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  1. README.md +23 -2
  2. biology_processes.html +716 -0
  3. computer_science_processes.html +59 -41
  4. index.html +70 -174
README.md CHANGED
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  sdk: static
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  license: mit
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- short_description: Cross-disciplinary programming methodology framework
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  ---
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- Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  sdk: static
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  license: mit
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+ short_description: Cross-disciplinary methodology for complex systems
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  ---
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+ ## Programming Framework
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+
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+ A systematic visualization methodology for analyzing complex systems across disciplines using Mermaid Markdown and a universal five-color code.
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+
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+ ### Universal Color Coding Table
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+
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+ | Color | Hex | Biology | Chemistry | Computer Science | Physics | Mathematics |
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+ | --- | --- | --- | --- | --- | --- | --- |
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+ | Red | `#ff6b6b` | Environmental signals, nutrients | Reactant supply, temperature | Input data, user commands | Energy input, force | Axioms, givens |
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+ | Yellow | `#ffd43b` | Enzymes, receptors | Catalysts, vessels | Data structures, algorithms | Fields, particles | Theorems, methods |
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+ | Green | `#51cf66` | Metabolic reactions | Chemical reactions | Algorithm execution | Quantum/force operations | Calculations, deductions |
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+ | Blue | `#74c0fc` | Metabolites, states | Intermediates, streams | Variables, memory states | States, measurement results | Intermediate results |
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+ | Violet | `#b197fc` | Biomolecules, responses | Final products | Program outputs | Phenomena, measured quantities | Proven results |
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+
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+ ### Explore the Space
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+
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+ - Biology evidence base: GLMP Space (Hugging Face) and repo
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+ - Chemistry processes: `chemistry_examples.html`
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+ - Computer Science: `computer_science_processes.html`
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+ - Physics: `physics_processes.html`
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+ - Mathematics: `mathematics_processes.html`
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+ - Full article: `programming_framework_article.html`
biology_processes.html ADDED
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+ <!DOCTYPE html>
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+ <html lang="en">
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+ <head>
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+ <meta charset="UTF-8" />
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+ <meta name="viewport" content="width=device-width, initial-scale=1" />
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+ <title>Biology Processes - Programming Framework Analysis</title>
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+ <style>
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+ body {
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+ font-family: 'Times New Roman', Times, serif, 'Arial Unicode MS';
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+ margin: 0;
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+ background: #ffffff;
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+ color: #000000;
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+ line-height: 1.6;
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+ font-size: 12pt;
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+ }
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+ .container {
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+ max-width: 1000px;
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+ margin: 0 auto;
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+ padding: 1.5rem;
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+ }
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+ h1, h2, h3 {
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+ color: #000000;
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+ margin-top: 1.5rem;
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+ margin-bottom: 0.75rem;
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+ }
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+ h1 {
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+ font-size: 18pt;
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+ text-align: center;
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+ }
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+ h2 {
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+ font-size: 16pt;
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+ border-bottom: 2px solid #000;
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+ padding-bottom: 0.5rem;
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+ }
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+ h3 {
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+ font-size: 14pt;
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+ }
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+ p {
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+ margin-bottom: 1rem;
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+ text-align: justify;
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+ }
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+ .figure {
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+ margin: 1rem 0;
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+ text-align: center;
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+ border: 1px solid #ccc;
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+ padding: 1rem;
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+ background: #f9f9f9;
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+ }
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+ .figure-caption {
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+ margin-top: 1rem;
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+ font-style: italic;
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+ text-align: left;
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+ }
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+ .mermaid {
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+ background: white;
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+ padding: 1rem;
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+ border-radius: 4px;
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+ }
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+ .color-legend {
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+ display: flex;
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+ flex-wrap: wrap;
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+ gap: 1rem;
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+ margin-top: 1rem;
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+ justify-content: center;
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+ }
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+ .color-legend span {
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+ display: inline-flex;
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+ align-items: center;
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+ gap: 0.5rem;
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+ padding: 0.25rem 0.5rem;
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+ border-radius: 999px;
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+ border: 1px solid rgba(0,0,0,.08);
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+ background: #fff;
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+ font-size: 0.9rem;
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+ }
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+ .color-box {
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+ width: 12px;
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+ height: 12px;
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+ border-radius: 2px;
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+ border: 1px solid rgba(0,0,0,.15);
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+ }
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+ .glmp-link {
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+ background: #e8f5e8;
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+ padding: 1rem;
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+ border-radius: 8px;
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+ margin: 1rem 0;
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+ border-left: 4px solid #28a745;
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+ }
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+ .glmp-link h3 {
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+ margin-top: 0;
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+ color: #28a745;
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+ }
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+ </style>
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+ <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
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+ <script>
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+ mermaid.initialize({
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+ startOnLoad: true,
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+ theme: 'default',
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+ flowchart: {
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+ useMaxWidth: false,
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+ htmlLabels: true,
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+ curve: 'linear',
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+ nodeSpacing: 50,
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+ rankSpacing: 50,
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+ padding: 20
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+ },
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+ themeVariables: {
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+ fontFamily: 'Arial Unicode MS, Arial, sans-serif'
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+ }
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+ });
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+ </script>
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+ </head>
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+ <body>
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+ <div class="container">
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+ <h1>Biology Processes - Programming Framework Analysis</h1>
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+
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+ <div class="glmp-link">
118
+ <h3>🔗 GLMP (Genome Logic Modeling Project) Connection</h3>
119
+ <p>This analysis is based on the comprehensive biological dataset from the <strong>Genome Logic Modeling Project (GLMP)</strong>, which contains 297+ analyzed biological processes across multiple organisms and systems.</p>
120
+ <p><strong>GLMP Resources:</strong></p>
121
+ <ul>
122
+ <li><a href="https://huggingface.co/spaces/garywelz/glmp" target="_blank">GLMP Hugging Face Space</a> - Live demonstration and evidence base</li>
