Upload biological_computing_overview.html

biological_computing_overview.html

@@ -147,15 +147,15 @@
                 <h2>📊 Collection Statistics</h2>
                 <div class="stats-grid">
                     <div class="stat-item">
-                        <div class="stat-number">297</div>
+                        <div class="stat-number">411</div>
                         <div>Total Processes</div>
                     </div>
                     <div class="stat-item">
-                        <div class="stat-number">36</div>
+                        <div class="stat-number">45</div>
                         <div>Individual Collections</div>
                     </div>
                     <div class="stat-item">
-                        <div class="stat-number">6</div>
+                        <div class="stat-number">7</div>
                         <div>Kingdoms/Systems</div>
                     </div>
                     <div class="stat-item">
@@ -165,12 +165,28 @@
                 </div>
             </div>
 
+            <h2>🧠 Neural Computation Systems</h2>
+            <div class="collection-grid">
+                <div class="collection-card">
+                    <h3>🧠 Neural Plasticity & Learning</h3>
+                    <p><strong>40 neural computation processes across 5 batch files</strong></p>
+                    <p>Advanced neural computation systems demonstrating sophisticated biological computing architectures in neural networks.</p>
+                    <ul>
+                        <li><a href="neural_plasticity_batch01_synaptic_plasticity.html">Synaptic Plasticity Mechanisms (LTP/LTD/Synaptic Scaling)</a></li>
+                        <li><a href="neural_plasticity_batch02_sensory_processing.html">Sensory Processing Algorithms (Visual/Auditory/Olfactory)</a></li>
+                        <li><a href="neural_plasticity_batch03_memory_formation.html">Memory Formation Systems (Consolidation/Retrieval/Extinction)</a></li>
+                        <li><a href="neural_plasticity_batch04_motor_control.html">Motor Control Systems (Planning/Execution/Learning)</a></li>
+                        <li><a href="neural_plasticity_batch05_decision_making.html">Neural Decision-Making (Winner-Take-All/Lateral Inhibition)</a></li>
+                    </ul>
+                </div>
+            </div>
+
             <h2>🏛️ Complete Collections</h2>
             <div class="collection-grid">
                 <!-- Cellular Process Collections -->
                 <div class="collection-card">
                     <h3>🧬 Yeast Cellular Processes</h3>
-                    <p><strong>110 processes across 15 batch files</strong></p>
+                    <p><strong>184 processes across 23 batch files</strong></p>
                     <p>Comprehensive eukaryotic cellular programming system demonstrating sophisticated computational architecture.</p>
                     <ul>
                         <li>Complete Collection (Individual Batch Files)</li>
@@ -189,24 +205,60 @@
                     </ul>
                 </div>
 
-                <!-- Viral Computing Systems -->
+                <!-- Model Organisms -->
+                <div class="collection-card">
+                    <h3>🌱 Arabidopsis thaliana</h3>
+                    <p><strong>8 photosynthesis and development processes</strong></p>
+                    <p>Plant model organism demonstrating photosynthetic computing and developmental programming.</p>
+                    <ul>
+                        <li><a href="a_thaliana_batch01_photosynthesis_development.html">Photosynthesis & Development</a></li>
+                        <li>Light harvesting, carbon fixation, developmental signaling, stress responses</li>
+                    </ul>
+                </div>
+
+                <div class="collection-card">
+                    <h3>🦟 Drosophila melanogaster</h3>
+                    <p><strong>8 development and genetics processes</strong></p>
+                    <p>Insect model organism demonstrating developmental programming and genetic regulation.</p>
+                    <ul>
+                        <li><a href="d_melanogaster_batch01_development_genetics.html">Development & Genetics</a></li>
+                        <li>Pattern formation, cell fate specification, genetic networks, morphogenesis</li>
+                    </ul>
+                </div>
+
+                <div class="collection-card">
+                    <h3>🪱 Caenorhabditis elegans</h3>
+                    <p><strong>8 development and behavior processes</strong></p>
+                    <p>Nematode model organism demonstrating behavioral computing and developmental logic.</p>
+                    <ul>
+                        <li><a href="c_elegans_batch01_development_behavior.html">Development & Behavior</a></li>
+                        <li>Cell lineage, neural circuits, behavioral responses, developmental timing</li>
+                    </ul>
+                </div>
+
+                <!-- Viral Systems -->
                 <div class="collection-card">
-                    <h3>🦠 Phage λ Decision Switch</h3>
-                    <p><strong>10 decision logic processes</strong></p>
-                    <p>The paradigm of biological binary decision-making implementing bistable switches and competitive inhibition.</p>
+                    <h3>🦠 Viral Computing Systems</h3>
+                    <p><strong>24 viral processes across 4 systems</strong></p>
+                    <p>Viral decision-making and programming systems demonstrating biological logic gates and temporal control.</p>
                     <ul>
-                        <li><a href="phage_lambda_decision_switch.html">Complete Analysis</a></li>
-                        <li>CII stabilization, CI auto-regulation, Cro antagonism, decision thresholding, lysogeny maintenance</li>
+                        <li><a href="phage_lambda_decision_switch.html">Phage λ Decision Switch (10 processes)</a></li>
+                        <li><a href="phage_t7_time_cascade.html">Phage T7 Time Cascade (10 processes)</a></li>
+                        <li><a href="sars_cov2_batch01_entry_replication.html">SARS-CoV-2 Entry & Replication (8 processes)</a></li>
+                        <li><a href="hiv1_batch01_replication_evasion.html">HIV-1 Replication & Immune Evasion (8 processes)</a></li>
                     </ul>
                 </div>
 
