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| <div class="header"> |
| <h1>🧬 Developmental Decision Systems</h1> |
| <p>Cell Fate Choice Mechanisms: Biological Computation of Differentiation Decisions</p> |
| <div class="stats"> |
| <div class="stat"> |
| <span class="stat-number">4</span> |
| <span class="stat-label">Processes</span> |
| </div> |
| <div class="stat"> |
| <span class="stat-number">4</span> |
| <span class="stat-label">Categories</span> |
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| <div class="stat"> |
| <span class="stat-number">Complete</span> |
| <span class="stat-label">Complete</span> |
| </div> |
| </div> |
| </div> |
| |
| <div class="intro"> |
| <h2>🎯 Developmental Decision Systems Overview</h2> |
| <p>This document showcases <strong>Cell Fate Choice Mechanisms</strong> as part of the Genome Logic Modeling Project (GLMP). These processes represent the fundamental computational mechanisms by which cells make binary decisions about differentiation and fate specification during development.</p> |
| <p>Each process is modeled using the <strong>Programming Framework</strong>, demonstrating how developmental decision-making operates as sophisticated biological computation with precise molecular algorithms for cell fate regulation.</p> |
| <p>The processes are organized into four main categories: <strong>Morphogen Sensing</strong>, <strong>Fate Decision Logic</strong>, <strong>Transcription Factor Competition</strong>, and <strong>Differentiation Execution</strong>.</p> |
| </div> |
| |
| <div class="content"> |
| |
| <div class="process-section"> |
| <div class="process-header"> |
| <h2>📡 Morphogen Sensing</h2> |
| <p>Gradient detection and positional information</p> |
| </div> |
| <div class="process-content"> |
| <h3>1. Morphogen Gradient Interpretation</h3> |
| <p class="process-description">The computational process by which cells interpret morphogen gradients to determine their position and fate within developing tissues, involving receptor binding, signal transduction, and threshold-based responses.</p> |
| <div class="mermaid"> |
| graph TD |
| A[High Morphogen] --> B{Above Threshold 1?} |
| C[Medium Morphogen] --> D{Above Threshold 2?} |
| E[Low Morphogen] --> F{Above Threshold 3?} |
| G[No Morphogen] --> H{Basal Level?} |
| |
| B -->|Yes| I[Fate A Signal] |
| B -->|No| J[Fate B Signal] |
| D -->|Yes| K[Fate B Signal] |
| D -->|No| L[Fate C Signal] |
| F -->|Yes| M[Fate C Signal] |
| F -->|No| N[Fate D Signal] |
| H -->|Yes| O[Fate D Signal] |
| H -->|No| P[Default Fate] |
| |
| I --> Q[High Concentration Response] |
| K --> R[Medium Concentration Response] |
| M --> S[Low Concentration Response] |
| O --> T[Basal Response] |
| |
| Q --> U[Fate A Specification] |
| R --> V[Fate B Specification] |
| S --> W[Fate C Specification] |
| T --> X[Fate D Specification] |
| P --> Y[Default Specification] |
| |
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| style Y fill:#b197fc,color:#fff |
| </div> |
| <div class="color-legend"> |
| <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span> |
| <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| </div> |
| </div> |
| </div> |
|
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| |
| <div class="process-section"> |
| <div class="process-header"> |
| <h2>🧠 Fate Decision Logic</h2> |
| <p>Binary fate choice and competitive inhibition</p> |
| </div> |
| <div class="process-content"> |
| <h3>2. Fate A vs Fate B Competitive Decision</h3> |
| <p class="process-description">The computational process by which cells implement a bistable switch between two alternative fates through competitive inhibition between transcription factors, demonstrating the same logic as bacterial quorum sensing and viral lysogeny decisions.</p> |
| <div class="mermaid"> |
| graph TD |
| A[Morphogen Signal] --> B{Signal Strength?} |
| C[Fate A TF] --> D{Fate A Above Threshold?} |
| E[Fate B TF] --> F{Fate B Above Threshold?} |
| |
| B -->|Strong| G[High Fate A Signal] |
| B -->|Weak| H[High Fate B Signal] |
| |
