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<title>C. elegans Batch 01: Development & Behavior - Programming Framework Analysis</title>
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<body>
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<div class="container">
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<div class="header">
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<h1>🧬 C. elegans Batch 01: Development & Behavior</h1>
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<p>Programming Framework Analysis - 8 Eukaryotic Processes</p>
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</div>
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<div class="content">
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<div class="intro">
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<h2>🧬 Development & Behavior Systems</h2>
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<p><strong>Batch Overview:</strong> This batch contains 8 fundamental C. elegans processes responsible for development and behavior. These processes represent the core computational systems that enable this model organism to develop from embryo to adult, exhibit complex behaviors, and respond to environmental cues.</p>
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<p>Each process demonstrates sophisticated biological programming with developmental pathways, neural circuits, behavioral responses, and aging mechanisms.</p>
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</div>
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<div class="toc">
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<h2>📋 Table of Contents - 8 Eukaryotic Processes</h2>
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<ul>
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<li><a href="#embryonic-development">1. Embryonic Development</a></li>
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<li><a href="#cell-fate-determination">2. Cell Fate Determination</a></li>
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<li><a href="#neural-development">3. Neural Development</a></li>
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<li><a href="#behavioral-circuits">4. Behavioral Circuits</a></li>
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<li><a href="#sensory-processing">5. Sensory Processing</a></li>
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<li><a href="#learning-memory">6. Learning & Memory</a></li>
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<li><a href="#aging-longevity">7. Aging & Longevity</a></li>
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<li><a href="#stress-response">8. Stress Response</a></li>
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</ul>
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</div>
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<div class="process-item" id="embryonic-development">
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<h3>1. Embryonic Development</h3>
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<p>Detailed analysis of C. elegans Embryonic Development using the Programming Framework, revealing computational logic and regulatory patterns for early development.</p>
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<div class="mermaid-container">
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<div class="mermaid">
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graph TD
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%% Development Triggers
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A[Fertilization] --> B[Zygote Formation]
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C[Maternal Factors] --> D[Asymmetric Division]
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E[Cell Division] --> F[Blastula Formation]
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G[Gastrulation] --> H[Germ Layer Formation]
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%% Zygote Development
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B --> I[Polarity Establishment]
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I --> J[Asymmetric Cleavage]
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J --> K[Cell Fate Specification]
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%% Maternal Control
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D --> L[Maternal mRNAs]
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L --> M[Translation Control]
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M --> N[Protein Gradients]
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%% Germ Layer Formation
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F --> O[Ectoderm Formation]
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O --> P[Mesoderm Formation]
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P --> Q[Endoderm Formation]
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%% Integration
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K --> R[Development Program]
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N --> R
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Q --> R
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H --> R
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R --> S[Embryonic Pattern]
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%% Styling - Programming Framework Colors
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style A fill:#ff6b6b,color:#fff
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style C fill:#ff6b6b,color:#fff
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style E fill:#ff6b6b,color:#fff
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style G fill:#ff6b6b,color:#fff
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style B fill:#ffd43b,color:#000
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style D fill:#ffd43b,color:#000
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style F fill:#ffd43b,color:#000
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style H fill:#ffd43b,color:#000
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style I fill:#ffd43b,color:#000
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style J fill:#51cf66,color:#fff
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style K fill:#51cf66,color:#fff
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style L fill:#ffd43b,color:#000
