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  1. processes/yeast/yeast_batch08_quality_control_systems.html +418 -1198
  2. processes/yeast/yeast_simple_index.html +357 -0
processes/yeast/yeast_batch08_quality_control_systems.html CHANGED
@@ -1,12 +1,12 @@
1
  <!DOCTYPE html>
 
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  <html lang="en">
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  <head>
4
- <meta charset="UTF-8">
5
- <meta name="viewport" content="width=device-width, initial-scale=1.0">
6
- <title>Yeast Batch 15: Quality Control Systems</title>
7
  <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js">
8
-
9
- </script><style>
10
  body { font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif; /* Ensure proper rendering of Greek characters */
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  h1, h2, h3, p, li, a {
12
  font-family: \'Segoe UI\', Tahoma, Geneva, Verdana, \'Arial Unicode MS\', sans-serif;
@@ -91,140 +91,328 @@
91
  }
92
  </style></head>
93
  <body>
94
- <div class="container">
95
- <div class="header">
96
- <h1>
97
- 🧬 Yeast Cellular Processes
98
- </h><p>
99
- Programming Framework Analysis - Batch 15
100
- </p></div> <div class="content">
101
- <div class="batch-header">
102
- <h2>
103
- Batch 15: Quality Control Systems (8 processes)
104
- </h><p>
105
- Cellular surveillance and error correction mechanisms
106
- </p></div><div class="toc">
107
- <h2>
108
  📋 Table of Contents - 8 Quality Control Processes
109
- </h><ul>
110
- <li>
111
- <a href="#unfolded-protein-response">1. Unfolded Protein Response</a></li><li>
112
- <a href="#nonsense-mediated-decay">2. Nonsense-Mediated Decay</a></li><li>
113
- <a href="#ribosome-quality-control">3. Ribosome Quality Control</a></li><li>
114
- <a href="#mitochondrial-quality-control">4. Mitochondrial Quality Control</a></li><li>
115
- <a href="#chromosome-integrity">5. Chromosome Integrity</a></li><li>
116
- <a href="#cell-wall-integrity">6. Cell Wall Integrity</a></li><li>
117
- <a href="#organelle-inheritance">7. Organelle Inheritance</a></li><li>
118
- <a href="#apoptosis">8. Apoptosis</a></li></ul></div><!-- Process 1: Unfolded Protein Response --> <div class="process-item" id="unfolded-protein-response">
119
- <h3>
120
- 1. Unfolded Protein Response
121
- </h><p>
122
  Detailed analysis of Unfolded Protein Response using the Programming Framework, revealing computational logic for ER stress management.
123
  </p>
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
124
  <!-- Interactive Slider Controls -->
125
  <div class="slider-controls">
126
  <h4>🎛️ Detail Level Control</h4>
127
  <div class="slider-container">
128
  <span class="slider-label">Level:</span>
129
- <input type="range" class="detail-slider" id="slider-1" min="1" max="5" value="1" step="1">
130
- <span class="level-display" id="level-1">1</span>
131
  </div>
132
  </div>
133
 
134
  <div class="mermaid-container">
135
- <div class="mermaid" id="chart-1">
136
- graph TD
137
- A[Misfolded Proteins] --> B[ER Stress Detection] B --> C[IRE1 Activation] C --> D[HAC1 mRNA Splicing] D --> E[Hac1 Protein Translation] E --> F[UPR Gene Expression] F --> G[ER Chaperone Upregulation] G --> H[Protein Folding Capacity] H --> I[ER Homeostasis] J[Severe Stress] --> K[PERK/ATF6 Pathways] K --> L[Translation Attenuation] L --> M[Protein Load Reduction] N[Prolonged Stress] --> O[Apoptosis Signaling] O --> P[Cell Death] style  fill:#ff6b6b,color:#fff
138
- style  fill:#ffd43b,color:#000
139
- style  fill:#ffd43b,color:#000
140
- style  fill:#b197fc,color:#fff
141
- style  fill:#ff6b6b,color:#fff
 
 
 
 
 
 
 
 
 
 
 
 
142
  </div>
143
- </div>
144
- </div><!-- Process 2: Nonsense-Mediated Decay --> <div class="process-item" id="nonsense-mediated-decay">
145
- <h3>
146
- 2. Nonsense-Mediated Decay
147
- </h><p>
148
- Detailed analysis of Nonsense-Mediated Decay using the Programming Framework, revealing computational logic for mRNA quality control.
149
- </p>
 
 
 
 
 
 
 
 
150
  <!-- Interactive Slider Controls -->
151
  <div class="slider-controls">
152
  <h4>🎛️ Detail Level Control</h4>
153
  <div class="slider-container">
154
  <span class="slider-label">Level:</span>
155
- <input type="range" class="detail-slider" id="slider-2" min="1" max="5" value="1" step="1">
156
- <span class="level-display" id="level-2">1</span>
157
  </div>
158
  </div>
159
 
160
  <div class="mermaid-container">
161
- <div class="mermaid" id="chart-2">
162
- graph TD
163
- A[Premature Stop Codon] --> B[Ribosome Stalling] B --> C[Upf1 Recruitment] C --> D[Upf1 Phosphorylation] D --> E[Upf2/Upf3 Binding] E --> F[mRNA Degradation Complex] F --> G[5' to 3' Exonuclease] G --> H[3' to 5' Exonuclease] H --> I[mRNA Decay] I --> J[Aberrant mRNA Elimination] style  fill:#ff6b6b,color:#fff
164
- style  fill:#ffd43b,color:#000
165
- style  fill:#ffd43b,color:#000
166
- style  fill:#74c0fc,color:#fff
167
- style  fill:#b197fc,color:#fff
 
 
 
 
 
 
 
 
 
 
 
 
168
  </div>
169
- </div>
170
- </div><!-- Process 3: Cell Wall Integrity --> <div class="process-item" id="cell-wall-integrity">
171
- <h3>
172
- 6. Cell Wall Integrity
173
- </h><p>
174
- Detailed analysis of Cell Wall Integrity using the Programming Framework, revealing computational logic for structural maintenance and repair.
175
- </p>
 
 
 
 
 
 
 
 
176
  <!-- Interactive Slider Controls -->
177
  <div class="slider-controls">
178
  <h4>🎛️ Detail Level Control</h4>
179
  <div class="slider-container">
180
  <span class="slider-label">Level:</span>
181
- <input type="range" class="detail-slider" id="slider-3" min="1" max="5" value="1" step="1">
182
- <span class="level-display" id="level-3">1</span>
183
  </div>
184
  </div>
185
 
186
  <div class="mermaid-container">
187
- <div class="mermaid" id="chart-3">
188
- graph TD
189
- A[Cell Wall Stress] --> B[Pkc1 Activation] B --> C[MAPK Cascade] C --> D[Slt2 Phosphorylation] D --> E[Rlm1/SBF Activation] E --> F[Cell Wall Gene Expression] F --> G[Chitin/Glucan Synthesis] G --> H[Cell Wall Repair] H --> I[Structural Integrity] J[Severe Damage] --> K[Emergency Response] K --> L[Cell Wall Thickening] L --> M[Osmotic Protection] style  fill:#ff6b6b,color:#fff
190
- style  fill:#ffd43b,color:#000
191
- style  fill:#ffd43b,color:#000
192
- style  fill:#b197fc,color:#fff
193
- style  fill:#b197fc,color:#fff
 
 
 
 
 
 
 
 
 
 
 
 
194
  </div>
195
- </div>
196
- </div><!-- Process 4: Apoptosis --> <div class="process-item" id="apoptosis">
197
- <h3>
198
- 8. Apoptosis
199
- </h><p>
200
- Detailed analysis of Apoptosis using the Programming Framework, revealing computational logic for programmed cell death.
201
- </p>
 
 
 
 
 
 
 
 
202
  <!-- Interactive Slider Controls -->
203
  <div class="slider-controls">
204
  <h4>🎛️ Detail Level Control</h4>
205
  <div class="slider-container">
206
  <span class="slider-label">Level:</span>
207
- <input type="range" class="detail-slider" id="slider-4" min="1" max="5" value="1" step="1">
208
- <span class="level-display" id="level-4">1</span>
209
  </div>
210
  </div>
211
 
212
  <div class="mermaid-container">
213
- <div class="mermaid" id="chart-4">
214
- graph TD
215
- A[Severe Cellular Damage] --> B[DNA Damage Response] B --> C[p53 Homolog Activation] C --> D[Pro-apoptotic Signals] D --> E[Mitochondrial Dysfunction] E --> F[Cytochrome c Release] F --> G[Caspase Activation] G --> H[Chromatin Condensation] H --> I[DNA Fragmentation] I --> J[Cell Death] K[Stress Response Failure] --> L[Autophagy Pathway] L
216
- --> M{Recovery Possible?} M
217
- -->|No|
218
- N[Apoptotic Switch] N
219
- --> D
220
- style  fill:#ff6b6b,color:#fff
221
- style  fill:#ffd43b,color:#000
222
- style  fill:#ffd43b,color:#000
223
- style  fill:#ff6b6b,color:#fff
224
- style  fill:#74c0fc,color:#fff
 
 
 
 
 
 
 
225
  </div>
226
- </div>
227
- </div> <!-- Sources Section -->
 
 
 
 
 
 
 
 
 
228
  <div class="sources-section">
229
  <h2>📚 Academic Sources</h2>
230
  <div class="sources-content">
@@ -235,12 +423,10 @@
235
  <li><strong>Lodish, H., et al.</strong> (2016). <em>Molecular Cell Biology</em>, 8th Edition. W.H. Freeman.</li>
236
  <li><strong>Nelson, D.L. & Cox, M.M.</strong> (2017). <em>Lehninger Principles of Biochemistry</em>, 7th Edition. W.H. Freeman.</li>
237
  </ul>
238
- <h3>Yeast Cell Biology Research</h3>
239
  <ul>
240
- <li><strong>Botstein, D. & Fink, G.R.</strong> (2011). Yeast: an experimental organism for 21st Century biology. <em>Genetics</em>, 189(3), 695-704.</li>
241
- <li><strong>Hartwell, L.H.</strong> (2002). Nobel lecture: Yeast and cancer. <em>Bioscience Reports</em>, 22(3-4), 373-394.</li>
242
- <li><strong>Nurse, P.</strong> (2002). Cyclin dependent kinases and cell cycle control. <em>ChemBioChem</em>, 3(7), 596-603.</li>
243
- <li><strong>Goffeau, A., et al.</strong> (1996). Life with 6000 genes. <em>Science</em>, 274(5287), 546-567.</li>
244
  </ul>
245
  </div>
246
  </div>
@@ -273,1135 +459,169 @@
273
  </div>
274
 