| D -->|Yes| I[Fate A Dominant] |
| D -->|No| J[Fate A Low] |
| F -->|Yes| K[Fate B Dominant] |
| F -->|No| L[Fate B Low] |
| |
| G --> M[Fate A Production] |
| H --> N[Fate B Production] |
| |
| I --> O[Fate A Auto-regulation] |
| J --> P[Fate A Inhibition] |
| K --> Q[Fate B Auto-regulation] |
| L --> R[Fate B Inhibition] |
| |
| O --> S[Fate A State] |
| P --> T[Decision Point] |
| Q --> U[Fate B State] |
| R --> T |
| |
| M --> T |
| N --> T |
| |
| T --> V{Fate A vs Fate B Balance?} |
| V -->|Fate A Wins| S |
| V -->|Fate B Wins| U |
| |
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| </div> |
| <div class="color-legend"> |
| <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span> |
| <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| </div> |
| </div> |
| </div> |
|
|
| |
| <div class="process-section"> |
| <div class="process-header"> |
| <h2>⚔️ Transcription Factor Competition</h2> |
| <p>TF binding competition and gene regulation</p> |
| </div> |
| <div class="process-content"> |
| <h3>3. TF Binding Site Competition</h3> |
| <p class="process-description">The computational process by which transcription factors compete for binding sites on target genes, implementing competitive inhibition and mutual repression to establish stable fate decisions.</p> |
| <div class="mermaid"> |
| graph TD |
| A[Fate A TF] --> B[TF A Binding] |
| C[Fate B TF] --> D[TF B Binding] |
| E[Target Gene] --> F[Promoter Region] |
| |
| B --> G{TF A Bound?} |
| D --> H{TF B Bound?} |
| F --> I[Binding Site Available] |
| |
| G -->|Yes| J[Fate A Gene Expression] |
| G -->|No| K[Fate A Gene Repression] |
| H -->|Yes| L[Fate B Gene Expression] |
| H -->|No| M[Fate B Gene Repression] |
| |
| I --> N[Competitive Binding] |
| N --> O[TF A vs TF B Competition] |
| O --> P{Stronger TF?} |
| |
| P -->|TF A| Q[TF A Wins Binding] |
| P -->|TF B| R[TF B Wins Binding] |
| |
| Q --> J |
| R --> L |
| |
| J --> S[Fate A Program] |
| L --> T[Fate B Program] |
| K --> U[Fate A Inhibition] |
| M --> V[Fate B Inhibition] |
| |
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| </div> |
| <div class="color-legend"> |
| <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span> |
| <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| </div> |
| </div> |
| </div> |
|
|
| |
| <div class="process-section"> |
| <div class="process-header"> |
| <h2>🔬 Differentiation Execution</h2> |
| <p>Final fate implementation and cell specialization</p> |
| </div> |
| <div class="process-content"> |
| <h3>4. Cell Specialization and Fate Commitment</h3> |
| <p class="process-description">The computational process by which cells execute their chosen fate through gene expression programs, protein synthesis, and morphological changes, demonstrating the complete cell fate decision cycle.</p> |
| <div class="mermaid"> |
| graph TD |
| A[Fate A Program] --> B[Fate A Genes] |
| C[Fate B Program] --> D[Fate B Genes] |
| |
| B --> E[Fate A Proteins] |
| D --> F[Fate B Proteins] |
| |
| E --> G[Fate A Morphology] |
| F --> H[Fate B Morphology] |
| |
| G --> I[Fate A Function] |
| H --> J[Fate B Function] |
| |
| I --> K[Fate A Commitment] |
| J --> L[Fate B Commitment] |
| |
| K --> M[Irreversible Fate A] |
| L --> N[Irreversible Fate B] |
| |
| M --> O[Fate A Specialization] |
| N --> P[Fate B Specialization] |
| |
| O --> Q[Fate A Identity] |
| P --> R[Fate B Identity] |
| |
| style A fill:#ff6b6b,color:#fff |
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| style R fill:#b197fc,color:#fff |
| </div> |
| <div class="color-legend"> |
| <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span> |
| <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| </div> |
| </div> |
| </div> |
|
|
| <div class="footer"> |
| <p><strong>Generated using the Programming Framework methodology</strong></p> |
| <p>This analysis demonstrates the computational nature of developmental decision systems</p> |
| <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p> |
| </div> |
| </div> |
| </div> |
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