123
+ <li><a href="https://github.com/garywelz/glmp" target="_blank">GLMP GitHub Repository</a> - Complete dataset and methodology</li>
124
+ </ul>
125
+ <p>The GLMP represents the most comprehensive biological computing system analysis ever created, demonstrating how biological systems function as sophisticated computational programs with complex regulatory logic, decision trees, and feedback mechanisms.</p>
126
+ </div>
127
+
128
+ <p>This document presents representative biological processes analyzed using the Programming Framework methodology. Each process is represented as a computational flowchart with standardized color coding: Red for triggers/inputs, Yellow for structures/objects, Green for processing/operations, Blue for intermediates/states, and Violet for products/outputs. Yellow nodes use black text for optimal readability, while all other colors use white text.</p>
129
+
130
+ <h2>1. β-Galactosidase Regulation System (E. coli)</h2>
131
+ <div class="figure">
132
+ <div class="mermaid">
133
+ graph TD
134
+ %% Environmental Inputs
135
+ A[Lactose in Environment] --> B[Lactose Transport]
136
+ C[Glucose in Environment] --> D[Glucose Transport]
137
+ E[Low Energy Status] --> F[Energy Stress Signal]
138
+
139
+ %% Transport Processes
140
+ B --> G[Lactose Permease LacY]
141
+ G --> H[Lactose Inside Cell]
142
+ H --> I[Lactose Availability]
143
+ D --> J[Glucose Transporters]
144
+ J --> K[Glucose Inside Cell]
145
+ K --> L[High Glucose Status]
146
+
147
+ %% Regulatory Logic Gates
148
+ I --> M{Is Lactose Present?}
149
+ L --> N{Is Glucose Present?}
150
+ F --> O{Is Energy Low?}
151
+
152
+ %% Repressor Logic
153
+ M -->|No| P[Lac Repressor Active]
154
+ M -->|Yes| Q[Lac Repressor Inactive]
155
+ P --> R[Repressor Binds Operator]
156
+ R --> S[Transcription Blocked]
157
+ Q --> T[Repressor Released]
158
+ T --> U[Operator Free]
159
+
160
+ %% CAP-cAMP Logic
161
+ N -->|Yes| V[Low cAMP Levels]
162
+ N -->|No| W[High cAMP Levels]
163
+ O --> W
164
+ W --> X[cAMP-CAP Complex]
165
+ V --> Y[No CAP Binding]
166
+ X --> Z[CAP Binds Promoter]
167
+ Y --> AA[No CAP Binding]
168
+
169
+ %% Transcription Control
170
+ U --> BB{Operator Free?}
171
+ Z --> CC{CAP Bound?}
172
+ BB -->|Yes| DD[RNA Polymerase Binding]
173
+ BB -->|No| EE[Transcription Blocked]
174
+ CC -->|Yes| FF[Strong Transcription]
175
+ CC -->|No| GG[Weak Transcription]
176
+
177
+ %% Gene Expression
178
+ DD --> HH[Transcription Initiation]
179
+ FF --> II[lacZ mRNA Synthesis]
180
+ FF --> JJ[lacY mRNA Synthesis]
181
+ FF --> KK[lacA mRNA Synthesis]
182
+
183
+ %% Protein Synthesis
184
+ II --> LL[LacZ Translation]
185
+ JJ --> MM[LacY Translation]
186
+ KK --> NN[LacA Translation]
187
+
188
+ %% Functional Proteins
189
+ LL --> OO[Beta-Galactosidase Enzyme]
190
+ MM --> PP[Lactose Permease]
191
+ NN --> QQ[Galactoside Acetyltransferase]
192
+
193
+ %% Metabolic Functions
194
+ OO --> RR[Lactose Hydrolysis]
195
+ PP --> SS[Lactose Transport]
196
+ QQ --> TT[Galactoside Modification]
197
+
198
+ %% Final Products
199
+ RR --> UU[Glucose + Galactose]
200
+ SS --> VV[Lactose Uptake]
201
+ TT --> WW[Detoxification]
202
+
203
+ %% Energy Production
204
+ UU --> XX[Glycolysis]
205
+ VV --> YY[Lactose Processing]
206
+ WW --> ZZ[Cell Protection]
207
+
208
+ %% System Equilibrium
209
+ XX --> AAA[Energy Production]
210
+ YY --> BBB[Lactose Consumption]
211
+ ZZ --> CCC[Cell Survival]
212
+
213
+ %% Feedback Control
214
+ AAA --> DDD[Energy Status Improved]
215
+ BBB --> EEE[Lactose Depletion]
216
+ CCC --> FFF[Reduced Energy Stress]
217
+
218
+ %% Dynamic Equilibrium
219
+ DDD --> GGG[Reduced Lactose Signal]
220
+ EEE --> HHH[Maintained Homeostasis]
221
+ FFF --> III[System Equilibrium]
222
+
223
+ %% Styling - Biological Color Scheme
224
+ %% Red: Triggers & Inputs
225
+ style A fill:#ff6b6b,color:#fff
226
+ style C fill:#ff6b6b,color:#fff
227
+ style E fill:#ff6b6b,color:#fff
228
+
229
+ %% Yellow: Structures & Objects
230
+ style G fill:#ffd43b,color:#000
231
+ style J fill:#ffd43b,color:#000
232
+ style P fill:#ffd43b,color:#000
233
+ style Q fill:#ffd43b,color:#000
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+ style X fill:#ffd43b,color:#000
235
+ style OO fill:#ffd43b,color:#000
236
+ style PP fill:#ffd43b,color:#000
237
+ style QQ fill:#ffd43b,color:#000
238
+
239
+ %% Green: Processing & Operations
240
+ style B fill:#51cf66,color:#fff
241
+ style D fill:#51cf66,color:#fff
242
+ style F fill:#51cf66,color:#fff
243
+ style H fill:#51cf66,color:#fff
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+ style K fill:#51cf66,color:#fff
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+ style R fill:#51cf66,color:#fff
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+ style T fill:#51cf66,color:#fff
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+ style W fill:#51cf66,color:#fff
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+ style Z fill:#51cf66,color:#fff
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+ style DD fill:#51cf66,color:#fff
250
+ style FF fill:#51cf66,color:#fff
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+ style HH fill:#51cf66,color:#fff
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+ style II fill:#51cf66,color:#fff
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+ style JJ fill:#51cf66,color:#fff
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+ style KK fill:#51cf66,color:#fff
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+ style LL fill:#51cf66,color:#fff
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+ style MM fill:#51cf66,color:#fff
257
+ style NN fill:#51cf66,color:#fff
258
+ style RR fill:#51cf66,color:#fff
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+ style SS fill:#51cf66,color:#fff
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+ style TT fill:#51cf66,color:#fff
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+ style XX fill:#51cf66,color:#fff
262
+ style YY fill:#51cf66,color:#fff
263
+ style ZZ fill:#51cf66,color:#fff
264
+ style DDD fill:#51cf66,color:#fff
265
+ style EEE fill:#51cf66,color:#fff
266
+ style FFF fill:#51cf66,color:#fff
267
+
268
+ %% Blue: Intermediates & States
269
+ style I fill:#74c0fc,color:#fff
270
+ style L fill:#74c0fc,color:#fff
271
+ style U fill:#74c0fc,color:#fff
272
+ style AA fill:#74c0fc,color:#fff
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+ style UU fill:#74c0fc,color:#fff
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+ style VV fill:#74c0fc,color:#fff
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+ style WW fill:#74c0fc,color:#fff
276
+ style AAA fill:#74c0fc,color:#fff
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+ style BBB fill:#74c0fc,color:#fff
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+ style CCC fill:#74c0fc,color:#fff
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+ style GGG fill:#74c0fc,color:#fff
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+ style HHH fill:#74c0fc,color:#fff
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+ style III fill:#74c0fc,color:#fff
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+
283
+ %% Violet: Products & Outputs
284
+ style M fill:#b197fc,color:#fff
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+ style N fill:#b197fc,color:#fff
286
+ style O fill:#b197fc,color:#fff
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+ style BB fill:#b197fc,color:#fff
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+ style CC fill:#b197fc,color:#fff
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+ style EE fill:#b197fc,color:#fff
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+ style GG fill:#b197fc,color:#fff
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+ </div>
292
+ <div class="color-legend">
293
+ <span><span class="color-box" style="background:#ff6b6b;"></span>Environmental Inputs</span>
294
+ <span><span class="color-box" style="background:#ffd43b;"></span>Enzymes & Proteins</span>
295
+ <span><span class="color-box" style="background:#51cf66;"></span>Metabolic Reactions</span>
296
+ <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates & States</span>
297
+ <span><span class="color-box" style="background:#b197fc;"></span>Products & Outputs</span>
298
+ </div>
299
+ <div class="figure-caption">
300
+ <strong>Figure 1.</strong> β-Galactosidase Regulation System. This comprehensive computational flowchart demonstrates the Programming Framework's ability to represent complex genetic regulatory networks with complete feedback loops and system equilibrium. The visualization shows environmental inputs (lactose, glucose, energy status), regulatory complexes and enzymes (Lac repressor, CAP-cAMP complex, β-galactosidase), intermediate states and logic gates, functional outputs (glucose + galactose, lactose uptake, detoxification), and dynamic feedback control mechanisms.
301
+ </div>
302
+ </div>
303
+
304
+ <h2>2. Yeast Cell Cycle Control System</h2>
305
+ <div class="figure">
306
+ <div class="mermaid">
307
+ graph TD
308
+ %% Environmental Inputs
309
+ A[Nutrient Availability] --> B[Nutrient Sensing]
310
+ C[Cell Size] --> D[Size Checkpoint]
311
+ E[DNA Damage] --> F[Damage Detection]
312
+
313
+ %% Sensing Mechanisms
314
+ B --> G[Nutrient Transporters]
315
+ D --> H[Size Sensors]
316
+ F --> I[DNA Repair Enzymes]
317
+
318
+ %% Signal Processing
319
+ G --> J[Nutrient Signal Processing]
320
+ H --> K[Size Signal Processing]
321
+ I --> L[Damage Signal Processing]
322
+
323
+ %% Decision Logic
324
+ J --> M{Nutrients Sufficient?}
325
+ K --> N{Size Adequate?}
326
+ L --> O{DNA Intact?}
327
+
328
+ %% Cell Cycle Progression
329
+ M -->|Yes| P[G1 Phase Entry]
330
+ N -->|Yes| Q[G1/S Transition]
331
+ O -->|Yes| R[S Phase Entry]
332
+
333
+ %% Checkpoint Controls
334
+ M -->|No| S[G1 Arrest]
335
+ N -->|No| T[Size Arrest]
336
+ O -->|No| U[DNA Repair Arrest]
337
+
338
+ %% DNA Replication
339
+ P --> V[DNA Replication Initiation]
340
+ Q --> W[Replication Fork Formation]
341
+ R --> X[DNA Synthesis]
342
+
343
+ %% Mitosis Preparation
344
+ V --> Y[G2 Phase Entry]
345
+ W --> Z[Replication Completion]
346
+ X --> AA[DNA Duplication]
347
+
348
+ %% Mitosis Control
349
+ Y --> BB[Mitosis Entry]
350
+ Z --> CC[Spindle Formation]
351
+ AA --> DD[Chromosome Condensation]
352
+
353
+ %% Cell Division
354
+ BB --> EE[Anaphase]
355
+ CC --> FF[Chromosome Separation]
356
+ DD --> GG[Cytokinesis]
357
+
358
+ %% Final Products
359
+ EE --> HH[Two Daughter Cells]
360
+ FF --> II[Chromosome Segregation]
361
+ GG --> JJ[Cell Division Complete]
362
+
363
+ %% Styling - Biological Color Scheme
364
+ %% Red: Triggers & Inputs
365
+ style A fill:#ff6b6b,color:#fff
366
+ style C fill:#ff6b6b,color:#fff
367
+ style E fill:#ff6b6b,color:#fff
368
+
369
+ %% Yellow: Structures & Objects
370
+ style G fill:#ffd43b,color:#000
371
+ style H fill:#ffd43b,color:#000
372
+ style I fill:#ffd43b,color:#000
373
+ style P fill:#ffd43b,color:#000
374
+ style Q fill:#ffd43b,color:#000
375
+ style R fill:#ffd43b,color:#000
376
+ style S fill:#ffd43b,color:#000
377
+ style T fill:#ffd43b,color:#000
378
+ style U fill:#ffd43b,color:#000
379
+
380
+ %% Green: Processing & Operations
381
+ style B fill:#51cf66,color:#fff
382
+ style D fill:#51cf66,color:#fff
383
+ style F fill:#51cf66,color:#fff
384
+ style J fill:#51cf66,color:#fff
385
+ style K fill:#51cf66,color:#fff
386
+ style L fill:#51cf66,color:#fff
387
+ style V fill:#51cf66,color:#fff
388
+ style W fill:#51cf66,color:#fff
389
+ style X fill:#51cf66,color:#fff
390
+ style Y fill:#51cf66,color:#fff
391
+ style Z fill:#51cf66,color:#fff
392
+ style AA fill:#51cf66,color:#fff
393
+ style BB fill:#51cf66,color:#fff
394
+ style CC fill:#51cf66,color:#fff
395
+ style DD fill:#51cf66,color:#fff
396
+ style EE fill:#51cf66,color:#fff
397
+ style FF fill:#51cf66,color:#fff
398
+ style GG fill:#51cf66,color:#fff
399
+
400
+ %% Blue: Intermediates & States
401
+ style M fill:#74c0fc,color:#fff
402
+ style N fill:#74c0fc,color:#fff
403
+ style O fill:#74c0fc,color:#fff
404
+
405
+ %% Violet: Products & Outputs
406
+ style HH fill:#b197fc,color:#fff
407
+ style II fill:#b197fc,color:#fff
408
+ style JJ fill:#b197fc,color:#fff
409
+ </div>
410
+ <div class="color-legend">
411
+ <span><span class="color-box" style="background:#ff6b6b;"></span>Environmental Inputs</span>