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style Q fill:#51cf66,color:#fff
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style R fill:#74c0fc,color:#fff
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style S fill:#b197fc,color:#fff
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</div>
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<div class="color-legend">
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<span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
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<span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
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<span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
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<span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
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<span><span class="color-box" style="background:#b197fc;"></span>Products</span>
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</div>
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</div>
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</div>
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<div class="process-item" id="cell-fate-determination">
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<h3>2. Cell Fate Determination</h3>
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<p>Detailed analysis of C. elegans Cell Fate Determination using the Programming Framework, revealing computational logic and regulatory patterns for cell differentiation.</p>
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<div class="mermaid-container">
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<div class="mermaid">
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graph TD
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%% Fate Components
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A[Cell Lineage] --> B[Fate Specification]
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C[Signaling Pathways] --> D[Cell-Cell Communication]
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E[Transcription Factors] --> F[Gene Expression]
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G[Epigenetic Control] --> H[Fate Maintenance]
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%% Lineage Control
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B --> I[Asymmetric Division]
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I --> J[Fate Determinants]
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J --> K[Cell Identity]
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%% Signaling Networks
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D --> L[Notch Signaling]
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L --> M[Wnt Pathway]
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M --> N[Cell Fate Decision]
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%% Transcription Control
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F --> O[Homeobox Genes]
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O --> P[Cell Type Genes]
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P --> Q[Differentiation]
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%% Integration
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K --> R[Fate Program]
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N --> R
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Q --> R
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H --> R
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R --> S[Cell Identity]
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%% Styling - Programming Framework Colors
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style A fill:#ff6b6b,color:#fff
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style C fill:#ff6b6b,color:#fff
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style E fill:#ff6b6b,color:#fff
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style G fill:#ff6b6b,color:#fff
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style B fill:#ffd43b,color:#000
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style D fill:#ffd43b,color:#000
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style F fill:#ffd43b,color:#000
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style H fill:#ffd43b,color:#000
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style I fill:#ffd43b,color:#000
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style S fill:#b197fc,color:#fff
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</div>
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<div class="color-legend">
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<span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
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<span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
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<span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
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<span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
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<span><span class="color-box" style="background:#b197fc;"></span>Products</span>
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</div>
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</div>
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</div>
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<div class="process-item" id="neural-development">
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<h3>3. Neural Development</h3>
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<p>Detailed analysis of C. elegans Neural Development using the Programming Framework, revealing computational logic and regulatory patterns for nervous system formation.</p>
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<div class="mermaid-container">
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<div class="mermaid">
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graph TD
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%% Neural Components
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A[Neural Precursors] --> B[Neurogenesis]
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C[Axon Guidance] --> D[Synapse Formation]
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E[Neural Circuits] --> F[Circuit Assembly]