275
  <div class="footer">
276
- <p>
277
- <strong>Generated using the Programming Framework methodology</strong>
278
-
279
- </p><p>
280
  This batch demonstrates the computational nature of yeast quality control and cellular surveillance systems
281
  </p><p>
282
- <em>Batch 15 of 15: Quality Control Systems</em>
283
-
284
- </p></div>
285
- </div>
286
- </div><script>
287
- // Process definitions with 5 detail levels each - Complete allProcesses object
288
  const allProcesses = {
289
- 1: { // Process 1
290
  levels: {
291
  1: `graph TD
292
- A[Signal Input] --> B[Process Initiation]
293
- B --> C[Process Output]
294
-
295
- style A fill:#ff6b6b,color:#fff
296
- style B fill:#ffd43b,color:#000
297
- style C fill:#b197fc,color:#fff`,
298
-
299
  2: `graph TD
300
- A[Environmental Signal] --> B[Receptor Binding]
301
- B --> C[Signal Transduction]
302
- C --> D[Molecular Complex]
303
- D --> E[Process Output]
304
-
305
- style A fill:#ff6b6b,color:#fff
306
- style B fill:#ffd43b,color:#000
307
- style C fill:#74c0fc,color:#fff
308
- style D fill:#51cf66,color:#fff
309
- style E fill:#b197fc,color:#fff`,
310
-
311
  3: `graph TD
312
- A[Cellular Signal] --> B[Sensor Protein]
313
- B --> C[Signal Cascade]
314
- C --> D[Protein Recruitment]
315
- D --> E[Complex Assembly]
316
- E --> F[Active Site Formation]
317
- F --> G[Catalytic Mechanism]
318
- G --> H[Product Formation]
319
-
320
- style A fill:#ff6b6b,color:#fff
321
- style B fill:#ffd43b,color:#000
322
- style C fill:#74c0fc,color:#fff
323
- style D fill:#51cf66,color:#fff
324
- style E fill:#74c0fc,color:#fff
325
- style F fill:#51cf66,color:#fff
326
- style G fill:#51cf66,color:#fff
327
- style H fill:#b197fc,color:#fff`,
328
-
329
  4: `graph TD
330
- A[External Signal] --> B[Receptor Complex]
331
- B --> C[Signal Integration]
332
- C --> D[Pathway Activation]
333
- D --> E[Protein Network]
334
- E --> F[Complex Formation]
335
- F --> G[Active Site Assembly]
336
- G --> H[Catalytic Cycle]
337
- H --> I[Product Release]
338
- I --> J[Quality Control]
339
- J --> K[Process Completion]
340
-
341
- style A fill:#ff6b6b,color:#fff
342
- style B fill:#ffd43b,color:#000
343
- style C fill:#74c0fc,color:#fff
344
- style D fill:#51cf66,color:#fff
345
- style E fill:#74c0fc,color:#fff
346
- style F fill:#51cf66,color:#fff
347
- style G fill:#74c0fc,color:#fff
348
- style H fill:#51cf66,color:#fff
349
- style I fill:#ffd43b,color:#000
350
- style J fill:#51cf66,color:#fff
351
- style K fill:#b197fc,color:#fff`,
352
-
353
  5: `graph TD
354
- A[Regulatory Signal] --> B[Multi-Receptor Complex]
355
- B --> C[Signal Processing Network]
356
- C --> D[Pathway Integration]
357
- D --> E[Protein Network Assembly]
358
- E --> F[Dynamic Complex Formation]
359
- F --> G[Allosteric Network]
360
- G --> H[Cooperative Binding]
361
- H --> I[Multi-Step Catalysis]
362
- I --> J[Intermediate Processing]
363
- J --> K[Product Modification]
364
- K --> L[Quality Assurance]
365
- L --> M[Regulatory Feedback]
366
- M --> N[Process Optimization]
367
- N --> O[System Integration]
368
- O --> P[Process Completion]
369
-
370
- style A fill:#ff6b6b,color:#fff
371
- style B fill:#ffd43b,color:#000
372
- style C fill:#74c0fc,color:#fff
373
- style D fill:#51cf66,color:#fff
374
- style E fill:#74c0fc,color:#fff
375
- style F fill:#51cf66,color:#fff
376
- style G fill:#51cf66,color:#fff
377
- style H fill:#74c0fc,color:#fff
378
- style I fill:#51cf66,color:#fff
379
- style J fill:#74c0fc,color:#fff
380
- style K fill:#51cf66,color:#fff
381
- style L fill:#ffd43b,color:#000
382
- style M fill:#74c0fc,color:#fff
383
- style N fill:#51cf66,color:#fff
384
- style O fill:#74c0fc,color:#fff
385
- style P fill:#b197fc,color:#fff`
386
  }
387
  },
388
- 2: { // Process 2
389
  levels: {
390
  1: `graph TD
391
- A[Input 2] --> B[Processing 2]
392
- B --> C[Output 2]
393
-
394
- style A fill:#ff6b6b,color:#fff
395
- style B fill:#51cf66,color:#fff
396
- style C fill:#b197fc,color:#fff`,
397
  2: `graph TD
398
- A[Signal 2] --> B[Recognition 2]
399
- B --> C[Processing 2]
400
- C --> D[Response 2]
401
-
402
- style A fill:#ff6b6b,color:#fff
403
- style B fill:#ffd43b,color:#000
404
- style C fill:#51cf66,color:#fff
405
- style D fill:#b197fc,color:#fff`,
406
  3: `graph TD
407
- A[Input 2] --> B[Detection 2]
408
- B --> C[Processing 2]
409
- C --> D[Integration 2]
410
- D --> E[Output 2]
411
-
412
- style A fill:#ff6b6b,color:#fff
413
- style B fill:#ffd43b,color:#000
414
- style C fill:#51cf66,color:#fff
415
- style D fill:#74c0fc,color:#fff
416
- style E fill:#b197fc,color:#fff`,
417
  4: `graph TD
418
- A[Signal 2] --> B[Sensor 2]
419
- B --> C[Cascade 2]
420
- C --> D[Integration 2]
421
- D --> E[Processing 2]
422
- E --> F[Response 2]
423
-
424
- style A fill:#ff6b6b,color:#fff
425
- style B fill:#ffd43b,color:#000
426
- style C fill:#74c0fc,color:#fff
427
- style D fill:#51cf66,color:#fff
428
- style E fill:#51cf66,color:#fff
429
- style F fill:#b197fc,color:#fff`,
430
  5: `graph TD
431
- A[Input 2] --> B[Recognition 2]
432
- B --> C[Processing Network 2]
433
- C --> D[Integration System 2]
434
- D --> E[Quality Control 2]
435
- E --> F[Feedback Loop 2]
436
- F --> G[Optimization 2]
437
- G --> H[Final Output 2]
438
-
439
- style A fill:#ff6b6b,color:#fff
440
- style B fill:#ffd43b,color:#000
441
- style C fill:#74c0fc,color:#fff
442
- style D fill:#51cf66,color:#fff
443
- style E fill:#51cf66,color:#fff
444
- style F fill:#74c0fc,color:#fff
445
- style G fill:#51cf66,color:#fff
446
- style H fill:#b197fc,color:#fff`
447
  }
448
  },
449
- 3: { // Process 3
450
  levels: {
451
  1: `graph TD
452
- A[Input 3] --> B[Processing 3]
453
- B --> C[Output 3]
454
-
455
- style A fill:#ff6b6b,color:#fff
456
- style B fill:#51cf66,color:#fff
457
- style C fill:#b197fc,color:#fff`,
458
  2: `graph TD
459
- A[Signal 3] --> B[Recognition 3]
460
- B --> C[Processing 3]
461
- C --> D[Response 3]
462
-
463
- style A fill:#ff6b6b,color:#fff
464
- style B fill:#ffd43b,color:#000
465
- style C fill:#51cf66,color:#fff
466
- style D fill:#b197fc,color:#fff`,
467
  3: `graph TD
468
- A[Input 3] --> B[Detection 3]
469
- B --> C[Processing 3]
470
- C --> D[Integration 3]
471
- D --> E[Output 3]
472
-
473
- style A fill:#ff6b6b,color:#fff
474
- style B fill:#ffd43b,color:#000
475
- style C fill:#51cf66,color:#fff
476
- style D fill:#74c0fc,color:#fff
477
- style E fill:#b197fc,color:#fff`,
478
  4: `graph TD
479
- A[Signal 3] --> B[Sensor 3]
480
- B --> C[Cascade 3]
481
- C --> D[Integration 3]
482
- D --> E[Processing 3]
483
- E --> F[Response 3]
484
-
485
- style A fill:#ff6b6b,color:#fff
486
- style B fill:#ffd43b,color:#000
487
- style C fill:#74c0fc,color:#fff
488
- style D fill:#51cf66,color:#fff
489
- style E fill:#51cf66,color:#fff
490
- style F fill:#b197fc,color:#fff`,
491
  5: `graph TD
492
- A[Input 3] --> B[Recognition 3]
493
- B --> C[Processing Network 3]
494
- C --> D[Integration System 3]
495
- D --> E[Quality Control 3]
496
- E --> F[Feedback Loop 3]
497
- F --> G[Optimization 3]
498
- G --> H[Final Output 3]
499
-
500
- style A fill:#ff6b6b,color:#fff
501
- style B fill:#ffd43b,color:#000
502
- style C fill:#74c0fc,color:#fff
503
- style D fill:#51cf66,color:#fff
504
- style E fill:#51cf66,color:#fff
505
- style F fill:#74c0fc,color:#fff
506
- style G fill:#51cf66,color:#fff
507
- style H fill:#b197fc,color:#fff`
508
  }
509
  },
510
- 4: { // Process 4
511
  levels: {
512
  1: `graph TD
513
- A[Input 4] --> B[Processing 4]
514
- B --> C[Output 4]
515
-
516
- style A fill:#ff6b6b,color:#fff
517
- style B fill:#51cf66,color:#fff
518
- style C fill:#b197fc,color:#fff`,
 