412
+ <span><span class="color-box" style="background:#ffd43b;"></span>Enzymes & Proteins</span>
413
+ <span><span class="color-box" style="background:#51cf66;"></span>Metabolic Reactions</span>
414
+ <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates & States</span>
415
+ <span><span class="color-box" style="background:#b197fc;"></span>Products & Outputs</span>
416
+ </div>
417
+ <div class="figure-caption">
418
+ <strong>Figure 2.</strong> Yeast Cell Cycle Control System. This biological process visualization demonstrates the computational logic of eukaryotic cell cycle regulation. The flowchart shows environmental inputs (nutrients, cell size, DNA damage), sensing mechanisms and regulatory proteins, signal processing and decision logic, cell cycle progression through G1, S, G2, and M phases, checkpoint controls, and final cell division products.
419
+ </div>
420
+ </div>
421
+
422
+ <h2>3. Photosynthesis Process (Plant Systems)</h2>
423
+ <div class="figure">
424
+ <div class="mermaid">
425
+ graph TD
426
+ %% Light Input
427
+ A[Sunlight] --> B[Light Absorption]
428
+ C[CO2 in Atmosphere] --> D[CO2 Diffusion]
429
+ E[Water in Soil] --> F[Water Uptake]
430
+
431
+ %% Light Reactions
432
+ B --> G[Chlorophyll Molecules]
433
+ G --> H[Photosystem II]
434
+ H --> I[Electron Transport Chain]
435
+ I --> J[Photosystem I]
436
+
437
+ %% Water Splitting
438
+ F --> K[Water Transport]
439
+ K --> L[Water Splitting Complex]
440
+ L --> M[Oxygen Evolution]
441
+ L --> N[Proton Release]
442
+ L --> O[Electron Donation]
443
+
444
+ %% Electron Transport
445
+ O --> P[Electron Flow]
446
+ P --> Q[NADP+ Reduction]
447
+ Q --> R[NADPH Production]
448
+ N --> S[Proton Gradient]
449
+ S --> T[ATP Synthesis]
450
+
451
+ %% Calvin Cycle
452
+ D --> U[CO2 Fixation]
453
+ U --> V[Ribulose-1,5-bisphosphate]
454
+ V --> W[3-Phosphoglycerate]
455
+ W --> X[Glyceraldehyde-3-phosphate]
456
+
457
+ %% Sugar Synthesis
458
+ X --> Y[Glucose Synthesis]
459
+ Y --> Z[Starch Formation]
460
+ Y --> AA[Sucrose Transport]
461
+
462
+ %% Final Products
463
+ M --> BB[Oxygen Gas]
464
+ R --> CC[NADPH Pool]
465
+ T --> DD[ATP Pool]
466
+ Z --> EE[Starch Storage]
467
+ AA --> FF[Sucrose Export]
468
+
469
+ %% Styling - Biological Color Scheme
470
+ %% Red: Triggers & Inputs
471
+ style A fill:#ff6b6b,color:#fff
472
+ style C fill:#ff6b6b,color:#fff
473
+ style E fill:#ff6b6b,color:#fff
474
+
475
+ %% Yellow: Structures & Objects
476
+ style G fill:#ffd43b,color:#000
477
+ style H fill:#ffd43b,color:#000
478
+ style J fill:#ffd43b,color:#000
479
+ style L fill:#ffd43b,color:#000
480
+ style V fill:#ffd43b,color:#000
481
+
482
+ %% Green: Processing & Operations
483
+ style B fill:#51cf66,color:#fff
484
+ style D fill:#51cf66,color:#fff
485
+ style F fill:#51cf66,color:#fff
486
+ style I fill:#51cf66,color:#fff
487
+ style K fill:#51cf66,color:#fff
488
+ style M fill:#51cf66,color:#fff
489
+ style N fill:#51cf66,color:#fff
490
+ style O fill:#51cf66,color:#fff
491
+ style P fill:#51cf66,color:#fff
492
+ style Q fill:#51cf66,color:#fff
493
+ style S fill:#51cf66,color:#fff
494
+ style T fill:#51cf66,color:#fff
495
+ style U fill:#51cf66,color:#fff
496
+ style W fill:#51cf66,color:#fff
497
+ style X fill:#51cf66,color:#fff
498
+ style Y fill:#51cf66,color:#fff
499
+ style Z fill:#51cf66,color:#fff
500
+ style AA fill:#51cf66,color:#fff
501
+
502
+ %% Blue: Intermediates & States
503
+ style R fill:#74c0fc,color:#fff
504
+ style DD fill:#74c0fc,color:#fff
505
+ style CC fill:#74c0fc,color:#fff
506
+
507
+ %% Violet: Products & Outputs
508
+ style BB fill:#b197fc,color:#fff
509
+ style EE fill:#b197fc,color:#fff
510
+ style FF fill:#b197fc,color:#fff
511
+ </div>
512
+ <div class="color-legend">
513
+ <span><span class="color-box" style="background:#ff6b6b;"></span>Environmental Inputs</span>
514
+ <span><span class="color-box" style="background:#ffd43b;"></span>Enzymes & Proteins</span>
515
+ <span><span class="color-box" style="background:#51cf66;"></span>Metabolic Reactions</span>
516
+ <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates & States</span>
517
+ <span><span class="color-box" style="background:#b197fc;"></span>Products & Outputs</span>
518
+ </div>
519
+ <div class="figure-caption">
520
+ <strong>Figure 3.</strong> Photosynthesis Process. This biological process visualization demonstrates the computational logic of photosynthetic energy conversion. The flowchart shows environmental inputs (sunlight, CO2, water), photosynthetic complexes and enzymes (chlorophyll, photosystems, Calvin cycle enzymes), light and dark reactions, electron transport and ATP synthesis, sugar synthesis pathways, and final products (oxygen, glucose, starch, sucrose).
521
+ </div>
522
+ </div>
523
+
524
+ <h2>4. Bacterial Quorum Sensing System</h2>
525
+ <div class="figure">
526
+ <div class="mermaid">
527
+ graph TD
528
+ %% Environmental Inputs
529
+ A[Cell Density] --> B[Density Sensing]
530
+ C[Autoinducer Molecules] --> D[Autoinducer Production]
531
+ E[Environmental Conditions] --> F[Stress Detection]
532
+
533
+ %% Sensing Mechanisms
534
+ B --> G[Density Sensors]
535
+ D --> H[Autoinducer Synthases]
536
+ F --> I[Stress Response Proteins]
537
+
538
+ %% Signal Processing
539
+ G --> J[Density Signal Processing]
540
+ H --> K[Autoinducer Accumulation]
541
+ I --> L[Stress Signal Processing]
542
+
543
+ %% Threshold Logic
544
+ J --> M{Autoinducer Above Threshold?}
545
+ K --> N{Quorum Reached?}
546
+ L --> O{Stress Conditions?}
547
+
548
+ %% Gene Regulation
549
+ M -->|Yes| P[LuxR Activation]
550
+ N -->|Yes| Q[Quorum Response]
551
+ O -->|Yes| R[Stress Response]
552
+
553
+ %% Response Pathways
554
+ P --> S[Target Gene Expression]
555
+ Q --> T[Biofilm Formation]
556
+ R --> U[Antibiotic Production]
557
+
558
+ %% Collective Behaviors
559
+ S --> V[Luminescence]
560
+ T --> W[Matrix Production]
561
+ U --> X[Antimicrobial Synthesis]
562
+
563
+ %% Final Products
564
+ V --> Y[Light Emission]
565
+ W --> Z[Biofilm Structure]
566
+ X --> AA[Antibiotic Molecules]
567
+
568
+ %% Styling - Biological Color Scheme
569
+ %% Red: Triggers & Inputs
570
+ style A fill:#ff6b6b,color:#fff
571
+ style C fill:#ff6b6b,color:#fff
572
+ style E fill:#ff6b6b,color:#fff
573
+
574
+ %% Yellow: Structures & Objects
575
+ style G fill:#ffd43b,color:#000
576
+ style H fill:#ffd43b,color:#000
577
+ style I fill:#ffd43b,color:#000
578
+ style P fill:#ffd43b,color:#000
579
+ style Q fill:#ffd43b,color:#000
580
+ style R fill:#ffd43b,color:#000
581
+
582
+ %% Green: Processing & Operations
583
+ style B fill:#51cf66,color:#fff
584
+ style D fill:#51cf66,color:#fff
585
+ style F fill:#51cf66,color:#fff
586
+ style J fill:#51cf66,color:#fff
587
+ style K fill:#51cf66,color:#fff
588
+ style L fill:#51cf66,color:#fff
589
+ style S fill:#51cf66,color:#fff
590
+ style T fill:#51cf66,color:#fff
591
+ style U fill:#51cf66,color:#fff
592
+ style V fill:#51cf66,color:#fff
593
+ style W fill:#51cf66,color:#fff
594
+ style X fill:#51cf66,color:#fff
595
+
596
+ %% Blue: Intermediates & States
597
+ style M fill:#74c0fc,color:#fff
598
+ style N fill:#74c0fc,color:#fff
599
+ style O fill:#74c0fc,color:#fff
600
+
601
+ %% Violet: Products & Outputs
602
+ style Y fill:#b197fc,color:#fff
603
+ style Z fill:#b197fc,color:#fff
604
+ style AA fill:#b197fc,color:#fff
605
+ </div>
606
+ <div class="color-legend">
607
+ <span><span class="color-box" style="background:#ff6b6b;"></span>Environmental Inputs</span>
608
+ <span><span class="color-box" style="background:#ffd43b;"></span>Enzymes & Proteins</span>
609
+ <span><span class="color-box" style="background:#51cf66;"></span>Metabolic Reactions</span>
610
+ <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates & States</span>
611
+ <span><span class="color-box" style="background:#b197fc;"></span>Products & Outputs</span>
612
+ </div>
613
+ <div class="figure-caption">
614
+ <strong>Figure 4.</strong> Bacterial Quorum Sensing System. This biological process visualization demonstrates the computational logic of bacterial communication and collective behavior. The flowchart shows environmental inputs (cell density, autoinducer molecules, stress conditions), sensing mechanisms and regulatory proteins, signal processing and threshold logic, gene regulation and response pathways, collective behaviors, and final products (light emission, biofilm structure, antibiotic molecules).
615
+ </div>
616
+ </div>
617
+
618
+ <h2>5. Circadian Clock System (Mammalian)</h2>
619
+ <div class="figure">
620
+ <div class="mermaid">
621
+ graph TD
622
+ %% Environmental Inputs
623
+ A[Light/Dark Cycle] --> B[Light Detection]
624
+ C[Temperature] --> D[Temperature Sensing]
625
+ E[Feeding Schedule] --> F[Metabolic Sensing]
626
+
627
+ %% Input Processing
628
+ B --> G[Retinal Photoreceptors]
629
+ D --> H[Temperature Sensors]
630
+ F --> I[Metabolic Sensors]
631
+
632
+ %% Signal Transmission
633
+ G --> J[Light Signal to SCN]
634
+ H --> K[Temperature Signal]
635
+ I --> L[Metabolic Signal]
636
+
637
+ %% Central Clock
638
+ J --> M[Suprachiasmatic Nucleus]
639
+ K --> N[Clock Gene Expression]
640
+ L --> O[Metabolic Clock]
641
+
642
+ %% Molecular Oscillator
643
+ M --> P[CLOCK-BMAL1 Complex]
644
+ N --> Q[PER-CRY Complex]
645
+ O --> R[REV-ERBα/β]
646
+
647
+ %% Feedback Loops
648
+ P --> S[Target Gene Activation]
649
+ Q --> T[Clock Gene Repression]
650
+ R --> U[BMAL1 Repression]
651
+
652
+ %% Output Pathways
653
+ S --> V[Hormone Secretion]
654
+ T --> W[Metabolic Regulation]
655
+ U --> X[Sleep-Wake Cycle]
656
+
657
+ %% Physiological Outputs
658
+ V --> Y[Cortisol Rhythm]
659
+ W --> Z[Glucose Metabolism]
660
+ X --> AA[Sleep Regulation]
661
+
662
+ %% Styling - Biological Color Scheme
663
+ %% Red: Triggers & Inputs
664
+ style A fill:#ff6b6b,color:#fff
665
+ style C fill:#ff6b6b,color:#fff
666
+ style E fill:#ff6b6b,color:#fff
667
+
668
+ %% Yellow: Structures & Objects
669
+ style G fill:#ffd43b,color:#000
670
+ style H fill:#ffd43b,color:#000
671
+ style I fill:#ffd43b,color:#000
672
+ style M fill:#ffd43b,color:#000
673
+ style P fill:#ffd43b,color:#000
674
+ style Q fill:#ffd43b,color:#000
675
+ style R fill:#ffd43b,color:#000
676
+
677
+ %% Green: Processing & Operations
678
+ style B fill:#51cf66,color:#fff
679
+ style D fill:#51cf66,color:#fff
680
+ style F fill:#51cf66,color:#fff
681
+ style J fill:#51cf66,color:#fff
682
+ style K fill:#51cf66,color:#fff
683
+ style L fill:#51cf66,color:#fff
684
+ style N fill:#51cf66,color:#fff
685
+ style O fill:#51cf66,color:#fff
686
+ style S fill:#51cf66,color:#fff
687
+ style T fill:#51cf66,color:#fff
688
+ style U fill:#51cf66,color:#fff
689
+ style V fill:#51cf66,color:#fff
690
+ style W fill:#51cf66,color:#fff
691
+ style X fill:#51cf66,color:#fff
692
+
693
+ %% Blue: Intermediates & States
694
+ style Y fill:#74c0fc,color:#fff
695
+ style Z fill:#74c0fc,color:#fff
696
+ style AA fill:#74c0fc,color:#fff
697
+
698
+ %% Violet: Products & Outputs
699
+ style Y fill:#b197fc,color:#fff
700
+ style Z fill:#b197fc,color:#fff
701
+ style AA fill:#b197fc,color:#fff
702
+ </div>
703
+ <div class="color-legend">
704
+ <span><span class="color-box" style="background:#ff6b6b;"></span>Environmental Inputs</span>
705
+ <span><span class="color-box" style="background:#ffd43b;"></span>Enzymes & Proteins</span>
706
+ <span><span class="color-box" style="background:#51cf66;"></span>Metabolic Reactions</span>
707
+ <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates & States</span>
708
+ <span><span class="color-box" style="background:#b197fc;"></span>Products & Outputs</span>
709
+ </div>
710
+ <div class="figure-caption">
711
+ <strong>Figure 5.</strong> Circadian Clock System. This biological process visualization demonstrates the computational logic of mammalian circadian rhythm regulation. The flowchart shows environmental inputs (light/dark cycle, temperature, feeding schedule), sensory mechanisms and clock proteins, signal transmission and central clock processing, molecular oscillator feedback loops, output pathways, and physiological outputs (hormone rhythms, metabolic regulation, sleep-wake cycles).
712
+ </div>
713
+ </div>
714
+ </div>
715
+ </body>
716
+ </html>
computer_science_processes.html CHANGED
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167
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168
 