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G[Neurotransmitters] --> H[Neural Function]
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%% Neurogenesis
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B --> I[Neural Progenitors]
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I --> J[Neuron Differentiation]
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J --> K[Neural Identity]
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%% Axon Guidance
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D --> L[Guidance Molecules]
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L --> M[Axon Pathfinding]
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M --> N[Target Recognition]
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%% Synapse Formation
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F --> O[Synaptic Proteins]
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O --> P[Synapse Assembly]
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P --> Q[Functional Synapses]
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%% Integration
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K --> R[Neural Program]
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N --> R
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Q --> R
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H --> R
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R --> S[Neural Circuit]
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%% Styling - Programming Framework Colors
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style A fill:#ff6b6b,color:#fff
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style C fill:#ff6b6b,color:#fff
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style E fill:#ff6b6b,color:#fff
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style G fill:#ff6b6b,color:#fff
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style B fill:#ffd43b,color:#000
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style D fill:#ffd43b,color:#000
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style F fill:#ffd43b,color:#000
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style H fill:#ffd43b,color:#000
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style I fill:#ffd43b,color:#000
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style J fill:#51cf66,color:#fff
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style K fill:#51cf66,color:#fff
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style L fill:#ffd43b,color:#000
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style M fill:#51cf66,color:#fff
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style O fill:#ffd43b,color:#000
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style Q fill:#51cf66,color:#fff
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style R fill:#74c0fc,color:#fff
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style S fill:#b197fc,color:#fff
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</div>
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<div class="color-legend">
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<span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
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<span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
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<span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
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<span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
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<span><span class="color-box" style="background:#b197fc;"></span>Products</span>
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</div>
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</div>
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</div>
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<div class="process-item" id="behavioral-circuits">
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<h3>4. Behavioral Circuits</h3>
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<p>Detailed analysis of C. elegans Behavioral Circuits using the Programming Framework, revealing computational logic and regulatory patterns for behavior generation.</p>
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<div class="mermaid-container">
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<div class="mermaid">
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graph TD
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%% Behavior Components
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A[Sensory Input] --> B[Sensory Neurons]
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C[Interneurons] --> D[Neural Processing]
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E[Motor Neurons] --> F[Motor Output]
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G[Behavioral State] --> H[Behavioral Control]
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%% Sensory Processing
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B --> I[Sensory Transduction]
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I --> J[Signal Integration]
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J --> K[Sensory Representation]
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%% Neural Processing
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D --> L[Interneuron Networks]
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L --> M[Information Processing]
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M --> N[Decision Making]
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%% Motor Control
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F --> O[Motor Pattern Generation]
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O --> P[Muscle Activation]
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P --> Q[Behavioral Response]
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%% Integration
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K --> R[Behavioral Program]
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N --> R
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Q --> R
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H --> R
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R --> S[Behavioral Output]
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%% Styling - Programming Framework Colors
