py
│ │ ├── generate_figures.py
│ │ ├── memory_kernel.py
│ │ └── spiral_operator.py
│ ├── stage5_regime_transitions/
│ │ ├── compute_delta_phi.py
│ │ ├── detect_regimes.py
│ │ ├── generate_figures.py
│ │ └── segmentation_utils.py
│ └── viz/
│ ├── generate_figure_8.py
│ ├── plot_ice.py
│ ├── plot_null_tests.py
│ ├── plot_regimes.py
│ └── plot_timeseries.py
│
├── VALIDATION_ANALYSIS.md
├── requirements.txt
├── LICENSE
├── .gitignore
└── README.md
Clone the repository and install the required dependencies:
git clone https://github.com/dfeen87/Cell-DNA-Dynamics.git
cd Cell-DNA-Dynamics
pip install -r requirements.txtPython 3.10+ is recommended for full compatibility.
The manuscript‑aligned workflow is organized modularly across Stages 1–5. Reproduction therefore proceeds via the stage‑specific scripts in src/stage1/ through src/stage5_regime_transitions/, together with the simulation utilities in src/simulation/ and the visualization scripts in src/viz/.
All manuscript figures can be reproduced deterministically by running each stage script in order:
python src/stage1/stage_i.py
python src/stage2/stage_ii.py
python src/stage3/stage_iii.py
python src/stage4_spiral_time/generate_figures.py
python src/stage5_regime_transitions/generate_figures.pyThe pipeline generates the following outputs:
- ICE curves
- ΔΦ instability profiles
- Spiral embeddings
- Regime segmentation plots
Outputs are saved to the corresponding stage subdirectories under figures/:
| Stage | Output directory |
|---|---|
| 1 | figures/stage1/ |
| 2 | figures/stage2/ |
| 3 | figures/stage3/ |
| 4 | figures/stage4_spiral_time/ |
| 5 | figures/stage5_regime_transitions/ |
These outputs correspond to the exact figures used in the manuscript.
Note: The final conceptual figures used in the manuscript are rendered directly in LaTeX/TikZ. Placeholder files in figures/simulations/ are retained only for repository structure and are not part of the validated numerical output set or the manuscript-linked quantitative results.
The repository includes two conceptual translational extensions:
| Extension | Description |
|---|---|
| Stage 6 | Cellular‑scale ICE mapping |
| Stage 7 | DNA‑associated chromatin dynamics mapping |
Important: These modules are:
- not validated
- not part of the manuscript
- not used in any figure or quantitative result
- included only as future‑work scaffolding
The PNG files in figures/extensions/ are placeholders only.
This separation ensures clarity for reviewers and prevents any misinterpretation of these exploratory layers as components of the validated pipeline.
Krüger, M., & Feeney, D. (2026). A Triadic Spiral-Time Framework for Cellular and DNA-Associated Dynamics: A Conservative Effective Modeling Proposal for Biological Stability Transitions. Zenodo. https://doi.org/10.5281/zenodo.19318103
Full BibTeX entries for referenced works are provided in docs/citations.bib.
This project was developed through a combination of original scientific design, hands‑on coding, and iterative refinement supported by advanced AI tooling.
The authors acknowledge Microsoft Copilot for its meaningful assistance in:
- structuring the repository
- improving clarity and reproducibility
- generating manuscript‑aligned documentation
- supporting the overall scientific workflow
All scientific ideas, interpretations, and final decisions remain the responsibility of the authors.
This project is released under the MIT License.