169
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170
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171
  style C fill:#ff6b6b,color:#fff
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174
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  style D fill:#ffd43b,color:#000
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@@ -186,6 +188,7 @@ graph TD
186
  style V fill:#ffd43b,color:#000
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  style Y fill:#ffd43b,color:#000
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189
  style P fill:#51cf66,color:#fff
190
  style Q fill:#51cf66,color:#fff
191
  style R fill:#51cf66,color:#fff
@@ -198,18 +201,17 @@ graph TD
198
  style II fill:#51cf66,color:#fff
199
  style JJ fill:#51cf66,color:#fff
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201
  style S fill:#74c0fc,color:#fff
202
  style T fill:#74c0fc,color:#fff
203
  style U fill:#74c0fc,color:#fff
204
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205
  style BB fill:#74c0fc,color:#fff
206
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207
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208
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209
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210
- style HH fill:#51cf66,color:#fff
211
- style II fill:#51cf66,color:#fff
212
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213
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214
  <div class="color-legend">
215
  <span><span class="color-box" style="background:#ff6b6b;"></span>Inputs & Data</span>
@@ -272,10 +274,12 @@ graph TD
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  AA --> CC
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274
  %% Styling - Computer Science Color Scheme
 
275
  style A fill:#ff6b6b,color:#fff
276
  style C fill:#ff6b6b,color:#fff
277
  style E fill:#ff6b6b,color:#fff
278
 