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style A fill:#ff6b6b,color:#fff
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style C fill:#ff6b6b,color:#fff
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style E fill:#ff6b6b,color:#fff
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style G fill:#ff6b6b,color:#fff
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style B fill:#ffd43b,color:#000
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style D fill:#ffd43b,color:#000
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style F fill:#ffd43b,color:#000
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style H fill:#ffd43b,color:#000
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style I fill:#ffd43b,color:#000
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style J fill:#51cf66,color:#fff
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style S fill:#b197fc,color:#fff
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</div>
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<div class="color-legend">
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<span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
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<span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
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<span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
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<span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
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<span><span class="color-box" style="background:#b197fc;"></span>Products</span>
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</div>
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</div>
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</div>
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<div class="process-item" id="sensory-processing">
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<h3>5. Sensory Processing</h3>
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<p>Detailed analysis of C. elegans Sensory Processing using the Programming Framework, revealing computational logic and regulatory patterns for environmental sensing.</p>
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<div class="mermaid-container">
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<div class="mermaid">
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graph TD
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%% Sensory Components
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A[Environmental Cues] --> B[Sensory Receptors]
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C[Signal Transduction] --> D[Neural Encoding]
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E[Sensory Integration] --> F[Perception]
|
|
|
G[Behavioral Response] --> H[Sensory Adaptation]
|
|
|
|
|
|
%% Receptor Activation
|
|
|
B --> I[Chemoreceptors]
|
|
|
I --> J[Mechanoreceptors]
|
|
|
J --> K[Thermoreceptors]
|
|
|
|
|
|
%% Signal Transduction
|
|
|
D --> L[G-Protein Coupling]
|
|
|
L --> M[Second Messengers]
|
|
|
M --> N[Ion Channel Activation]
|
|
|
|
|
|
%% Neural Encoding
|
|
|
F --> O[Action Potentials]
|
|
|
O --> P[Neural Codes]
|
|
|
P --> Q[Sensory Representation]
|
|
|
|
|
|
%% Integration
|
|
|
K --> R[Sensory Program]
|
|
|
N --> R
|
|
|
Q --> R
|
|
|
H --> R
|
|
|
R --> S[Environmental Response]
|
|
|
|
|
|
%% Styling - Programming Framework Colors
|
|
|
style A fill:#ff6b6b,color:#fff
|
|
|
style C fill:#ff6b6b,color:#fff
|
|
|
style E fill:#ff6b6b,color:#fff
|
|
|
style G fill:#ff6b6b,color:#fff
|
|
|
style B fill:#ffd43b,color:#000
|
|
|
style D fill:#ffd43b,color:#000
|
|
|
style F fill:#ffd43b,color:#000
|
|
|
style H fill:#ffd43b,color:#000
|
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|
style I fill:#ffd43b,color:#000
|
|
|
style J fill:#51cf66,color:#fff
|
|
|
style K fill:#51cf66,color:#fff
|
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|
style L fill:#ffd43b,color:#000
|
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|
style M fill:#51cf66,color:#fff
|
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style N fill:#51cf66,color:#fff
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style O fill:#ffd43b,color:#000
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style P fill:#51cf66,color:#fff
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style Q fill:#51cf66,color:#fff
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style R fill:#74c0fc,color:#fff
|
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style S fill:#b197fc,color:#fff
|
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</div>
|
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|
<div class="color-legend">
|
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|
<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>
|
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|
<span><span class="color-box" style="background:#b197fc;"></span>Products</span>
|
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|
</div>
|
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|
</div>
|
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|
</div>
|
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|
|
|
<div class="process-item" id="learning-memory">
|
|
|
<h3>6. Learning & Memory</h3>
|
|
|
<p>Detailed analysis of C. elegans Learning & Memory using the Programming Framework, revealing computational logic and regulatory patterns for behavioral plasticity.</p>
|
|
|
<div class="mermaid-container">
|
|
|
<div class="mermaid">
|
|
|
graph TD
|
|
|
%% Learning Components
|
|
|
A[Experience] --> B[Neural Plasticity]
|
|
|
C[Synaptic Changes] --> D[Memory Formation]
|
|
|
E[Memory Storage] --> F[Memory Retrieval]
|
|
|
G[Behavioral Change] --> H[Learning Outcome]
|
|
|
|
|
|
%% Neural Plasticity
|
|
|
B --> I[Synaptic Strengthening]
|
|
|
I --> J[Synaptic Weakening]
|
|
|
J --> K[Circuit Modification]
|
|
|
|
|
|
%% Memory Formation
|
|
|
D --> L[Short-term Memory]
|
|
|
L --> M[Long-term Memory]
|
|
|
M --> N[Memory Consolidation]
|
|
|
|
|
|
%% Memory Storage
|
|
|
F --> O[Neural Circuits]
|
|
|
O --> P[Synaptic Networks]
|
|
|
P --> Q[Memory Traces]
|
|
|
|
|
|
%% Integration
|
|
|
K --> R[Learning Program]
|
|
|
N --> R
|
|
|
Q --> R
|
|
|
H --> R
|
|
|
R --> S[Behavioral Adaptation]