+                <!-- Bacterial Pathogens -->
                 <div class="collection-card">
-                    <h3>⏰ T7 Phage Time Cascade</h3>
-                    <p><strong>10 temporal programming processes</strong></p>
-                    <p>Sophisticated temporal programming with precisely ordered gene expression and genetic timers.</p>
+                    <h3>🦠 Bacterial Pathogen Systems</h3>
+                    <p><strong>32 pathogenicity processes across 4 species</strong></p>
+                    <p>Pathogenic bacterial computing systems demonstrating virulence programming and host interaction logic.</p>
                     <ul>
-                        <li><a href="phage_t7_time_cascade.html">Complete Analysis</a></li>
-                        <li>Host takeover, T7 RNAP expression, class II/III promoters, replication timing, lysis execution</li>
+                        <li><a href="s_enterica_batch01_invasion_virulence.html">Salmonella enterica Invasion & Virulence (8 processes)</a></li>
+                        <li><a href="s_aureus_batch01_pathogenicity_biofilm.html">Staphylococcus aureus Pathogenicity & Biofilm (8 processes)</a></li>
+                        <li><a href="m_tuberculosis_batch01_dormancy_persistence.html">Mycobacterium tuberculosis Dormancy & Persistence (8 processes)</a></li>
+                        <li><a href="p_aeruginosa_batch01_virulence_pathogenicity.html">Pseudomonas aeruginosa Virulence & Pathogenicity (8 processes)</a></li>
                     </ul>
                 </div>
 
@@ -305,16 +357,17 @@
 
             <div class="intro">
                 <h2>🔬 Scientific Impact</h2>
-                <p>This collection represents a paradigm shift in our understanding of biological systems. By systematically applying the Programming Framework methodology across 297 biological processes, we have demonstrated that:</p>
+                <p>This collection represents a paradigm shift in our understanding of biological systems. By systematically applying the Programming Framework methodology across 411 biological processes, we have demonstrated that:</p>
                 <ul>
                     <li><strong>Biology IS computation</strong> - not just analogous to it</li>
                     <li><strong>Universal computational patterns</strong> exist across all kingdoms of life</li>
                     <li><strong>Complex behaviors emerge</strong> from well-defined algorithmic processes</li>
                     <li><strong>Engineering principles</strong> can be directly applied to biological systems</li>
                     <li><strong>Predictive models</strong> can be built from computational logic</li>
+                    <li><strong>Neural systems</strong> implement sophisticated learning and decision-making algorithms</li>
                 </ul>
                 <div class="highlight">
-                    <strong>Innovation Achievement:</strong> This work demonstrates how individual researchers, working with AI tools, can make significant contributions to our understanding of life's computational nature - representing a new era in computational biology research.
+                    <strong>Innovation Achievement:</strong> This work demonstrates how individual researchers, working with AI tools, can make significant contributions to our understanding of life's computational nature - representing a new era in computational biology research spanning cellular processes, neural computation, viral programming, and pathogenic systems.
                 </div>
             </div>