 
279
  style B fill:#ffd43b,color:#000
280
  style D fill:#ffd43b,color:#000
281
  style F fill:#ffd43b,color:#000
@@ -285,7 +289,6 @@ graph TD
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  style J fill:#ffd43b,color:#000
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  style K fill:#ffd43b,color:#000
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  style L fill:#ffd43b,color:#000
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- style M fill:#74c0fc,color:#fff
289
  style N fill:#ffd43b,color:#000
290
  style O fill:#ffd43b,color:#000
291
  style P fill:#ffd43b,color:#000
@@ -294,15 +297,17 @@ graph TD
294
  style S fill:#ffd43b,color:#000
295
  style T fill:#ffd43b,color:#000
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  style U fill:#ffd43b,color:#000
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298
- style W fill:#74c0fc,color:#fff
299
  style X fill:#ffd43b,color:#000
300
  style Y fill:#ffd43b,color:#000
301
  style Z fill:#ffd43b,color:#000
302
  style AA fill:#ffd43b,color:#000
303
- style BB fill:#ffd43b,color:#000
304
- style CC fill:#ffd43b,color:#000
305
 
 
 
 
 
 
 
306
  style BB fill:#74c0fc,color:#fff
307
  style CC fill:#74c0fc,color:#fff
308
  </div>
@@ -358,10 +363,12 @@ graph TD
358
  U --> X[Solution Verification]
359
 
360
  %% Styling - Computer Science Color Scheme
 
361
  style A fill:#ff6b6b,color:#fff
362
  style C fill:#ff6b6b,color:#fff
363
  style E fill:#ff6b6b,color:#fff
364
 
 
365
  style B fill:#ffd43b,color:#000
366
  style D fill:#ffd43b,color:#000
367
  style F fill:#ffd43b,color:#000
@@ -374,16 +381,18 @@ graph TD
374
  style M fill:#ffd43b,color:#000
375
  style N fill:#ffd43b,color:#000
376
  style O fill:#ffd43b,color:#000
377
- style P fill:#ffd43b,color:#000
378
- style Q fill:#ffd43b,color:#000
379
- style R fill:#ffd43b,color:#000
380
- style S fill:#ffd43b,color:#000
381
- style T fill:#ffd43b,color:#000
382
- style U fill:#ffd43b,color:#000
383
- style V fill:#ffd43b,color:#000
384
- style W fill:#ffd43b,color:#000
385
- style X fill:#ffd43b,color:#000
386
 
 
 
 
 
 
 
 
 
 
 
 
387
  style X fill:#74c0fc,color:#fff
388
  </div>
389
  <div class="color-legend">
@@ -438,10 +447,12 @@ graph TD
438
  U --> X[Algorithm Termination]
439
 
440
  %% Styling - Computer Science Color Scheme
 
441
  style A fill:#ff6b6b,color:#fff
442
  style C fill:#ff6b6b,color:#fff
443
  style E fill:#ff6b6b,color:#fff
444
 
 
445
  style B fill:#ffd43b,color:#000
446
  style D fill:#ffd43b,color:#000
447
  style F fill:#ffd43b,color:#000
@@ -451,19 +462,21 @@ graph TD
451
  style J fill:#ffd43b,color:#000
452
  style K fill:#ffd43b,color:#000
453
  style L fill:#ffd43b,color:#000
454
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455
- style N fill:#ffd43b,color:#000
456
- style O fill:#ffd43b,color:#000
457
- style P fill:#ffd43b,color:#000
458
- style Q fill:#ffd43b,color:#000
459
- style R fill:#ffd43b,color:#000
460
- style S fill:#ffd43b,color:#000
461
- style T fill:#ffd43b,color:#000
462
- style U fill:#ffd43b,color:#000
463
- style V fill:#ffd43b,color:#000
464
- style W fill:#ffd43b,color:#000
465
- style X fill:#ffd43b,color:#000
466
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
467
  style X fill:#74c0fc,color:#fff
468
  </div>
469
  <div class="color-legend">
@@ -518,10 +531,12 @@ graph TD
518
  U --> X[Memory Management Complete]
519
 
520
  %% Styling - Computer Science Color Scheme
 
521
  style A fill:#ff6b6b,color:#fff
522
  style C fill:#ff6b6b,color:#fff
523
  style E fill:#ff6b6b,color:#fff
524
 
 
525
  style B fill:#ffd43b,color:#000
526
  style D fill:#ffd43b,color:#000
527
  style F fill:#ffd43b,color:#000
@@ -534,16 +549,18 @@ graph TD
534
  style M fill:#ffd43b,color:#000
535
  style N fill:#ffd43b,color:#000
536
  style O fill:#ffd43b,color:#000
537
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538
- style Q fill:#ffd43b,color:#000
539
- style R fill:#ffd43b,color:#000
540
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541
- style T fill:#ffd43b,color:#000
542
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543
- style V fill:#ffd43b,color:#000
544
- style W fill:#ffd43b,color:#000
545
- style X fill:#ffd43b,color:#000
546
 
 
 
 
 
 
 
 
 
 
 
 
547
  style X fill:#74c0fc,color:#fff
548
  </div>
549
  <div class="color-legend">
@@ -559,4 +576,5 @@ graph TD
559
  </div>
560
  </div>
561
  </body>
562
- </html>
 