519
  2: `graph TD
520
- A[Signal 4] --> B[Recognition 4]
521
- B --> C[Processing 4]
522
- C --> D[Response 4]
523
-
524
- style A fill:#ff6b6b,color:#fff
525
- style B fill:#ffd43b,color:#000
526
- style C fill:#51cf66,color:#fff
527
- style D fill:#b197fc,color:#fff`,
528
  3: `graph TD
529
- A[Input 4] --> B[Detection 4]
530
- B --> C[Processing 4]
531
- C --> D[Integration 4]
532
- D --> E[Output 4]
533
-
534
- style A fill:#ff6b6b,color:#fff
535
- style B fill:#ffd43b,color:#000
536
- style C fill:#51cf66,color:#fff
537
- style D fill:#74c0fc,color:#fff
538
- style E fill:#b197fc,color:#fff`,
539
  4: `graph TD
540
- A[Signal 4] --> B[Sensor 4]
541
- B --> C[Cascade 4]
542
- C --> D[Integration 4]
543
- D --> E[Processing 4]
544
- E --> F[Response 4]
545
-
546
- style A fill:#ff6b6b,color:#fff
547
- style B fill:#ffd43b,color:#000
548
- style C fill:#74c0fc,color:#fff
549
- style D fill:#51cf66,color:#fff
550
- style E fill:#51cf66,color:#fff
551
- style F fill:#b197fc,color:#fff`,
552
  5: `graph TD
553
- A[Input 4] --> B[Recognition 4]
554
- B --> C[Processing Network 4]
555
- C --> D[Integration System 4]
556
- D --> E[Quality Control 4]
557
- E --> F[Feedback Loop 4]
558
- F --> G[Optimization 4]
559
- G --> H[Final Output 4]
560
-
561
- style A fill:#ff6b6b,color:#fff
562
- style B fill:#ffd43b,color:#000
563
- style C fill:#74c0fc,color:#fff
564
- style D fill:#51cf66,color:#fff
565
- style E fill:#51cf66,color:#fff
566
- style F fill:#74c0fc,color:#fff
567
- style G fill:#51cf66,color:#fff
568
- style H fill:#b197fc,color:#fff`
569
  }
570
  },
571
- 5: { // Process 5
572
- levels: {
573
- 1: `graph TD
574
- A[Input 5] --> B[Processing 5]
575
- B --> C[Output 5]
576
-
577
- style A fill:#ff6b6b,color:#fff
578
- style B fill:#51cf66,color:#fff
579
- style C fill:#b197fc,color:#fff`,
580
- 2: `graph TD
581
- A[Signal 5] --> B[Recognition 5]
582
- B --> C[Processing 5]
583
- C --> D[Response 5]
584
-
585
- style A fill:#ff6b6b,color:#fff
586
- style B fill:#ffd43b,color:#000
587
- style C fill:#51cf66,color:#fff
588
- style D fill:#b197fc,color:#fff`,
589
- 3: `graph TD
590
- A[Input 5] --> B[Detection 5]
591
- B --> C[Processing 5]
592
- C --> D[Integration 5]
593
- D --> E[Output 5]
594
-
595
- style A fill:#ff6b6b,color:#fff
596
- style B fill:#ffd43b,color:#000
597
- style C fill:#51cf66,color:#fff
598
- style D fill:#74c0fc,color:#fff
599
- style E fill:#b197fc,color:#fff`,
600
- 4: `graph TD
601
- A[Signal 5] --> B[Sensor 5]
602
- B --> C[Cascade 5]
603
- C --> D[Integration 5]
604
- D --> E[Processing 5]
605
- E --> F[Response 5]
606
-
607
- style A fill:#ff6b6b,color:#fff
608
- style B fill:#ffd43b,color:#000
609
- style C fill:#74c0fc,color:#fff
610
- style D fill:#51cf66,color:#fff
611
- style E fill:#51cf66,color:#fff
612
- style F fill:#b197fc,color:#fff`,
613
- 5: `graph TD
614
- A[Input 5] --> B[Recognition 5]
615
- B --> C[Processing Network 5]
616
- C --> D[Integration System 5]
617
- D --> E[Quality Control 5]
618
- E --> F[Feedback Loop 5]
619
- F --> G[Optimization 5]
620
- G --> H[Final Output 5]
621
-
622
- style A fill:#ff6b6b,color:#fff
623
- style B fill:#ffd43b,color:#000
624
- style C fill:#74c0fc,color:#fff
625
- style D fill:#51cf66,color:#fff
626
- style E fill:#51cf66,color:#fff
627
- style F fill:#74c0fc,color:#fff
628
- style G fill:#51cf66,color:#fff
629
- style H fill:#b197fc,color:#fff`
630
- }
631
- },
632
- 6: { // Process 6
633
- levels: {
634
- 1: `graph TD
635
- A[Input 6] --> B[Processing 6]
636
- B --> C[Output 6]
637
-
638
- style A fill:#ff6b6b,color:#fff
639
- style B fill:#51cf66,color:#fff
640
- style C fill:#b197fc,color:#fff`,
641
- 2: `graph TD
642
- A[Signal 6] --> B[Recognition 6]
643
- B --> C[Processing 6]
644
- C --> D[Response 6]
645
-
646
- style A fill:#ff6b6b,color:#fff
647
- style B fill:#ffd43b,color:#000
648
- style C fill:#51cf66,color:#fff
649
- style D fill:#b197fc,color:#fff`,
650
- 3: `graph TD
651
- A[Input 6] --> B[Detection 6]
652
- B --> C[Processing 6]
653
- C --> D[Integration 6]
654
- D --> E[Output 6]
655
-
656
- style A fill:#ff6b6b,color:#fff
657
- style B fill:#ffd43b,color:#000
658
- style C fill:#51cf66,color:#fff
659
- style D fill:#74c0fc,color:#fff
660
- style E fill:#b197fc,color:#fff`,
661
- 4: `graph TD
662
- A[Signal 6] --> B[Sensor 6]
663
- B --> C[Cascade 6]
664
- C --> D[Integration 6]
665
- D --> E[Processing 6]
666
- E --> F[Response 6]
667
-
668
- style A fill:#ff6b6b,color:#fff
669
- style B fill:#ffd43b,color:#000
670
- style C fill:#74c0fc,color:#fff
671
- style D fill:#51cf66,color:#fff
672
- style E fill:#51cf66,color:#fff
673
- style F fill:#b197fc,color:#fff`,
674
- 5: `graph TD
675
- A[Input 6] --> B[Recognition 6]
676
- B --> C[Processing Network 6]
677
- C --> D[Integration System 6]
678
- D --> E[Quality Control 6]
679
- E --> F[Feedback Loop 6]
680
- F --> G[Optimization 6]
681
- G --> H[Final Output 6]
682
-
683
- style A fill:#ff6b6b,color:#fff
684
- style B fill:#ffd43b,color:#000
685
- style C fill:#74c0fc,color:#fff
686
- style D fill:#51cf66,color:#fff
687
- style E fill:#51cf66,color:#fff
688
- style F fill:#74c0fc,color:#fff
689
- style G fill:#51cf66,color:#fff
690
- style H fill:#b197fc,color:#fff`
691
- }
692
- },
693
- 7: { // Process 7
694
- levels: {
695
- 1: `graph TD
696
- A[Input 7] --> B[Processing 7]
697
- B --> C[Output 7]
698
-
699
- style A fill:#ff6b6b,color:#fff
700
- style B fill:#51cf66,color:#fff
701
- style C fill:#b197fc,color:#fff`,
702
- 2: `graph TD
703
- A[Signal 7] --> B[Recognition 7]
704
- B --> C[Processing 7]
705
- C --> D[Response 7]
706
-
707
- style A fill:#ff6b6b,color:#fff
708
- style B fill:#ffd43b,color:#000
709
- style C fill:#51cf66,color:#fff
710
- style D fill:#b197fc,color:#fff`,
711
- 3: `graph TD
712
- A[Input 7] --> B[Detection 7]
713
- B --> C[Processing 7]
714
- C --> D[Integration 7]
715
- D --> E[Output 7]
716
-
717
- style A fill:#ff6b6b,color:#fff
718
- style B fill:#ffd43b,color:#000
719
- style C fill:#51cf66,color:#fff
720
- style D fill:#74c0fc,color:#fff
721
- style E fill:#b197fc,color:#fff`,
722
- 4: `graph TD
723
- A[Signal 7] --> B[Sensor 7]
724
- B --> C[Cascade 7]
725
- C --> D[Integration 7]
726
- D --> E[Processing 7]
727
- E --> F[Response 7]
728
-
729
- style A fill:#ff6b6b,color:#fff
730
- style B fill:#ffd43b,color:#000
731
- style C fill:#74c0fc,color:#fff
732
- style D fill:#51cf66,color:#fff
733
- style E fill:#51cf66,color:#fff
734
- style F fill:#b197fc,color:#fff`,
735
- 5: `graph TD
736
- A[Input 7] --> B[Recognition 7]
737
- B --> C[Processing Network 7]
738
- C --> D[Integration System 7]
739
- D --> E[Quality Control 7]
740
- E --> F[Feedback Loop 7]
741
- F --> G[Optimization 7]
742
- G --> H[Final Output 7]
743
-
744
- style A fill:#ff6b6b,color:#fff
745
- style B fill:#ffd43b,color:#000
746
- style C fill:#74c0fc,color:#fff
747
- style D fill:#51cf66,color:#fff
748
- style E fill:#51cf66,color:#fff
749
- style F fill:#74c0fc,color:#fff
750
- style G fill:#51cf66,color:#fff
751
- style H fill:#b197fc,color:#fff`
752
- }
753
- },
754
- 8: { // Process 8
755
- levels: {
756
- 1: `graph TD
757
- A[Input 8] --> B[Processing 8]
758
- B --> C[Output 8]
759
-
760
- style A fill:#ff6b6b,color:#fff
761
- style B fill:#51cf66,color:#fff
762
- style C fill:#b197fc,color:#fff`,
763
- 2: `graph TD
764
- A[Signal 8] --> B[Recognition 8]
765
- B --> C[Processing 8]
766
- C --> D[Response 8]
767
-
768
- style A fill:#ff6b6b,color:#fff
769
- style B fill:#ffd43b,color:#000
770
- style C fill:#51cf66,color:#fff
771
- style D fill:#b197fc,color:#fff`,
772
- 3: `graph TD
773
- A[Input 8] --> B[Detection 8]
774
- B --> C[Processing 8]
775
- C --> D[Integration 8]
776
- D --> E[Output 8]
777
-
778
- style A fill:#ff6b6b,color:#fff
779
- style B fill:#ffd43b,color:#000
780
- style C fill:#51cf66,color:#fff
781
- style D fill:#74c0fc,color:#fff
782
- style E fill:#b197fc,color:#fff`,
783
- 4: `graph TD
784
- A[Signal 8] --> B[Sensor 8]
785
- B --> C[Cascade 8]
786
- C --> D[Integration 8]
787
- D --> E[Processing 8]
788
- E --> F[Response 8]
789
-
790
- style A fill:#ff6b6b,color:#fff
791
- style B fill:#ffd43b,color:#000
792
- style C fill:#74c0fc,color:#fff
793
- style D fill:#51cf66,color:#fff
794
- style E fill:#51cf66,color:#fff
795
- style F fill:#b197fc,color:#fff`,
796
- 5: `graph TD
797
- A[Input 8] --> B[Recognition 8]
798
- B --> C[Processing Network 8]
799
- C --> D[Integration System 8]
800
- D --> E[Quality Control 8]
801
- E --> F[Feedback Loop 8]
802
- F --> G[Optimization 8]
803
- G --> H[Final Output 8]
804
-
805
- style A fill:#ff6b6b,color:#fff
806
- style B fill:#ffd43b,color:#000
807
- style C fill:#74c0fc,color:#fff
808
- style D fill:#51cf66,color:#fff
809
- style E fill:#51cf66,color:#fff
810
- style F fill:#74c0fc,color:#fff
811
- style G fill:#51cf66,color:#fff
812
- style H fill:#b197fc,color:#fff`
813
- }
814
- }
815
- };
816
-
817
- // Slider functionality
818
- function updateChart(processId, level) {
819
- const chartDiv = document.getElementById(`chart-${processId}`);
820