|
|
|
|
|
|
%% Styling - Programming Framework Colors
|
|
|
style A fill:#ff6b6b,color:#fff
|
|
|
style C fill:#ff6b6b,color:#fff
|
|
|
style E fill:#ff6b6b,color:#fff
|
|
|
style G fill:#ff6b6b,color:#fff
|
|
|
style B fill:#ffd43b,color:#000
|
|
|
style D fill:#ffd43b,color:#000
|
|
|
style F fill:#ffd43b,color:#000
|
|
|
style H fill:#ffd43b,color:#000
|
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|
style I fill:#ffd43b,color:#000
|
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style J fill:#51cf66,color:#fff
|
|
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style K fill:#51cf66,color:#fff
|
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style L fill:#ffd43b,color:#000
|
|
|
style M fill:#51cf66,color:#fff
|
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style N fill:#51cf66,color:#fff
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style O fill:#ffd43b,color:#000
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style P fill:#51cf66,color:#fff
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style Q fill:#51cf66,color:#fff
|
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style R fill:#74c0fc,color:#fff
|
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style S fill:#b197fc,color:#fff
|
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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-item" id="aging-longevity">
|
|
|
<h3>7. Aging & Longevity</h3>
|
|
|
<p>Detailed analysis of C. elegans Aging & Longevity using the Programming Framework, revealing computational logic and regulatory patterns for lifespan regulation.</p>
|
|
|
<div class="mermaid-container">
|
|
|
<div class="mermaid">
|
|
|
graph TD
|
|
|
%% Aging Components
|
|
|
A[Age-related Changes] --> B[Insulin/IGF Signaling]
|
|
|
C[Oxidative Stress] --> D[DNA Damage]
|
|
|
E[Protein Homeostasis] --> F[Metabolic Changes]
|
|
|
G[Longevity Pathways] --> H[Lifespan Control]
|
|
|
|
|
|
%% Insulin Signaling
|
|
|
B --> I[DAF-2/DAF-16]
|
|
|
I --> J[FOXO Transcription]
|
|
|
J --> K[Stress Resistance]
|
|
|
|
|
|
%% Oxidative Damage
|
|
|
D --> L[ROS Production]
|
|
|
L --> M[Antioxidant Response]
|
|
|
M --> N[Oxidative Protection]
|
|
|
|
|
|
%% Protein Homeostasis
|
|
|
F --> O[Proteasome Function]
|
|
|
O --> P[Autophagy]
|
|
|
P --> Q[Protein Quality Control]
|
|
|
|
|
|
%% Integration
|
|
|
K --> R[Aging Program]
|
|
|
N --> R
|
|
|
Q --> R
|
|
|
H --> R
|
|
|
R --> S[Lifespan Regulation]
|
|
|
|
|
|
%% Styling - Programming Framework Colors
|
|
|
style A fill:#ff6b6b,color:#fff
|
|
|
style C fill:#ff6b6b,color:#fff
|
|
|
style E fill:#ff6b6b,color:#fff
|
|
|
style G fill:#ff6b6b,color:#fff
|
|
|
style B fill:#ffd43b,color:#000
|
|
|
style D fill:#ffd43b,color:#000
|
|
|
style F fill:#ffd43b,color:#000
|
|
|
style H fill:#ffd43b,color:#000
|
|
|
style I fill:#ffd43b,color:#000
|
|
|
style J fill:#51cf66,color:#fff
|
|
|
style K fill:#51cf66,color:#fff
|
|
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style L fill:#ffd43b,color:#000
|
|
|
style M fill:#51cf66,color:#fff
|
|
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style N fill:#51cf66,color:#fff
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style O fill:#ffd43b,color:#000
|
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style P fill:#51cf66,color:#fff
|
|
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style Q fill:#51cf66,color:#fff
|
|
|
style R fill:#74c0fc,color:#fff
|
|
|
style S 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="process-item" id="stress-response">
|
|
|
<h3>8. Stress Response</h3>
|
|
|
<p>Detailed analysis of C. elegans Stress Response using the Programming Framework, revealing computational logic and regulatory patterns for environmental adaptation.</p>
|
|
|
<div class="mermaid-container">
|
|
|
<div class="mermaid">
|
|
|
graph TD
|
|
|
%% Stress Components
|
|
|
A[Environmental Stress] --> B[Stress Detection]
|
|
|
C[Stress Signaling] --> D[Stress Response]
|
|
|
E[Adaptation] --> F[Stress Tolerance]
|
|
|
G[Recovery] --> H[Homeostasis]
|
|
|
|
|
|
%% Stress Detection
|
|
|
B --> I[Heat Shock]
|
|
|
I --> J[Oxidative Stress]
|
|
|
J --> K[Osmotic Stress]
|
|
|
|
|
|
%% Stress Signaling
|
|
|
D --> L[HSF-1 Activation]
|
|
|
L --> M[Stress Proteins]
|
|
|
M --> N[Protective Response]
|
|
|
|
|
|
%% Adaptation
|
|
|
F --> O[Metabolic Changes]
|
|
|
O --> P[Behavioral Changes]
|
|
|
P --> Q[Physiological Adaptation]
|
|
|
|
|
|
%% Integration
|
|
|
K --> R[Stress Program]
|
|
|
N --> R
|
|
|
Q --> R
|
|
|
H --> R
|
|
|
R --> S[Stress Survival]
|
|
|
|
|
|
%% Styling - Programming Framework Colors
|
|
|
style A fill:#ff6b6b,color:#fff
|
|
|
style C fill:#ff6b6b,color:#fff
|
|
|
style E fill:#ff6b6b,color:#fff
|
|
|
style G fill:#ff6b6b,color:#fff
|
|
|
style B fill:#ffd43b,color:#000
|
|
|
style D fill:#ffd43b,color:#000
|
|
|
style F fill:#ffd43b,color:#000
|
|
|
style H fill:#ffd43b,color:#000
|
|
|
style I fill:#ffd43b,color:#000
|
|
|
style J fill:#51cf66,color:#fff
|
|
|
style K fill:#51cf66,color:#fff
|
|
|
style L fill:#ffd43b,color:#000
|
|
|
style M fill:#51cf66,color:#fff
|
|
|
style N fill:#51cf66,color:#fff
|
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|
style O fill:#ffd43b,color:#000
|
|
|
style P fill:#51cf66,color:#fff
|
|
|
style Q fill:#51cf66,color:#fff
|
|
|
style R fill:#74c0fc,color:#fff
|
|
|
style S 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 batch demonstrates the computational nature of C. elegans development and behavior systems</p>
|
|
|
<p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
|
|
|
<p><em>Batch 01 of 8: Development & Behavior</em></p>
|
|
|
</div>
|
|
|
</div>
|
|
|
</div>
|
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|
|
|
|
<script>
|
|
|
mermaid.initialize({
|
|
|
startOnLoad: true,
|
|
|
theme: 'default',
|
|
|
flowchart: {
|
|
|
useMaxWidth: false,
|
|
|
htmlLabels: true,
|
|
|
curve: 'linear',
|
|
|
nodeSpacing: 30,
|
|
|
rankSpacing: 40,
|
|
|
padding: 10
|
|
|
},
|
|
|
themeVariables: {
|
|
|
fontFamily: 'Arial, sans-serif',
|
|
|
fontSize: '14px',
|
|
|
primaryColor: '#ff6b6b',
|
|
|
lineColor: '#333333',
|
|
|
secondaryColor: '#feca57',
|
|
|
tertiaryColor: '#4ecdc4'
|
|
|
}
|
|
|
});
|
|
|
</script>
|
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|
</body>
|
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</html>
|
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|