 
167
  GG --> JJ[Stability Assessment Unstable]
168
 
169
  %% Styling - Computer Science Color Scheme
170
+ %% Red: Inputs & Triggers
171
  style A fill:#ff6b6b,color:#fff
172
  style C fill:#ff6b6b,color:#fff
173
  style E fill:#ff6b6b,color:#fff
174
 
175
+ %% Yellow: Structures & Objects
176
  style B fill:#ffd43b,color:#000
177
  style D fill:#ffd43b,color:#000
178
  style F fill:#ffd43b,color:#000
 
188
  style V fill:#ffd43b,color:#000
189
  style Y fill:#ffd43b,color:#000
190
 
191
+ %% Green: Processing & Operations
192
  style P fill:#51cf66,color:#fff
193
  style Q fill:#51cf66,color:#fff
194
  style R fill:#51cf66,color:#fff
 
201
  style II fill:#51cf66,color:#fff
202
  style JJ fill:#51cf66,color:#fff
203
 
204
+ %% Blue: Intermediates & States
205
  style S fill:#74c0fc,color:#fff
206
  style T fill:#74c0fc,color:#fff
207
  style U fill:#74c0fc,color:#fff
208
  style X fill:#74c0fc,color:#fff
209
  style BB fill:#74c0fc,color:#fff
210
  style CC fill:#74c0fc,color:#fff
 
211
  style FF fill:#74c0fc,color:#fff
212
+
213
+ %% Violet: Products & Outputs
214
+ style EE fill:#b197fc,color:#fff
 
215
  </div>
216
  <div class="color-legend">
217
  <span><span class="color-box" style="background:#ff6b6b;"></span>Inputs & Data</span>
 
274
  AA --> CC
275
 
276
  %% Styling - Computer Science Color Scheme
277
+ %% Red: Inputs & Triggers
278
  style A fill:#ff6b6b,color:#fff
279
  style C fill:#ff6b6b,color:#fff
280
  style E fill:#ff6b6b,color:#fff
281
 
282
+ %% Yellow: Structures & Objects
283
  style B fill:#ffd43b,color:#000
284
  style D fill:#ffd43b,color:#000
285
  style F fill:#ffd43b,color:#000
 
289
  style J fill:#ffd43b,color:#000
290
  style K fill:#ffd43b,color:#000
291
  style L fill:#ffd43b,color:#000
 
292
  style N fill:#ffd43b,color:#000
293
  style O fill:#ffd43b,color:#000
294
  style P fill:#ffd43b,color:#000
 
297
  style S fill:#ffd43b,color:#000
298
  style T fill:#ffd43b,color:#000
299
  style U fill:#ffd43b,color:#000
 
 
300
  style X fill:#ffd43b,color:#000
301
  style Y fill:#ffd43b,color:#000
302
  style Z fill:#ffd43b,color:#000
303
  style AA fill:#ffd43b,color:#000
 
 
304
 
305
+ %% Green: Processing & Operations
306
+ style M fill:#51cf66,color:#fff
307
+ style V fill:#51cf66,color:#fff
308
+ style W fill:#51cf66,color:#fff
309
+
310
+ %% Blue: Intermediates & States
311
  style BB fill:#74c0fc,color:#fff
312
  style CC fill:#74c0fc,color:#fff
313
  </div>
 
363
  U --> X[Solution Verification]
364
 
365
  %% Styling - Computer Science Color Scheme
366
+ %% Red: Inputs & Triggers
367
  style A fill:#ff6b6b,color:#fff
368
  style C fill:#ff6b6b,color:#fff
369
  style E fill:#ff6b6b,color:#fff
370
 
371
+ %% Yellow: Structures & Objects
372
  style B fill:#ffd43b,color:#000
373
  style D fill:#ffd43b,color:#000
374
  style F fill:#ffd43b,color:#000
 
381
  style M fill:#ffd43b,color:#000
382
  style N fill:#ffd43b,color:#000
383
  style O fill:#ffd43b,color:#000
 
 
 
 
 
 
 
 
 
384
 
385
+ %% Green: Processing & Operations
386
+ style P fill:#51cf66,color:#fff
387
+ style Q fill:#51cf66,color:#fff
388
+ style R fill:#51cf66,color:#fff
389
+ style S fill:#51cf66,color:#fff
390
+ style T fill:#51cf66,color:#fff
391
+ style U fill:#51cf66,color:#fff
392
+
393
+ %% Blue: Intermediates & States
394
+ style V fill:#74c0fc,color:#fff
395
+ style W fill:#74c0fc,color:#fff
396
  style X fill:#74c0fc,color:#fff
397
  </div>
398
  <div class="color-legend">
 
447
  U --> X[Algorithm Termination]
448
 
449
  %% Styling - Computer Science Color Scheme
450
+ %% Red: Inputs & Triggers
451
  style A fill:#ff6b6b,color:#fff
452
  style C fill:#ff6b6b,color:#fff
453
  style E fill:#ff6b6b,color:#fff
454
 
455
+ %% Yellow: Structures & Objects
456
  style B fill:#ffd43b,color:#000
457
  style D fill:#ffd43b,color:#000
458
  style F fill:#ffd43b,color:#000
 
462
  style J fill:#ffd43b,color:#000
463
  style K fill:#ffd43b,color:#000
464
  style L fill:#ffd43b,color:#000
 
 
 
 
 
 
 
 
 
 
 
 
465
 
466
+ %% Green: Processing & Operations
467
+ style M fill:#51cf66,color:#fff
468
+ style N fill:#51cf66,color:#fff
469
+ style O fill:#51cf66,color:#fff
470
+ style P fill:#51cf66,color:#fff
471
+ style Q fill:#51cf66,color:#fff
472
+ style R fill:#51cf66,color:#fff
473
+ style S fill:#51cf66,color:#fff
474
+ style T fill:#51cf66,color:#fff
475
+ style U fill:#51cf66,color:#fff
476
+
477
+ %% Blue: Intermediates & States
478
+ style V fill:#74c0fc,color:#fff
479
+ style W fill:#74c0fc,color:#fff
480
  style X fill:#74c0fc,color:#fff
481
  </div>
482
  <div class="color-legend">
 
531
  U --> X[Memory Management Complete]
532
 
533
  %% Styling - Computer Science Color Scheme
534
+ %% Red: Inputs & Triggers
535
  style A fill:#ff6b6b,color:#fff
536
  style C fill:#ff6b6b,color:#fff
537
  style E fill:#ff6b6b,color:#fff
538
 
539
+ %% Yellow: Structures & Objects
540
  style B fill:#ffd43b,color:#000
541
  style D fill:#ffd43b,color:#000
542
  style F fill:#ffd43b,color:#000
 
549
  style M fill:#ffd43b,color:#000
550
  style N fill:#ffd43b,color:#000
551
  style O fill:#ffd43b,color:#000
 
 
 
 
 
 
 
 
 
552
 
553
+ %% Green: Processing & Operations
554
+ style P fill:#51cf66,color:#fff
555
+ style Q fill:#51cf66,color:#fff
556
+ style R fill:#51cf66,color:#fff
557
+ style S fill:#51cf66,color:#fff
558
+ style T fill:#51cf66,color:#fff
559
+ style U fill:#51cf66,color:#fff
560
+
561
+ %% Blue: Intermediates & States
562
+ style V fill:#74c0fc,color:#fff
563
+ style W fill:#74c0fc,color:#fff
564
  style X fill:#74c0fc,color:#fff
565
  </div>
566
  <div class="color-legend">
 
576
  </div>
577
  </div>
578
  </body>
579
+ </html>
580
+
index.html CHANGED
@@ -8,17 +8,18 @@
8
  <link href="https://cdnjs.cloudflare.com/ajax/libs/prism/1.29.0/themes/prism.min.css" rel="stylesheet">
9
  <script src="https://cdnjs.cloudflare.com/ajax/libs/prism/1.29.0/components/prism-core.min.js"></script>
10
  <script src="https://cdnjs.cloudflare.com/ajax/libs/prism/1.29.0/plugins/autoloader/prism-autoloader.min.js"></script>
 
 
11
  </head>
12
  <body>
13
  <div class="container">
14
  <header>
15
  <h1>🚀 Programming Framework</h1>
16
- <p>A comprehensive framework for programming education and practice</p>
17
  </header>
18
 