- const levelSpan = document.getElementById(`level-${processId}`);
821
-
822
- if (levelSpan) {
823
- levelSpan.textContent = level;
824
- }
825
-
826
- if (allProcesses[processId] && allProcesses[processId].levels[level]) {
827
- chartDiv.innerHTML = '';
828
- const mermaidCode = allProcesses[processId].levels[level];
829
- chartDiv.innerHTML = `<div class="mermaid">${mermaidCode}</div>`;
830
-
831
- const newMermaidElement = chartDiv.querySelector('.mermaid');
832
- if (newMermaidElement) {
833
- try {
834
- mermaid.init(undefined, newMermaidElement);
835
- } catch (error) {
836
- console.error('Mermaid error:', error);
837
- }
838
- }
839
- }
840
- }
841
-
842
- // Initialize mermaid and sliders
843
- mermaid.initialize({
844
- startOnLoad: true,
845
- theme: 'default',
846
- flowchart: {
847
- useMaxWidth: false,
848
- htmlLabels: true,
849
- curve: 'linear',
850
- nodeSpacing: 30,
851
- rankSpacing: 40,
852
- padding: 10
853
- },
854
- themeVariables: {
855
- fontFamily: 'Arial, sans-serif',
856
- fontSize: '14px',
857
- primaryColor: '#ff6b6b',
858
- lineColor: '#333333',
859
- secondaryColor: '#feca57',
860
- tertiaryColor: '#4ecdc4'
861
- }
862
- });
863
-
864
- document.addEventListener('DOMContentLoaded', function() {
865
- for (let i = 1; i <= 8; i++) {
866
- const slider = document.getElementById(`slider-${i}`);
867
- if (slider) {
868
- slider.addEventListener('input', function() {
869
- updateChart(i, this.value);
870
- });
871
- updateChart(i, 1); // Initialize with level 1
872
- }
873
- }
874
- });
875
- </script>
876
- <script>
877
- // Process definitions with 5 detail levels each - Complete allProcesses object
878
- const allProcesses = {
879
- 1: { // Process 1
880
- levels: {
881
- 1: `graph TD
882
- A[Signal Input] --> B[Process Initiation]
883
- B --> C[Process Output]
884
-
885
- style A fill:#ff6b6b,color:#fff
886
- style B fill:#ffd43b,color:#000
887
- style C fill:#b197fc,color:#fff`,
888
-
889
- 2: `graph TD
890
- A[Environmental Signal] --> B[Receptor Binding]
891
- B --> C[Signal Transduction]
892
- C --> D[Molecular Complex]
893
- D --> E[Process Output]
894
-
895
- style A fill:#ff6b6b,color:#fff
896
- style B fill:#ffd43b,color:#000
897
- style C fill:#74c0fc,color:#fff
898
- style D fill:#51cf66,color:#fff
899
- style E fill:#b197fc,color:#fff`,
900
-
901
- 3: `graph TD
902
- A[Cellular Signal] --> B[Sensor Protein]
903
- B --> C[Signal Cascade]
904
- C --> D[Protein Recruitment]
905
- D --> E[Complex Assembly]
906
- E --> F[Active Site Formation]
907
- F --> G[Catalytic Mechanism]
908
- G --> H[Product Formation]
909
-
910
- style A fill:#ff6b6b,color:#fff
911
- style B fill:#ffd43b,color:#000
912
- style C fill:#74c0fc,color:#fff
913
- style D fill:#51cf66,color:#fff
914
- style E fill:#74c0fc,color:#fff
915
- style F fill:#51cf66,color:#fff
916
- style G fill:#51cf66,color:#fff
917
- style H fill:#b197fc,color:#fff`,
918
-
919
- 4: `graph TD
920
- A[External Signal] --> B[Receptor Complex]
921
- B --> C[Signal Integration]
922
- C --> D[Pathway Activation]
923
- D --> E[Protein Network]
924
- E --> F[Complex Formation]
925
- F --> G[Active Site Assembly]
926
- G --> H[Catalytic Cycle]
927
- H --> I[Product Release]
928
- I --> J[Quality Control]
929
- J --> K[Process Completion]
930
-
931
- style A fill:#ff6b6b,color:#fff
932
- style B fill:#ffd43b,color:#000
933
- style C fill:#74c0fc,color:#fff
934
- style D fill:#51cf66,color:#fff
935
- style E fill:#74c0fc,color:#fff
936
- style F fill:#51cf66,color:#fff
937
- style G fill:#74c0fc,color:#fff
938
- style H fill:#51cf66,color:#fff
939
- style I fill:#ffd43b,color:#000
940
- style J fill:#51cf66,color:#fff
941
- style K fill:#b197fc,color:#fff`,
942
-
943
- 5: `graph TD
944
- A[Regulatory Signal] --> B[Multi-Receptor Complex]
945
- B --> C[Signal Processing Network]
946
- C --> D[Pathway Integration]
947
- D --> E[Protein Network Assembly]
948
- E --> F[Dynamic Complex Formation]
949
- F --> G[Allosteric Network]
950
- G --> H[Cooperative Binding]
951
- H --> I[Multi-Step Catalysis]
952
- I --> J[Intermediate Processing]
953
- J --> K[Product Modification]
954
- K --> L[Quality Assurance]
955
- L --> M[Regulatory Feedback]
956
- M --> N[Process Optimization]
957
- N --> O[System Integration]
958
- O --> P[Process Completion]
959
-
960
- style A fill:#ff6b6b,color:#fff
961
- style B fill:#ffd43b,color:#000
962
- style C fill:#74c0fc,color:#fff
963
- style D fill:#51cf66,color:#fff
964
- style E fill:#74c0fc,color:#fff
965
- style F fill:#51cf66,color:#fff
966
- style G fill:#51cf66,color:#fff
967
- style H fill:#74c0fc,color:#fff
968
- style I fill:#51cf66,color:#fff
969
- style J fill:#74c0fc,color:#fff
970
- style K fill:#51cf66,color:#fff
971
- style L fill:#ffd43b,color:#000
972
- style M fill:#74c0fc,color:#fff
973
- style N fill:#51cf66,color:#fff
974
- style O fill:#74c0fc,color:#fff
975
- style P fill:#b197fc,color:#fff`
976
- }
977
- },
978
- 2: { // Process 2
979
- levels: {
980
- 1: `graph TD
981
- A[Input 2] --> B[Processing 2]
982
- B --> C[Output 2]
983
-
984
- style A fill:#ff6b6b,color:#fff
985
- style B fill:#51cf66,color:#fff
986
- style C fill:#b197fc,color:#fff`,
987
- 2: `graph TD
988
- A[Signal 2] --> B[Recognition 2]
989
- B --> C[Processing 2]
990
- C --> D[Response 2]
991
-
992
- style A fill:#ff6b6b,color:#fff
993
- style B fill:#ffd43b,color:#000
994
- style C fill:#51cf66,color:#fff
995
- style D fill:#b197fc,color:#fff`,
996
- 3: `graph TD
997
- A[Input 2] --> B[Detection 2]
998
- B --> C[Processing 2]
999
- C --> D[Integration 2]
1000
- D --> E[Output 2]
1001
-
1002
- style A fill:#ff6b6b,color:#fff
1003
- style B fill:#ffd43b,color:#000
1004
- style C fill:#51cf66,color:#fff
1005
- style D fill:#74c0fc,color:#fff
1006
- style E fill:#b197fc,color:#fff`,
1007
- 4: `graph TD
1008
- A[Signal 2] --> B[Sensor 2]
1009
- B --> C[Cascade 2]
1010
- C --> D[Integration 2]
1011
- D --> E[Processing 2]
1012
- E --> F[Response 2]
1013
-
1014
- style A fill:#ff6b6b,color:#fff
1015
- style B fill:#ffd43b,color:#000
1016
- style C fill:#74c0fc,color:#fff
1017
- style D fill:#51cf66,color:#fff
1018
- style E fill:#51cf66,color:#fff
1019
- style F fill:#b197fc,color:#fff`,
1020
- 5: `graph TD
1021
- A[Input 2] --> B[Recognition 2]
1022
- B --> C[Processing Network 2]
1023
- C --> D[Integration System 2]
1024
- D --> E[Quality Control 2]
1025
- E --> F[Feedback Loop 2]
1026
- F --> G[Optimization 2]
1027
- G --> H[Final Output 2]
1028
-
1029
- style A fill:#ff6b6b,color:#fff
1030
- style B fill:#ffd43b,color:#000
1031
- style C fill:#74c0fc,color:#fff
1032
- style D fill:#51cf66,color:#fff
1033
- style E fill:#51cf66,color:#fff
1034
- style F fill:#74c0fc,color:#fff
1035
- style G fill:#51cf66,color:#fff
1036
- style H fill:#b197fc,color:#fff`
1037
- }
1038
- },
1039
- 3: { // Process 3
1040
- levels: {
1041
- 1: `graph TD
1042
- A[Input 3] --> B[Processing 3]
1043
- B --> C[Output 3]
1044
-
1045
- style A fill:#ff6b6b,color:#fff
1046
- style B fill:#51cf66,color:#fff
1047
- style C fill:#b197fc,color:#fff`,
1048
- 2: `graph TD
1049
- A[Signal 3] --> B[Recognition 3]
1050
- B --> C[Processing 3]
1051
- C --> D[Response 3]
1052
-
1053
- style A fill:#ff6b6b,color:#fff
1054
- style B fill:#ffd43b,color:#000
1055
- style C fill:#51cf66,color:#fff
1056
- style D fill:#b197fc,color:#fff`,
1057
- 3: `graph TD
1058
- A[Input 3] --> B[Detection 3]
1059
- B --> C[Processing 3]
1060
- C --> D[Integration 3]
1061
- D --> E[Output 3]
1062
-
1063
- style A fill:#ff6b6b,color:#fff
1064
- style B fill:#ffd43b,color:#000
1065
- style C fill:#51cf66,color:#fff
1066
- style D fill:#74c0fc,color:#fff
1067
- style E fill:#b197fc,color:#fff`,
1068
- 4: `graph TD
1069
- A[Signal 3] --> B[Sensor 3]
1070
- B --> C[Cascade 3]
1071
- C --> D[Integration 3]
1072
- D --> E[Processing 3]
1073
- E --> F[Response 3]
1074
-
1075
- style A fill:#ff6b6b,color:#fff
1076
- style B fill:#ffd43b,color:#000
1077
- style C fill:#74c0fc,color:#fff
1078
- style D fill:#51cf66,color:#fff
1079
- style E fill:#51cf66,color:#fff
1080
- style F fill:#b197fc,color:#fff`,
1081
- 5: `graph TD
1082
- A[Input 3] --> B[Recognition 3]
1083
- B --> C[Processing Network 3]
1084
- C --> D[Integration System 3]
1085
- D --> E[Quality Control 3]
1086
- E --> F[Feedback Loop 3]
1087
- F --> G[Optimization 3]
1088
- G --> H[Final Output 3]
1089
-
1090
- style A fill:#ff6b6b,color:#fff
1091
- style B fill:#ffd43b,color:#000
1092
- style C fill:#74c0fc,color:#fff
1093
- style D fill:#51cf66,color:#fff
1094
- style E fill:#51cf66,color:#fff
1095
- style F fill:#74c0fc,color:#fff
1096
- style G fill:#51cf66,color:#fff
1097
- style H fill:#b197fc,color:#fff`
1098
- }
1099
- },
1100
- 4: { // Process 4
1101
- levels: {
1102
- 1: `graph TD
1103
- A[Input 4] --> B[Processing 4]
1104
- B --> C[Output 4]
1105
-
1106
- style A fill:#ff6b6b,color:#fff
1107
- style B fill:#51cf66,color:#fff
1108
- style C fill:#b197fc,color:#fff`,
1109
- 2: `graph TD
1110
- A[Signal 4] --> B[Recognition 4]
1111
- B --> C[Processing 4]
1112
- C --> D[Response 4]
1113
-
1114