19
  <nav class="tabs">
20
  <button class="tab-btn active" data-tab="overview">Overview</button>
21
- <button class="tab-btn" data-tab="methodology">Methodology</button>
22
  <button class="tab-btn" data-tab="examples">Examples</button>
23
  <button class="tab-btn" data-tab="resources">Resources</button>
24
  </nav>
@@ -27,77 +28,64 @@
27
  <!-- Overview Tab -->
28
  <div class="tab-content active" id="overview">
29
  <div class="card">
30
- <h2>What is the Programming Framework?</h2>
31
- <p>The Programming Framework is a systematic approach to learning and mastering programming concepts through structured methodology, practical examples, and progressive skill development.</p>
32
-
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
33
  <div class="features">
34
  <div class="feature">
35
- <h3>🎯 Systematic Learning</h3>
36
- <p>Structured approach to programming education with clear progression paths</p>
 
37
  </div>
38
  <div class="feature">
39
- <h3>🔧 Practical Application</h3>
40
- <p>Real-world examples and hands-on exercises to reinforce concepts</p>
 
41
  </div>
42
  <div class="feature">
43
- <h3>📈 Progressive Development</h3>
44
- <p>Build skills incrementally from fundamentals to advanced techniques</p>
 
45
  </div>
46
  <div class="feature">
47
- <h3>🌐 Multi-Language Support</h3>
48
- <p>Learn concepts that apply across multiple programming languages</p>
 
 
 
 
 
 
49
  </div>
50
- </div>
51
- </div>
52
- </div>
53
-
54
- <!-- Methodology Tab -->
55
- <div class="tab-content" id="methodology">
56
- <div class="card">
57
- <h2>Programming Framework Methodology</h2>
58
-
59
- <div class="methodology-step">
60
- <h3>1. Foundation Building</h3>
61
- <p>Establish core programming concepts and principles</p>
62
- <ul>
63
- <li>Variables and data types</li>
64
- <li>Control structures</li>
65
- <li>Functions and methods</li>
66
- <li>Basic algorithms</li>
67
- </ul>
68
- </div>
69
-
70
- <div class="methodology-step">
71
- <h3>2. Problem Analysis</h3>
72
- <p>Learn to break down complex problems into manageable components</p>
73
- <ul>
74
- <li>Requirements gathering</li>
75
- <li>Problem decomposition</li>
76
- <li>Algorithm design</li>
77
- <li>Pseudocode development</li>
78
- </ul>
79
- </div>
80
-
81
- <div class="methodology-step">
82
- <h3>3. Implementation</h3>
83
- <p>Translate solutions into working code</p>
84
- <ul>
85
- <li>Code organization</li>
86
- <li>Best practices</li>
87
- <li>Testing and debugging</li>
88
- <li>Documentation</li>
89
- </ul>
90
- </div>
91
-
92
- <div class="methodology-step">
93
- <h3>4. Optimization</h3>
94
- <p>Improve code efficiency and maintainability</p>
95
- <ul>
96
- <li>Performance analysis</li>
97
- <li>Code refactoring</li>
98
- <li>Design patterns</li>
99
- <li>Advanced algorithms</li>
100
- </ul>
101
  </div>
102
  </div>
103
  </div>
@@ -105,124 +93,37 @@
105
  <!-- Examples Tab -->
106
  <div class="tab-content" id="examples">
107
  <div class="card">
108
- <h2>Framework Examples</h2>
109
-
110
- <div class="example">
111
- <h3>Problem: Find the Maximum Number in an Array</h3>
112
- <div class="framework-application">
113
- <h4>Framework Application:</h4>
114
- <ol>
115
- <li><strong>Foundation:</strong> Understand arrays and loops</li>
116
- <li><strong>Analysis:</strong> Need to compare each element with current maximum</li>
117
- <li><strong>Implementation:</strong> Write iterative solution</li>
118
- <li><strong>Optimization:</strong> Consider edge cases and efficiency</li>
119
- </ol>
120
- </div>
121
- <div class="code-example">
122
- <h4>Example Implementation (Python):</h4>
123
- <pre><code class="language-python">def find_max(arr):
124
- if not arr:
125
- return None
126
-
127
- max_val = arr[0]
128
- for num in arr[1:]:
129
- if num > max_val:
130
- max_val = num
131
-
132
- return max_val
133
-
134
- # Test the function
135
- numbers = [3, 7, 2, 9, 1, 5]
136
- result = find_max(numbers)
137
- print(f"Maximum number: {result}") # Output: Maximum number: 9</code></pre>
138
- </div>
139
- </div>
140
-
141
- <div class="example">
142
- <h3>Problem: Reverse a String</h3>
143
- <div class="framework-application">
144
- <h4>Framework Application:</h4>
145
- <ol>
146
- <li><strong>Foundation:</strong> String manipulation and indexing</li>
147
- <li><strong>Analysis:</strong> Process characters from end to beginning</li>
148
- <li><strong>Implementation:</strong> Build reversed string character by character</li>
149
- <li><strong>Optimization:</strong> Use built-in methods or efficient algorithms</li>
150
- </ol>
151
- </div>
152
- <div class="code-example">
153
- <h4>Example Implementation (JavaScript):</h4>
154
- <pre><code class="language-javascript">function reverseString(str) {
155
- let reversed = '';
156
- for (let i = str.length - 1; i >= 0; i--) {
157
- reversed += str[i];
158
- }
159
- return reversed;
160
- }
161
-
162
- // Test the function
163
- const text = "Programming Framework";
164
- const result = reverseString(text);
165
- console.log(result); // Output: krowemarF gnimmargorP</code></pre>
166
- </div>
167
- </div>
168
  </div>
169
  </div>
170
 
171
  <!-- Resources Tab -->
172
  <div class="tab-content" id="resources">
173
  <div class="card">
174
- <h2>Learning Resources</h2>
175
-
176
  <div class="resources-grid">
177
  <div class="resource">
178
- <h3>📚 Books</h3>
179
  <ul>
180
- <li>"Clean Code" by Robert C. Martin</li>
181
- <li>"Design Patterns" by Gang of Four</li>
182
- <li>"Introduction to Algorithms" by CLRS</li>
183
- <li>"The Pragmatic Programmer" by Hunt & Thomas</li>
184
- </ul>
185
- </div>
186
-
187
- <div class="resource">
188
- <h3>🌐 Online Platforms</h3>
189
- <ul>
190
- <li>LeetCode - Algorithm practice</li>
191
- <li>HackerRank - Coding challenges</li>
192
- <li>Codecademy - Interactive tutorials</li>
193
- <li>freeCodeCamp - Project-based learning</li>
194
- </ul>
195
- </div>
196
-
197
- <div class="resource">
198
- <h3>🎥 Video Courses</h3>
199
- <ul>
200
- <li>MIT OpenCourseWare</li>
201
- <li>Stanford CS50</li>
202
- <li>Coursera Algorithms courses</li>
203
- <li>YouTube programming channels</li>
204
- </ul>
205
- </div>
206
-
207
- <div class="resource">
208
- <h3>🛠️ Tools</h3>
209
- <ul>
210
- <li>Git - Version control</li>
211
- <li>VS Code - Code editor</li>
212
- <li>Docker - Containerization</li>
213
- <li>Postman - API testing</li>
214
  </ul>
215
  </div>
216
-
217
  <div class="resource">
218
- <h3>📖 Documentation</h3>
219
  <ul>
220
- <li><a href="ProgFrame_README.md" target="_blank">Programming Framework README</a></li>
221
- <li><a href="programming_framework_article.html" target="_blank">Academic Article</a></li>
222
- <li><a href="computer_science_processes.html" target="_blank">Computer Science Examples</a></li>
223
- <li><a href="chemistry_examples.html" target="_blank">Chemistry Examples</a></li>
224
- <li><a href="physics_processes.html" target="_blank">Physics Examples</a></li>
225
- <li><a href="mathematics_processes.html" target="_blank">Mathematics Examples</a></li>
226
  </ul>
227
  </div>
228
  </div>
@@ -235,14 +136,9 @@ console.log(result); // Output: krowemarF gnimmargorP</code></pre>
235
  // Tab functionality
236
  document.querySelectorAll('.tab-btn').forEach(button => {
237
  button.addEventListener('click', () => {
238
- // Remove active class from all tabs and content
239
  document.querySelectorAll('.tab-btn').forEach(btn => btn.classList.remove('active'));
240
  document.querySelectorAll('.tab-content').forEach(content => content.classList.remove('active'));
241
-
242
- // Add active class to clicked tab
243
  button.classList.add('active');
244
-
245
- // Show corresponding content
246
  const tabId = button.getAttribute('data-tab');
247
  document.getElementById(tabId).classList.add('active');
248
  });
 