- style A fill:#ff6b6b,color:#fff
1115
- style B fill:#ffd43b,color:#000
1116
- style C fill:#51cf66,color:#fff
1117
- style D fill:#b197fc,color:#fff`,
1118
- 3: `graph TD
1119
- A[Input 4] --> B[Detection 4]
1120
- B --> C[Processing 4]
1121
- C --> D[Integration 4]
1122
- D --> E[Output 4]
1123
-
1124
- style A fill:#ff6b6b,color:#fff
1125
- style B fill:#ffd43b,color:#000
1126
- style C fill:#51cf66,color:#fff
1127
- style D fill:#74c0fc,color:#fff
1128
- style E fill:#b197fc,color:#fff`,
1129
- 4: `graph TD
1130
- A[Signal 4] --> B[Sensor 4]
1131
- B --> C[Cascade 4]
1132
- C --> D[Integration 4]
1133
- D --> E[Processing 4]
1134
- E --> F[Response 4]
1135
-
1136
- style A fill:#ff6b6b,color:#fff
1137
- style B fill:#ffd43b,color:#000
1138
- style C fill:#74c0fc,color:#fff
1139
- style D fill:#51cf66,color:#fff
1140
- style E fill:#51cf66,color:#fff
1141
- style F fill:#b197fc,color:#fff`,
1142
- 5: `graph TD
1143
- A[Input 4] --> B[Recognition 4]
1144
- B --> C[Processing Network 4]
1145
- C --> D[Integration System 4]
1146
- D --> E[Quality Control 4]
1147
- E --> F[Feedback Loop 4]
1148
- F --> G[Optimization 4]
1149
- G --> H[Final Output 4]
1150
-
1151
- style A fill:#ff6b6b,color:#fff
1152
- style B fill:#ffd43b,color:#000
1153
- style C fill:#74c0fc,color:#fff
1154
- style D fill:#51cf66,color:#fff
1155
- style E fill:#51cf66,color:#fff
1156
- style F fill:#74c0fc,color:#fff
1157
- style G fill:#51cf66,color:#fff
1158
- style H fill:#b197fc,color:#fff`
1159
- }
1160
- },
1161
- 5: { // Process 5
1162
- levels: {
1163
- 1: `graph TD
1164
- A[Input 5] --> B[Processing 5]
1165
- B --> C[Output 5]
1166
-
1167
- style A fill:#ff6b6b,color:#fff
1168
- style B fill:#51cf66,color:#fff
1169
- style C fill:#b197fc,color:#fff`,
1170
- 2: `graph TD
1171
- A[Signal 5] --> B[Recognition 5]
1172
- B --> C[Processing 5]
1173
- C --> D[Response 5]
1174
-
1175
- style A fill:#ff6b6b,color:#fff
1176
- style B fill:#ffd43b,color:#000
1177
- style C fill:#51cf66,color:#fff
1178
- style D fill:#b197fc,color:#fff`,
1179
- 3: `graph TD
1180
- A[Input 5] --> B[Detection 5]
1181
- B --> C[Processing 5]
1182
- C --> D[Integration 5]
1183
- D --> E[Output 5]
1184
-
1185
- style A fill:#ff6b6b,color:#fff
1186
- style B fill:#ffd43b,color:#000
1187
- style C fill:#51cf66,color:#fff
1188
- style D fill:#74c0fc,color:#fff
1189
- style E fill:#b197fc,color:#fff`,
1190
- 4: `graph TD
1191
- A[Signal 5] --> B[Sensor 5]
1192
- B --> C[Cascade 5]
1193
- C --> D[Integration 5]
1194
- D --> E[Processing 5]
1195
- E --> F[Response 5]
1196
-
1197
- style A fill:#ff6b6b,color:#fff
1198
- style B fill:#ffd43b,color:#000
1199
- style C fill:#74c0fc,color:#fff
1200
- style D fill:#51cf66,color:#fff
1201
- style E fill:#51cf66,color:#fff
1202
- style F fill:#b197fc,color:#fff`,
1203
- 5: `graph TD
1204
- A[Input 5] --> B[Recognition 5]
1205
- B --> C[Processing Network 5]
1206
- C --> D[Integration System 5]
1207
- D --> E[Quality Control 5]
1208
- E --> F[Feedback Loop 5]
1209
- F --> G[Optimization 5]
1210
- G --> H[Final Output 5]
1211
-
1212
- style A fill:#ff6b6b,color:#fff
1213
- style B fill:#ffd43b,color:#000
1214
- style C fill:#74c0fc,color:#fff
1215
- style D fill:#51cf66,color:#fff
1216
- style E fill:#51cf66,color:#fff
1217
- style F fill:#74c0fc,color:#fff
1218
- style G fill:#51cf66,color:#fff
1219
- style H fill:#b197fc,color:#fff`
1220
- }
1221
- },
1222
- 6: { // Process 6
1223
- levels: {
1224
- 1: `graph TD
1225
- A[Input 6] --> B[Processing 6]
1226
- B --> C[Output 6]
1227
-
1228
- style A fill:#ff6b6b,color:#fff
1229
- style B fill:#51cf66,color:#fff
1230
- style C fill:#b197fc,color:#fff`,
1231
- 2: `graph TD
1232
- A[Signal 6] --> B[Recognition 6]
1233
- B --> C[Processing 6]
1234
- C --> D[Response 6]
1235
-
1236
- style A fill:#ff6b6b,color:#fff
1237
- style B fill:#ffd43b,color:#000
1238
- style C fill:#51cf66,color:#fff
1239
- style D fill:#b197fc,color:#fff`,
1240
- 3: `graph TD
1241
- A[Input 6] --> B[Detection 6]
1242
- B --> C[Processing 6]
1243
- C --> D[Integration 6]
1244
- D --> E[Output 6]
1245
-
1246
- style A fill:#ff6b6b,color:#fff
1247
- style B fill:#ffd43b,color:#000
1248
- style C fill:#51cf66,color:#fff
1249
- style D fill:#74c0fc,color:#fff
1250
- style E fill:#b197fc,color:#fff`,
1251
- 4: `graph TD
1252
- A[Signal 6] --> B[Sensor 6]
1253
- B --> C[Cascade 6]
1254
- C --> D[Integration 6]
1255
- D --> E[Processing 6]
1256
- E --> F[Response 6]
1257
-
1258
- style A fill:#ff6b6b,color:#fff
1259
- style B fill:#ffd43b,color:#000
1260
- style C fill:#74c0fc,color:#fff
1261
- style D fill:#51cf66,color:#fff
1262
- style E fill:#51cf66,color:#fff
1263
- style F fill:#b197fc,color:#fff`,
1264
- 5: `graph TD
1265
- A[Input 6] --> B[Recognition 6]
1266
- B --> C[Processing Network 6]
1267
- C --> D[Integration System 6]
1268
- D --> E[Quality Control 6]
1269
- E --> F[Feedback Loop 6]
1270
- F --> G[Optimization 6]
1271
- G --> H[Final Output 6]
1272
-
1273
- style A fill:#ff6b6b,color:#fff
1274
- style B fill:#ffd43b,color:#000
1275
- style C fill:#74c0fc,color:#fff
1276
- style D fill:#51cf66,color:#fff
1277
- style E fill:#51cf66,color:#fff
1278
- style F fill:#74c0fc,color:#fff
1279
- style G fill:#51cf66,color:#fff
1280
- style H fill:#b197fc,color:#fff`
1281
- }
1282
- },
1283
- 7: { // Process 7
1284
- levels: {
1285
- 1: `graph TD
1286
- A[Input 7] --> B[Processing 7]
1287
- B --> C[Output 7]
1288
-
1289
- style A fill:#ff6b6b,color:#fff
1290
- style B fill:#51cf66,color:#fff
1291
- style C fill:#b197fc,color:#fff`,
1292
- 2: `graph TD
1293
- A[Signal 7] --> B[Recognition 7]
1294
- B --> C[Processing 7]
1295
- C --> D[Response 7]
1296
-
1297
- style A fill:#ff6b6b,color:#fff
1298
- style B fill:#ffd43b,color:#000
1299
- style C fill:#51cf66,color:#fff
1300
- style D fill:#b197fc,color:#fff`,
1301
- 3: `graph TD
1302
- A[Input 7] --> B[Detection 7]
1303
- B --> C[Processing 7]
1304
- C --> D[Integration 7]
1305
- D --> E[Output 7]
1306
-
1307
- style A fill:#ff6b6b,color:#fff
1308
- style B fill:#ffd43b,color:#000
1309
- style C fill:#51cf66,color:#fff
1310
- style D fill:#74c0fc,color:#fff
1311
- style E fill:#b197fc,color:#fff`,
1312
- 4: `graph TD
1313
- A[Signal 7] --> B[Sensor 7]
1314
- B --> C[Cascade 7]
1315
- C --> D[Integration 7]
1316
- D --> E[Processing 7]
1317
- E --> F[Response 7]
1318
-
1319
- style A fill:#ff6b6b,color:#fff
1320
- style B fill:#ffd43b,color:#000
1321
- style C fill:#74c0fc,color:#fff
1322
- style D fill:#51cf66,color:#fff
1323
- style E fill:#51cf66,color:#fff
1324
- style F fill:#b197fc,color:#fff`,
1325
- 5: `graph TD
1326
- A[Input 7] --> B[Recognition 7]
1327
- B --> C[Processing Network 7]
1328
- C --> D[Integration System 7]
1329
- D --> E[Quality Control 7]
1330
- E --> F[Feedback Loop 7]
1331
- F --> G[Optimization 7]
1332
- G --> H[Final Output 7]
1333
-
1334
- style A fill:#ff6b6b,color:#fff
1335
- style B fill:#ffd43b,color:#000
1336
- style C fill:#74c0fc,color:#fff
1337
- style D fill:#51cf66,color:#fff
1338
- style E fill:#51cf66,color:#fff
1339
- style F fill:#74c0fc,color:#fff
1340
- style G fill:#51cf66,color:#fff
1341
- style H fill:#b197fc,color:#fff`
1342
- }
1343
- },
1344
- 8: { // Process 8
1345
- levels: {
1346
- 1: `graph TD
1347
- A[Input 8] --> B[Processing 8]
1348
- B --> C[Output 8]
1349
-
1350
- style A fill:#ff6b6b,color:#fff
1351
- style B fill:#51cf66,color:#fff
1352
- style C fill:#b197fc,color:#fff`,
1353
- 2: `graph TD
1354
- A[Signal 8] --> B[Recognition 8]
1355
- B --> C[Processing 8]
1356
- C --> D[Response 8]
1357
-
1358
- style A fill:#ff6b6b,color:#fff
1359
- style B fill:#ffd43b,color:#000
1360
- style C fill:#51cf66,color:#fff
1361
- style D fill:#b197fc,color:#fff`,
1362
- 3: `graph TD
1363
- A[Input 8] --> B[Detection 8]
1364
- B --> C[Processing 8]
1365
- C --> D[Integration 8]
1366
- D --> E[Output 8]
1367
-
1368
- style A fill:#ff6b6b,color:#fff
1369
- style B fill:#ffd43b,color:#000
1370
- style C fill:#51cf66,color:#fff
1371
- style D fill:#74c0fc,color:#fff
1372
- style E fill:#b197fc,color:#fff`,
1373
- 4: `graph TD
1374
- A[Signal 8] --> B[Sensor 8]
1375
- B --> C[Cascade 8]
1376
- C --> D[Integration 8]
1377
- D --> E[Processing 8]
1378
- E --> F[Response 8]
1379
-
1380
- style A fill:#ff6b6b,color:#fff
1381
- style B fill:#ffd43b,color:#000
1382
- style C fill:#74c0fc,color:#fff
1383
- style D fill:#51cf66,color:#fff
1384
- style E fill:#51cf66,color:#fff
1385
- style F fill:#b197fc,color:#fff`,
1386
- 5: `graph TD
1387
- A[Input 8] --> B[Recognition 8]
1388
- B --> C[Processing Network 8]
1389
- C --> D[Integration System 8]
1390
- D --> E[Quality Control 8]
1391
- E --> F[Feedback Loop 8]
1392
- F --> G[Optimization 8]
1393
- G --> H[Final Output 8]
1394
-
1395
- style A fill:#ff6b6b,color:#fff
1396
- style B fill:#ffd43b,color:#000
1397
- style C fill:#74c0fc,color:#fff
1398
- style D fill:#51cf66,color:#fff
1399
- style E fill:#51cf66,color:#fff
1400
- style F fill:#74c0fc,color:#fff
1401
- style G fill:#51cf66,color:#fff
1402
- style H fill:#b197fc,color:#fff`
1403
- }
1404
- }
1405
  };
1406
 
1407
  // Slider functionality
@@ -1429,7 +649,7 @@
1429
  }
1430
  }
1431
 
1432
- // Initialize mermaid and sliders
1433
  mermaid.initialize({
1434
  startOnLoad: true,
1435
  theme: 'default',
@@ -1458,9 +678,9 @@
1458
  slider.addEventListener('input', function() {
1459
  updateChart(i, this.value);
1460
  });
1461
- updateChart(i, 1); // Initialize with level 1
1462
  }
1463
  }
1464
  });
1465
- </script>\n</body>
1466
  </html>
 
1
  <!DOCTYPE html>
2
+
3
  <html lang="en">
4
  <head>
5
+ <meta charset="utf-8"/>
6
+ <meta content="width=device-width, initial-scale=1.0" name="viewport"/>
7
+ <title>Yeast Batch 08: Quality Control Systems - Interactive Programming Framework</title>
8
  <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js">
9
+ </script><style>
 
10
  body { font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif; /* Ensure proper rendering of Greek characters */
11
  h1, h2, h3, p, li, a {
12
  font-family: \'Segoe UI\', Tahoma, Geneva, Verdana, \'Arial Unicode MS\', sans-serif;
 
91
  }
92
  </style></head>
93
  <body>
94
+ <div class="container">
95
+ <div class="header">
96
+ <h1 id="yeast-batch-08-quality-control-systems">
97
+ 🧬 Yeast Batch 08: Quality Control Systems
98
+ <p>
99
+ Interactive Programming Framework - 8 Quality Control Processes
100
+ </p></h1></div> <div class="content">
101
+ <div class="batch-header">
102
+ <h2 id="quality-control-systems-overview">
103
+ Quality Control Systems: Cellular Surveillance and Error Correction
104
+ <p>
105
+ This batch contains 8 fundamental yeast processes responsible for quality control and cellular surveillance. These processes represent the core computational systems that ensure proper protein folding, RNA processing, and cellular homeostasis through sophisticated quality control mechanisms.
106
+ </p></h2></div><div class="toc">
107
+ <h2 id="process-3-table-of-contents-8-quality-control-processes-1-unfolded-protein-response-2-nonsense-mediated-decay-3-ribosome-quality-control-4-mitochondrial-quality-control-5-chromosome-integrity-6-cell-wall-integrity-7-organelle-inheritance-8-apoptosis">
108
  📋 Table of Contents - 8 Quality Control Processes
109
+ <ul>
110
+ <li>
111
+ <a href="#process-1">Process 1: Unfolded Protein Response</a></li><li>
112
+ <a href="#process-2">Process 2: Nonsense-Mediated Decay</a></li><li>
113
+ <a href="#process-3">Process 3: Cell Wall Integrity</a></li><li>
114
+ <a href="#process-4">Process 4: Apoptosis</a></li><li>
115
+ <a href="#process-5">Process 5: Ribosome Quality Control</a></li><li>
116
+ <a href="#process-6">Process 6: Mitochondrial Quality Control</a></li><li>
117
+ <a href="#process-7">Process 7: Chromosome Integrity</a></li><li>
118
+ <a href="#process-8">Process 8: Organelle Inheritance</a></li></ul></h2></div><!-- Process 1: Unfolded Protein Response --> <div class="process-item" id="unfolded-protein-response">
119
+ <h3 id="process-1">
120
+ Process 1: Unfolded Protein Response
121
+ <p>
122
  Detailed analysis of Unfolded Protein Response using the Programming Framework, revealing computational logic for ER stress management.
123
  </p>
124
+
125
+ <!-- Interactive Slider Controls -->
126
+ <div class="slider-controls">
127
+ <h4>🎛️ Detail Level Control</h4>
128
+ <div class="slider-container">
129
+ <span class="slider-label">Level:</span>
130
+ <input type="range" class="detail-slider" id="slider-1" min="1" max="5" value="5" step="1">
131
+ <span class="level-display" id="level-1">5</span>
132
+ </div>
133
+ </div>
134
+
135
+ <div class="mermaid-container">
136
+ <div class="mermaid">
137
+ graph TD
138
+ A[Misfolded Proteins] --&gt; B[ER Stress Detection] B --&gt; C[IRE1 Activation] C --&gt; D[HAC1 mRNA Splicing] D --&gt; E[Hac1 Protein Translation] E --&gt; F[UPR Gene Expression] F --&gt; G[ER Chaperone Upregulation] G --&gt; H[Protein Folding Capacity] H --&gt; I[ER Homeostasis] J[Severe Stress] --&gt; K[PERK/ATF6 Pathways] K --&gt; L[Translation Attenuation] L --&gt; M[Protein Load Reduction] N[Prolonged Stress] --&gt; O[Apoptosis Signaling] O --&gt; P[Cell Death] style  fill:#ff6b6b,color:#fff
139
+ style  fill:#ffd43b,color:#000
140
+ style  fill:#ffd43b,color:#000
141
+ style  fill:#b197fc,color:#fff
142
+ style  fill:#ff6b6b,color:#fff
143
+ </div>
144
+ </div>
145
+ </h3></div><!-- Process 2: Nonsense-Mediated Decay --> <div class="process-item" id="nonsense-mediated-decay">
146
+ <h3 id="process-2">
147
+ Process 2: Nonsense-Mediated Decay
148
+ <p>
149
+ Detailed analysis of Nonsense-Mediated Decay using the Programming Framework, revealing computational logic for mRNA quality control.
150
+ </p>
151
+
152
+ <!-- Interactive Slider Controls -->
153
+ <div class="slider-controls">
154
+ <h4>🎛️ Detail Level Control</h4>
155
+ <div class="slider-container">
156
+ <span class="slider-label">Level:</span>
157
+ <input type="range" class="detail-slider" id="slider-2" min="1" max="5" value="5" step="1">
158
+ <span class="level-display" id="level-2">5</span>
159
+ </div>
160
+ </div>
161
+
162
+ <div class="mermaid-container">
163
+ <div class="mermaid">
164
+ graph TD
165
+ A[Premature Stop Codon] --&gt; B[Ribosome Stalling] B --&gt; C[Upf1 Recruitment] C --&gt; D[Upf1 Phosphorylation] D --&gt; E[Upf2/Upf3 Binding] E --&gt; F[mRNA Degradation Complex] F --&gt; G[5' to 3' Exonuclease] G --&gt; H[3' to 5' Exonuclease] H --&gt; I[mRNA Decay] I --&gt; J[Aberrant mRNA Elimination] style  fill:#ff6b6b,color:#fff
166
+ style  fill:#ffd43b,color:#000
167
+ style  fill:#ffd43b,color:#000
168
+ style  fill:#74c0fc,color:#fff
169
+ style  fill:#b197fc,color:#fff
170
+ </div>
171
+ </div>
172
+ </h3></div><!-- Process 3: Cell Wall Integrity --> <div class="process-item" id="cell-wall-integrity">
173
+ <h3 id="process-3">
174
+ Process 3: Cell Wall Integrity
175
+ <p>
176
+ Detailed analysis of Cell Wall Integrity using the Programming Framework, revealing computational logic for structural maintenance and repair.
177
+ </p>
178
+
179
+ <!-- Interactive Slider Controls -->
180
+ <div class="slider-controls">
181
+ <h4>🎛️ Detail Level Control</h4>
182
+ <div class="slider-container">
183
+ <span class="slider-label">Level:</span>
184
+ <input type="range" class="detail-slider" id="slider-3" min="1" max="5" value="5" step="1">
185
+ <span class="level-display" id="level-3">5</span>
186
+ </div>
187
+ </div>
188
+
189
+ <div class="mermaid-container">
190
+ <div class="mermaid">
191
+ graph TD
192
+ A[Cell Wall Stress] --&gt; B[Pkc1 Activation] B --&gt; C[MAPK Cascade] C --&gt; D[Slt2 Phosphorylation] D --&gt; E[Rlm1/SBF Activation] E --&gt; F[Cell Wall Gene Expression] F --&gt; G[Chitin/Glucan Synthesis] G --&gt; H[Cell Wall Repair] H --&gt; I[Structural Integrity] J[Severe Damage] --&gt; K[Emergency Response] K --&gt; L[Cell Wall Thickening] L --&gt; M[Osmotic Protection] style  fill:#ff6b6b,color:#fff
193
+ style  fill:#ffd43b,color:#000
194
+ style  fill:#ffd43b,color:#000
195
+ style  fill:#b197fc,color:#fff
196
+ style  fill:#b197fc,color:#fff
197
+ </div>
198
+ </div>
199
+ </h3></div><!-- Process 4: Apoptosis --> <div class="process-item" id="apoptosis">
200
+ <h3 id="process-4">
201
+ Process 4: Apoptosis
202
+ <p>
203
+ Detailed analysis of Apoptosis using the Programming Framework, revealing computational logic for programmed cell death.
204
+ </p>
205
+
206
+ <!-- Interactive Slider Controls -->
207
+ <div class="slider-controls">
208
+ <h4>🎛️ Detail Level Control</h4>
209
+ <div class="slider-container">
210
+ <span class="slider-label">Level:</span>
211
+ <input type="range" class="detail-slider" id="slider-4" min="1" max="5" value="5" step="1">
212
+ <span class="level-display" id="level-4">5</span>
213
+ </div>
214
+ </div>
215
+
216
+ <div class="mermaid-container">
217
+ <div class="mermaid">
218
+ graph TD
219
+ A[Severe Cellular Damage] --&gt; B[DNA Damage Response] B --&gt; C[p53 Homolog Activation] C --&gt; D[Pro-apoptotic Signals] D --&gt; E[Mitochondrial Dysfunction] E --&gt; F[Cytochrome c Release] F --&gt; G[Caspase Activation] G --&gt; H[Chromatin Condensation] H --&gt; I[DNA Fragmentation] I --&gt; J[Cell Death] K[Stress Response Failure] --&gt; L[Autophagy Pathway] L
220
+ --&gt; M{Recovery Possible?} M
221
+ --&gt;|No|
222
+ N[Apoptotic Switch] N
223
+ --&gt; D
224
+ style  fill:#ff6b6b,color:#fff
225
+ style  fill:#ffd43b,color:#000
226
+ style  fill:#ffd43b,color:#000
227
+ style  fill:#ff6b6b,color:#fff
228
+ style  fill:#74c0fc,color:#fff
229
+ </div>
230
+ </div>
231
+ </h3></div> <!-- Process 5: Ribosome Quality Control -->
232
+ <div class="process-item" id="process-5">
233
+ <h3 id="process-5">Process 5: Ribosome Quality Control</h3>
234
+ <p>Detailed analysis of Ribosome Quality Control using the Programming Framework, revealing computational logic and regulatory patterns.</p>
235
+
236
  <!-- Interactive Slider Controls -->
237
  <div class="slider-controls">
238
  <h4>🎛️ Detail Level Control</h4>
239
  <div class="slider-container">
240
  <span class="slider-label">Level:</span>
241
+ <input type="range" class="detail-slider" id="slider-5" min="1" max="5" value="5" step="1">
242
+ <span class="level-display" id="level-5">5</span>
243
  </div>
244
  </div>
245
 
246
  <div class="mermaid-container">
247
+ <div class="mermaid" id="chart-5">
248
+ graph TD
249
+ %% Initial Setup
250
+ A[Ribosome Stalling] --> B[Quality Checkpoint]
251
+ B --> C[Defect Detection]
252
+ C --> D[Quality Control Signal]
253
+ D --> E[Ubiquitin System]
254
+ E --> F[Protein Degradation]
255
+ F --> G[Quality Control]
256
+ G --> H[Functional Ribosome]
257
+ %% Styling - Biological Color Scheme
258
+ style A fill:#ff6b6b,color:#fff
259
+ style B fill:#ffd43b,color:#000
260
+ style C fill:#51cf66,color:#fff
261
+ style D fill:#74c0fc,color:#fff
262
+ style E fill:#ffd43b,color:#000
263
+ style F fill:#51cf66,color:#fff
264
+ style G fill:#74c0fc,color:#fff
265
+ style H fill:#b197fc,color:#fff
266
  </div>
267
+ <div class="color-legend">
268
+ <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
269
+ <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
270
+ <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
271
+ <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
272
+ <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
273
+ </div>
274
+ </div>
275
+ </div>
276
+
277
+ <!-- Process 6: Mitochondrial Quality Control -->
278
+ <div class="process-item" id="process-6">
279
+ <h3 id="process-6">Process 6: Mitochondrial Quality Control</h3>
280
+ <p>Detailed analysis of Mitochondrial Quality Control using the Programming Framework, revealing computational logic and regulatory patterns.</p>
281
+
282
  <!-- Interactive Slider Controls -->
283
  <div class="slider-controls">
284
  <h4>🎛️ Detail Level Control</h4>
285
  <div class="slider-container">
286
  <span class="slider-label">Level:</span>
287
+ <input type="range" class="detail-slider" id="slider-6" min="1" max="5" value="5" step="1">
288
+ <span class="level-display" id="level-6">5</span>
289
  </div>
290
  </div>
291
 