8
  <link href="https://cdnjs.cloudflare.com/ajax/libs/prism/1.29.0/themes/prism.min.css" rel="stylesheet">
9
  <script src="https://cdnjs.cloudflare.com/ajax/libs/prism/1.29.0/components/prism-core.min.js"></script>
10
  <script src="https://cdnjs.cloudflare.com/ajax/libs/prism/1.29.0/plugins/autoloader/prism-autoloader.min.js"></script>
11
+ <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
12
+ <script>mermaid.initialize({startOnLoad:true});</script>
13
  </head>
14
  <body>
15
  <div class="container">
16
  <header>
17
  <h1>🚀 Programming Framework</h1>
18
+ <p>A cross-disciplinary visualization methodology for complex systems using Mermaid Markdown and a universal five-color code.</p>
19
  </header>
20
 
21
  <nav class="tabs">
22
  <button class="tab-btn active" data-tab="overview">Overview</button>
 
23
  <button class="tab-btn" data-tab="examples">Examples</button>
24
  <button class="tab-btn" data-tab="resources">Resources</button>
25
  </nav>
 
28
  <!-- Overview Tab -->
29
  <div class="tab-content active" id="overview">
30
  <div class="card">
31
+ <h2>Universal Color Coding</h2>
32
+ <div class="resources-grid">
33
+ <div class="resource">
34
+ <h3>Red (#ff6b6b)</h3>
35
+ <p>Triggers & Inputs</p>
36
+ <p>Biology: Environmental signals · Chemistry: Reactant supply · CS: Input data · Physics: Energy input · Math: Axioms</p>
37
+ </div>
38
+ <div class="resource">
39
+ <h3>Yellow (#ffd43b)</h3>
40
+ <p>Structures & Objects</p>
41
+ <p>Biology: Enzymes · Chemistry: Catalysts · CS: Data structures · Physics: Fields · Math: Theorems</p>
42
+ </div>
43
+ <div class="resource">
44
+ <h3>Green (#51cf66)</h3>
45
+ <p>Processing & Operations</p>
46
+ <p>Biology: Reactions · Chemistry: Reactions · CS: Execution · Physics: Operations · Math: Deductions</p>
47
+ </div>
48
+ <div class="resource">
49
+ <h3>Blue (#74c0fc)</h3>
50
+ <p>Intermediates & States</p>
51
+ <p>Biology: Metabolites · Chemistry: Intermediates · CS: Variables · Physics: States · Math: Intermediates</p>
52
+ </div>
53
+ <div class="resource">
54
+ <h3>Violet (#b197fc)</h3>
55
+ <p>Products & Outputs</p>
56
+ <p>Biology: Biomolecules · Chemistry: Final products · CS: Program outputs · Physics: Phenomena · Math: Results</p>
57
+ </div>
58
+ </div>
59
+ </div>
60
+
61
+ <div class="card">
62
+ <h2>Mini Examples</h2>
63
  <div class="features">
64
  <div class="feature">
65
+ <h3>Biology</h3>
66
+ <div class="mermaid">graph TD; A[Glucose Input]-->B[Transport]; B-->C[Metabolism]; C-->D[ATP]; style A fill:#ff6b6b,color:#fff; style B fill:#ffd43b,color:#000; style C fill:#51cf66,color:#fff; style D fill:#b197fc,color:#fff;</div>
67
+ <p><a href="programming_framework_article.html" target="_blank">Read article</a> · <a href="https://huggingface.co/spaces/garywelz/glmp" target="_blank">GLMP Space</a></p>
68
  </div>
69
  <div class="feature">
70
+ <h3>Chemistry</h3>
71
+ <div class="mermaid">graph TD; A[Reactants]-->B[Catalyst]; B-->C[Reaction]; C-->D[Products]; style A fill:#ff6b6b,color:#fff; style B fill:#ffd43b,color:#000; style C fill:#51cf66,color:#fff; style D fill:#b197fc,color:#fff;</div>
72
+ <p><a href="chemistry_examples.html" target="_blank">Chemistry examples</a></p>
73
  </div>
74
  <div class="feature">
75
+ <h3>Computer Science</h3>
76
+ <div class="mermaid">graph TD; A[Input Array]-->B[Partition]; B-->C[Recurse]; C-->D[Sorted Output]; style A fill:#ff6b6b,color:#fff; style B fill:#51cf66,color:#fff; style C fill:#74c0fc,color:#fff; style D fill:#b197fc,color:#fff;</div>
77
+ <p><a href="computer_science_processes.html" target="_blank">CS processes</a></p>
78
  </div>
79
  <div class="feature">
80
+ <h3>Physics</h3>
81
+ <div class="mermaid">graph TD; A[Energy Input]-->B[State Prep]; B-->C[Evolution]; C-->D[Measurement]; style A fill:#ff6b6b,color:#fff; style B fill:#ffd43b,color:#000; style C fill:#51cf66,color:#fff; style D fill:#b197fc,color:#fff;</div>
82
+ <p><a href="physics_processes.html" target="_blank">Physics processes</a></p>
83
+ </div>
84
+ <div class="feature">
85
+ <h3>Mathematics</h3>
86
+ <div class="mermaid">graph TD; A[Axioms]-->B[Deduction]; B-->C[Intermediate]; C-->D[Theorem]; style A fill:#ff6b6b,color:#fff; style B fill:#51cf66,color:#fff; style C fill:#74c0fc,color:#fff; style D fill:#b197fc,color:#fff;</div>
87
+ <p><a href="mathematics_processes.html" target="_blank">Math processes</a></p>
88
  </div>
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
89
  </div>
90
  </div>
91
  </div>
 
93
  <!-- Examples Tab -->
94
  <div class="tab-content" id="examples">
95
  <div class="card">
96
+ <h2>Explore Examples</h2>
97
+ <ul>
98
+ <li><a href="programming_framework_article.html" target="_blank">Full article with biology examples</a></li>
99
+ <li><a href="chemistry_examples.html" target="_blank">Chemistry examples</a></li>
100
+ <li><a href="computer_science_processes.html" target="_blank">Computer Science processes</a></li>
101
+ <li><a href="physics_processes.html" target="_blank">Physics processes</a></li>
102
+ <li><a href="mathematics_processes.html" target="_blank">Mathematics processes</a></li>
103
+ </ul>
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
104
  </div>
105
  </div>
106
 
107
  <!-- Resources Tab -->
108
  <div class="tab-content" id="resources">
109
  <div class="card">
110
+ <h2>Resources</h2>
 
111
  <div class="resources-grid">
112
  <div class="resource">
113
+ <h3>Documentation</h3>
114
  <ul>
115
+ <li><a href="programming_framework_article.html" target="_blank">Academic Article</a></li>
116
+ <li><a href="https://huggingface.co/spaces/garywelz/glmp" target="_blank">GLMP Space (biology evidence base)</a></li>
117
+ <li><a href="https://github.com/garywelz/glmp" target="_blank">GLMP GitHub</a></li>
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
118
  </ul>
119
  </div>
 
120
  <div class="resource">
121
+ <h3>Discipline Pages</h3>
122
  <ul>
123
+ <li><a href="chemistry_examples.html" target="_blank">Chemistry</a></li>
124
+ <li><a href="computer_science_processes.html" target="_blank">Computer Science</a></li>
125
+ <li><a href="physics_processes.html" target="_blank">Physics</a></li>
126
+ <li><a href="mathematics_processes.html" target="_blank">Mathematics</a></li>
 
 
127
  </ul>
128
  </div>
129
  </div>
 
136
  // Tab functionality
137
  document.querySelectorAll('.tab-btn').forEach(button => {
138
  button.addEventListener('click', () => {
 
139
  document.querySelectorAll('.tab-btn').forEach(btn => btn.classList.remove('active'));
140
  document.querySelectorAll('.tab-content').forEach(content => content.classList.remove('active'));
 
 
141
  button.classList.add('active');
 
 
142
  const tabId = button.getAttribute('data-tab');
143
  document.getElementById(tabId).classList.add('active');
144
  });