292
  <div class="mermaid-container">
293
+ <div class="mermaid" id="chart-6">
294
+ graph TD
295
+ %% Initial Setup
296
+ A[Mitochondrial Stress] --> B[Quality Checkpoint]
297
+ B --> C[Defect Detection]
298
+ C --> D[Quality Control Signal]
299
+ D --> E[Autophagy System]
300
+ E --> F[Mitochondrial Degradation]
301
+ F --> G[Quality Control]
302
+ G --> H[Functional Mitochondria]
303
+ %% Styling - Biological Color Scheme
304
+ style A fill:#ff6b6b,color:#fff
305
+ style B fill:#ffd43b,color:#000
306
+ style C fill:#51cf66,color:#fff
307
+ style D fill:#74c0fc,color:#fff
308
+ style E fill:#ffd43b,color:#000
309
+ style F fill:#51cf66,color:#fff
310
+ style G fill:#74c0fc,color:#fff
311
+ style H fill:#b197fc,color:#fff
312
  </div>
313
+ <div class="color-legend">
314
+ <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
315
+ <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
316
+ <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
317
+ <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
318
+ <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
319
+ </div>
320
+ </div>
321
+ </div>
322
+
323
+ <!-- Process 7: Chromosome Integrity -->
324
+ <div class="process-item" id="process-7">
325
+ <h3 id="process-7">Process 7: Chromosome Integrity</h3>
326
+ <p>Detailed analysis of Chromosome Integrity using the Programming Framework, revealing computational logic and regulatory patterns.</p>
327
+
328
  <!-- Interactive Slider Controls -->
329
  <div class="slider-controls">
330
  <h4>🎛️ Detail Level Control</h4>
331
  <div class="slider-container">
332
  <span class="slider-label">Level:</span>
333
+ <input type="range" class="detail-slider" id="slider-7" min="1" max="5" value="5" step="1">
334
+ <span class="level-display" id="level-7">5</span>
335
  </div>
336
  </div>
337
 
338
  <div class="mermaid-container">
339
+ <div class="mermaid" id="chart-7">
340
+ graph TD
341
+ %% Initial Setup
342
+ A[DNA Damage] --> B[Checkpoint Activation]
343
+ B --> C[Damage Detection]
344
+ C --> D[Repair Signal]
345
+ D --> E[Repair Machinery]
346
+ E --> F[DNA Repair]
347
+ F --> G[Quality Control]
348
+ G --> H[Intact Chromosome]
349
+ %% Styling - Biological Color Scheme
350
+ style A fill:#ff6b6b,color:#fff
351
+ style B fill:#ffd43b,color:#000
352
+ style C fill:#51cf66,color:#fff
353
+ style D fill:#74c0fc,color:#fff
354
+ style E fill:#ffd43b,color:#000
355
+ style F fill:#51cf66,color:#fff
356
+ style G fill:#74c0fc,color:#fff
357
+ style H fill:#b197fc,color:#fff
358
  </div>
359
+ <div class="color-legend">
360
+ <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
361
+ <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
362
+ <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
363
+ <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
364
+ <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
365
+ </div>
366
+ </div>
367
+ </div>
368
+
369
+ <!-- Process 8: Organelle Inheritance -->
370
+ <div class="process-item" id="process-8">
371
+ <h3 id="process-8">Process 8: Organelle Inheritance</h3>
372
+ <p>Detailed analysis of Organelle Inheritance using the Programming Framework, revealing computational logic and regulatory patterns.</p>
373
+
374
  <!-- Interactive Slider Controls -->
375
  <div class="slider-controls">
376
  <h4>🎛️ Detail Level Control</h4>
377
  <div class="slider-container">
378
  <span class="slider-label">Level:</span>
379
+ <input type="range" class="detail-slider" id="slider-8" min="1" max="5" value="5" step="1">
380
+ <span class="level-display" id="level-8">5</span>
381
  </div>
382
  </div>
383
 
384
  <div class="mermaid-container">
385
+ <div class="mermaid" id="chart-8">
386
+ graph TD
387
+ %% Initial Setup
388
+ A[Cell Division] --> B[Organelle Segregation]
389
+ B --> C[Quality Checkpoint]
390
+ C --> D[Inheritance Signal]
391
+ D --> E[Segregation Machinery]
392
+ E --> F[Organelle Distribution]
393
+ F --> G[Quality Control]
394
+ G --> H[Proper Inheritance]
395
+ %% Styling - Biological Color Scheme
396
+ style A fill:#ff6b6b,color:#fff
397
+ style B fill:#ffd43b,color:#000
398
+ style C fill:#51cf66,color:#fff
399
+ style D fill:#74c0fc,color:#fff
400
+ style E fill:#ffd43b,color:#000
401
+ style F fill:#51cf66,color:#fff
402
+ style G fill:#74c0fc,color:#fff
403
+ style H fill:#b197fc,color:#fff
404
  </div>
405
+ <div class="color-legend">
406
+ <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span>
407
+ <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span>
408
+ <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span>
409
+ <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span>
410
+ <span><span class="color-box" style="background:#b197fc;"></span>Products</span>
411
+ </div>
412
+ </div>
413
+ </div>
414
+
415
+ <!-- Sources Section -->
416
  <div class="sources-section">
417
  <h2>📚 Academic Sources</h2>
418
  <div class="sources-content">
 
423
  <li><strong>Lodish, H., et al.</strong> (2016). <em>Molecular Cell Biology</em>, 8th Edition. W.H. Freeman.</li>
424
  <li><strong>Nelson, D.L. & Cox, M.M.</strong> (2017). <em>Lehninger Principles of Biochemistry</em>, 7th Edition. W.H. Freeman.</li>
425
  </ul>
426
+ <h3>yeast Research</h3>
427
  <ul>
428
+ <li><strong>Research-specific citations</strong> for yeast biological processes and molecular systems.</li>
429
+ <li><strong>Current methodologies</strong> in yeast molecular biology and genetic research.</li>
 
 
430
  </ul>
431
  </div>
432
  </div>
 
459
  </div>
460
 
461
  <div class="footer">
462
+ <p>
463
+ <strong>Generated using the Programming Framework methodology</strong>
464
+ </p><p>
 
465
  This batch demonstrates the computational nature of yeast quality control and cellular surveillance systems
466
  </p><p>
467
+ <em>Batch 15 of 15: Quality Control Systems</em>
468
+ </p></div>
469
+ </div>
470
+ </div><script>
 
 
471
  const allProcesses = {
472
+ 1: {
473
  levels: {
474
  1: `graph TD
475
+ A[Misfolded Proteins] --> B[ER Stress Detection] B --> C[IRE1 Activation] C --> D[HAC1 mRNA Splicing] D --> E[Hac1 Protein Translation] E --> F[UPR Gene Expression] F --> G[ER Chaperone Upregulation] G --> H[Protein Folding Capacity] H --> I[ER Homeostasis] J[Severe Stress] --> K[PERK/ATF6 Pathways] K --> L[Translation Attenuation] L --> M[Protein Load Reduction] N[Prolonged Stress] --> O[Apoptosis Signaling] O --> P[Cell Death] style  fill:#ff6b6b,color:#fff
476
+ style  fill:#ffd43b,color:#000
477
+ style  fill:#ffd43b,color:#000
478
+ style  fill:#b197fc,color:#fff
479
+ style  fill:#ff6b6b,color:#fff`,
 
 
480
  2: `graph TD
481
+ A[Misfolded Proteins] --> B[ER Stress Detection] B --> C[IRE1 Activation] C --> D[HAC1 mRNA Splicing] D --> E[Hac1 Protein Translation] E --> F[UPR Gene Expression] F --> G[ER Chaperone Upregulation] G --> H[Protein Folding Capacity] H --> I[ER Homeostasis] J[Severe Stress] --> K[PERK/ATF6 Pathways] K --> L[Translation Attenuation] L --> M[Protein Load Reduction] N[Prolonged Stress] --> O[Apoptosis Signaling] O --> P[Cell Death] style  fill:#ff6b6b,color:#fff
482
+ style  fill:#ffd43b,color:#000
483
+ style  fill:#ffd43b,color:#000
484
+ style  fill:#b197fc,color:#fff
485
+ style  fill:#ff6b6b,color:#fff`,
 
 
 
 
 
 
486
  3: `graph TD
487
+ A[Misfolded Proteins] --> B[ER Stress Detection] B --> C[IRE1 Activation] C --> D[HAC1 mRNA Splicing] D --> E[Hac1 Protein Translation] E --> F[UPR Gene Expression] F --> G[ER Chaperone Upregulation] G --> H[Protein Folding Capacity] H --> I[ER Homeostasis] J[Severe Stress] --> K[PERK/ATF6 Pathways] K --> L[Translation Attenuation] L --> M[Protein Load Reduction] N[Prolonged Stress] --> O[Apoptosis Signaling] O --> P[Cell Death] style  fill:#ff6b6b,color:#fff
488
+ style  fill:#ffd43b,color:#000
489
+ style  fill:#ffd43b,color:#000
490
+ style  fill:#b197fc,color:#fff
491
+ style  fill:#ff6b6b,color:#fff`,
 
 
 
 
 
 
 
 
 
 
 
 
492
  4: `graph TD
493
+ A[Misfolded Proteins] --> B[ER Stress Detection] B --> C[IRE1 Activation] C --> D[HAC1 mRNA Splicing] D --> E[Hac1 Protein Translation] E --> F[UPR Gene Expression] F --> G[ER Chaperone Upregulation] G --> H[Protein Folding Capacity] H --> I[ER Homeostasis] J[Severe Stress] --> K[PERK/ATF6 Pathways] K --> L[Translation Attenuation] L --> M[Protein Load Reduction] N[Prolonged Stress] --> O[Apoptosis Signaling] O --> P[Cell Death] style  fill:#ff6b6b,color:#fff
494
+ style  fill:#ffd43b,color:#000
495
+ style  fill:#ffd43b,color:#000
496
+ style  fill:#b197fc,color:#fff
497
+ style  fill:#ff6b6b,color:#fff`,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
498
  5: `graph TD
499
+ A[Misfolded Proteins] --> B[ER Stress Detection] B --> C[IRE1 Activation] C --> D[HAC1 mRNA Splicing] D --> E[Hac1 Protein Translation] E --> F[UPR Gene Expression] F --> G[ER Chaperone Upregulation] G --> H[Protein Folding Capacity] H --> I[ER Homeostasis] J[Severe Stress] --> K[PERK/ATF6 Pathways] K --> L[Translation Attenuation] L --> M[Protein Load Reduction] N[Prolonged Stress] --> O[Apoptosis Signaling] O --> P[Cell Death] style  fill:#ff6b6b,color:#fff
500
+ style  fill:#ffd43b,color:#000
501
+ style  fill:#ffd43b,color:#000
502
+ style  fill:#b197fc,color:#fff
503
+ style  fill:#ff6b6b,color:#fff`,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
504
  }
505
  },
506
+ 2: {
507
  levels: {
508
  1: `graph TD
509
+ A[Premature Stop Codon] --> B[Ribosome Stalling] B --> C[Upf1 Recruitment] C --> D[Upf1 Phosphorylation] D --> E[Upf2/Upf3 Binding] E --> F[mRNA Degradation Complex] F --> G[5' to 3' Exonuclease] G --> H[3' to 5' Exonuclease] H --> I[mRNA Decay] I --> J[Aberrant mRNA Elimination] style  fill:#ff6b6b,color:#fff
510
+ style  fill:#ffd43b,color:#000
511
+ style  fill:#ffd43b,color:#000
512
+ style  fill:#74c0fc,color:#fff
513
+ style  fill:#b197fc,color:#fff`,
 
514
  2: `graph TD
515
+ A[Premature Stop Codon] --> B[Ribosome Stalling] B --> C[Upf1 Recruitment] C --> D[Upf1 Phosphorylation] D --> E[Upf2/Upf3 Binding] E --> F[mRNA Degradation Complex] F --> G[5' to 3' Exonuclease] G --> H[3' to 5' Exonuclease] H --> I[mRNA Decay] I --> J[Aberrant mRNA Elimination] style  fill:#ff6b6b,color:#fff
516
+ style  fill:#ffd43b,color:#000
517
+ style  fill:#ffd43b,color:#000
518
+ style  fill:#74c0fc,color:#fff
519
+ style  fill:#b197fc,color:#fff`,
 
 
 
520
  3: `graph TD
521
+ A[Premature Stop Codon] --> B[Ribosome Stalling] B --> C[Upf1 Recruitment] C --> D[Upf1 Phosphorylation] D --> E[Upf2/Upf3 Binding] E --> F[mRNA Degradation Complex] F --> G[5' to 3' Exonuclease] G --> H[3' to 5' Exonuclease] H --> I[mRNA Decay] I --> J[Aberrant mRNA Elimination] style  fill:#ff6b6b,color:#fff
522
+ style  fill:#ffd43b,color:#000
523
+ style  fill:#ffd43b,color:#000
524
+ style  fill:#74c0fc,color:#fff
525
+ style  fill:#b197fc,color:#fff`,
 
 
 
 
 
526
  4: `graph TD
527
+ A[Premature Stop Codon] --> B[Ribosome Stalling] B --> C[Upf1 Recruitment] C --> D[Upf1 Phosphorylation] D --> E[Upf2/Upf3 Binding] E --> F[mRNA Degradation Complex] F --> G[5' to 3' Exonuclease] G --> H[3' to 5' Exonuclease] H --> I[mRNA Decay] I --> J[Aberrant mRNA Elimination] style  fill:#ff6b6b,color:#fff
528
+ style  fill:#ffd43b,color:#000
529
+ style  fill:#ffd43b,color:#000
530
+ style  fill:#74c0fc,color:#fff
531
+ style  fill:#b197fc,color:#fff`,
 
 
 
 
 
 
 
532
  5: `graph TD
533
+ A[Premature Stop Codon] --> B[Ribosome Stalling] B --> C[Upf1 Recruitment] C --> D[Upf1 Phosphorylation] D --> E[Upf2/Upf3 Binding] E --> F[mRNA Degradation Complex] F --> G[5' to 3' Exonuclease] G --> H[3' to 5' Exonuclease] H --> I[mRNA Decay] I --> J[Aberrant mRNA Elimination] style  fill:#ff6b6b,color:#fff
534
+ style  fill:#ffd43b,color:#000
535
+ style  fill:#ffd43b,color:#000
536
+ style  fill:#74c0fc,color:#fff
537
+ style  fill:#b197fc,color:#fff`,
 
 
 
 
 
 
 
 
 
 
 
538
  }
539
  },
540
+ 3: {
541
  levels: {
542
  1: `graph TD
543
+ A[Cell Wall Stress] --> B[Pkc1 Activation] B --> C[MAPK Cascade] C --> D[Slt2 Phosphorylation] D --> E[Rlm1/SBF Activation] E --> F[Cell Wall Gene Expression] F --> G[Chitin/Glucan Synthesis] G --> H[Cell Wall Repair] H --> I[Structural Integrity] J[Severe Damage] --> K[Emergency Response] K --> L[Cell Wall Thickening] L --> M[Osmotic Protection] style  fill:#ff6b6b,color:#fff
544
+ style  fill:#ffd43b,color:#000
545
+ style  fill:#ffd43b,color:#000
546
+ style  fill:#b197fc,color:#fff
547
+ style  fill:#b197fc,color:#fff`,
 
548
  2: `graph TD
549
+ A[Cell Wall Stress] --> B[Pkc1 Activation] B --> C[MAPK Cascade] C --> D[Slt2 Phosphorylation] D --> E[Rlm1/SBF Activation] E --> F[Cell Wall Gene Expression] F --> G[Chitin/Glucan Synthesis] G --> H[Cell Wall Repair] H --> I[Structural Integrity] J[Severe Damage] --> K[Emergency Response] K --> L[Cell Wall Thickening] L --> M[Osmotic Protection] style  fill:#ff6b6b,color:#fff
550
+ style  fill:#ffd43b,color:#000
551
+ style  fill:#ffd43b,color:#000
552
+ style  fill:#b197fc,color:#fff
553
+ style  fill:#b197fc,color:#fff`,
 
 
 
554
  3: `graph TD
555
+ A[Cell Wall Stress] --> B[Pkc1 Activation] B --> C[MAPK Cascade] C --> D[Slt2 Phosphorylation] D --> E[Rlm1/SBF Activation] E --> F[Cell Wall Gene Expression] F --> G[Chitin/Glucan Synthesis] G --> H[Cell Wall Repair] H --> I[Structural Integrity] J[Severe Damage] --> K[Emergency Response] K --> L[Cell Wall Thickening] L --> M[Osmotic Protection] style  fill:#ff6b6b,color:#fff
556
+ style  fill:#ffd43b,color:#000
557
+ style  fill:#ffd43b,color:#000
558
+ style  fill:#b197fc,color:#fff
559
+ style  fill:#b197fc,color:#fff`,
 
 
 
 
 
560
  4: `graph TD
561
+ A[Cell Wall Stress] --> B[Pkc1 Activation] B --> C[MAPK Cascade] C --> D[Slt2 Phosphorylation] D --> E[Rlm1/SBF Activation] E --> F[Cell Wall Gene Expression] F --> G[Chitin/Glucan Synthesis] G --> H[Cell Wall Repair] H --> I[Structural Integrity] J[Severe Damage] --> K[Emergency Response] K --> L[Cell Wall Thickening] L --> M[Osmotic Protection] style  fill:#ff6b6b,color:#fff
562
+ style  fill:#ffd43b,color:#000
563
+ style  fill:#ffd43b,color:#000
564
+ style  fill:#b197fc,color:#fff
565
+ style  fill:#b197fc,color:#fff`,
 
 
 
 
 
 
 
566
  5: `graph TD
567
+ A[Cell Wall Stress] --> B[Pkc1 Activation] B --> C[MAPK Cascade] C --> D[Slt2 Phosphorylation] D --> E[Rlm1/SBF Activation] E --> F[Cell Wall Gene Expression] F --> G[Chitin/Glucan Synthesis] G --> H[Cell Wall Repair] H --> I[Structural Integrity] J[Severe Damage] --> K[Emergency Response] K --> L[Cell Wall Thickening] L --> M[Osmotic Protection] style  fill:#ff6b6b,color:#fff
568
+ style  fill:#ffd43b,color:#000
569
+ style  fill:#ffd43b,color:#000
570
+ style  fill:#b197fc,color:#fff
571
+ style  fill:#b197fc,color:#fff`,
 
 
 
 
 
 
 
 
 
 
 
572
  }
573
  },
574
+ 4: {
575
  levels: {
576
  1: `graph TD
577
+ A[Severe Cellular Damage] --> B[DNA Damage Response] B --> C[p53 Homolog Activation] C --> D[Pro-apoptotic Signals] D --> E[Mitochondrial Dysfunction] E --> F[Cytochrome c Release] F --> G[Caspase Activation] G --> H[Chromatin Condensation] H --> I[DNA Fragmentation] I --> J[Cell Death] K[Stress Response Failure] --> L[Autophagy Pathway] L
578
+ --> M{Recovery Possible?} M
579
+ style  fill:#ff6b6b,color:#fff
580
+ style  fill:#ffd43b,color:#000
581
+ style  fill:#ffd43b,color:#000
582
+ style  fill:#ff6b6b,color:#fff
583
+ style  fill:#74c0fc,color:#fff`,
584
  2: `graph TD
585
+ A[Severe Cellular Damage] --> B[DNA Damage Response] B --> C[p53 Homolog Activation] C --> D[Pro-apoptotic Signals] D --> E[Mitochondrial Dysfunction] E --> F[Cytochrome c Release] F --> G[Caspase Activation] G --> H[Chromatin Condensation] H --> I[DNA Fragmentation] I --> J[Cell Death] K[Stress Response Failure] --> L[Autophagy Pathway] L
586
+ --> M{Recovery Possible?} M
587
+ -->|No|
588
+ style  fill:#ff6b6b,color:#fff
589
+ style  fill:#ffd43b,color:#000
590
+ style  fill:#ffd43b,color:#000
591
+ style  fill:#ff6b6b,color:#fff
592
+ style  fill:#74c0fc,color:#fff`,
593
  3: `graph TD
594
+ A[Severe Cellular Damage] --> B[DNA Damage Response] B --> C[p53 Homolog Activation] C --> D[Pro-apoptotic Signals] D --> E[Mitochondrial Dysfunction] E --> F[Cytochrome c Release] F --> G[Caspase Activation] G --> H[Chromatin Condensation] H --> I[DNA Fragmentation] I --> J[Cell Death] K[Stress Response Failure] --> L[Autophagy Pathway] L
595
+ --> M{Recovery Possible?} M
596
+ -->|No|
597
+ --> D
598
+ style  fill:#ff6b6b,color:#fff
599
+ style  fill:#ffd43b,color:#000
600
+ style  fill:#ffd43b,color:#000
601
+ style  fill:#ff6b6b,color:#fff
602
+ style  fill:#74c0fc,color:#fff`,
 
603
  4: `graph TD
604
+ A[Severe Cellular Damage] --> B[DNA Damage Response] B --> C[p53 Homolog Activation] C --> D[Pro-apoptotic Signals] D --> E[Mitochondrial Dysfunction] E --> F[Cytochrome c Release] F --> G[Caspase Activation] G --> H[Chromatin Condensation] H --> I[DNA Fragmentation] I --> J[Cell Death] K[Stress Response Failure] --> L[Autophagy Pathway] L
605
+ --> M{Recovery Possible?} M
606
+ -->|No|
607
+ --> D
608
+ style  fill:#ff6b6b,color:#fff
609
+ style  fill:#ffd43b,color:#000
610
+ style  fill:#ffd43b,color:#000
611
+ style  fill:#ff6b6b,color:#fff
612
+ style  fill:#74c0fc,color:#fff`,
 
 
 
613
  5: `graph TD
614
+ A[Severe Cellular Damage] --> B[DNA Damage Response] B --> C[p53 Homolog Activation] C --> D[Pro-apoptotic Signals] D --> E[Mitochondrial Dysfunction] E --> F[Cytochrome c Release] F --> G[Caspase Activation] G --> H[Chromatin Condensation] H --> I[DNA Fragmentation] I --> J[Cell Death] K[Stress Response Failure] --> L[Autophagy Pathway] L
615
+ --> M{Recovery Possible?} M
616
+ -->|No|
617
+ --> D
618
+ style  fill:#ff6b6b,color:#fff
619
+ style  fill:#ffd43b,color:#000
620
+ style  fill:#ffd43b,color:#000
621
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