| { |
| "$fractal": { |
| "version": "1.0.0", |
| "root_pattern": "genetic_circuit", |
| "compression": { |
| "ratio": 15.8, |
| "symbolic_residue": { |
| "regulatory_motifs": "recursive_biocircuit_0x7fa1", |
| "protein_domains": "recursive_biocircuit_0x3bc2" |
| }, |
| "attention_efficiency": 18.4 |
| }, |
| "interpretability_map": { |
| "gene_expression_cascade": "scale_invariant_patterns", |
| "regulatory_networks": "recursive_feedback_loops" |
| } |
| }, |
| "content": { |
| "⧖depth": 0, |
| "🜏pattern": "synthetic_genetic_system", |
| "∴seed": { |
| "organism": "E.coli_chassis", |
| "circuit_type": "oscillator", |
| "design_framework": "fractal_biobricks" |
| }, |
| "⇌children": { |
| "⇌promoter_module": { |
| "⧖depth": 1, |
| "🜏pattern": "regulatory_region", |
| "∴seed": { |
| "type": "inducible", |
| "strength": "strong", |
| "regulation": "positive" |
| }, |
| "⇌children": { |
| "⇌operator_sites": { |
| "⧖depth": 2, |
| "🜏pattern": "dna_binding_motif", |
| "∴seed": { |
| "consensus": "TGTGA...TCACA", |
| "affinity": 0.87 |
| }, |
| "⇌children": { |
| "⇌site_1": { |
| "⧖depth": 3, |
| "🜏pattern": "operator_instance", |
| "☍anchor": "#/patterns/recursive_biocircuit_0x7fa1", |
| "∴seed": { |
| "position": -35, |
| "orientation": "forward" |
| } |
| }, |
| "⇌site_2": { |
| "⧖depth": 3, |
| "🜏pattern": "operator_instance", |
| "☍anchor": "#/patterns/recursive_biocircuit_0x7fa1", |
| "∴seed": { |
| "position": -10, |
| "orientation": "forward" |
| } |
| } |
| } |
| }, |
| "⇌transcription_factors": { |
| "⧖depth": 2, |
| "🜏pattern": "regulatory_proteins", |
| "∴seed": { |
| "family": "LacI", |
| "multimerization": "dimer" |
| } |
| } |
| } |
| }, |
| "⇌coding_sequence": { |
| "⧖depth": 1, |
| "🜏pattern": "protein_coding_region", |
| "∴seed": { |
| "product": "fluorescent_reporter", |
| "codon_optimization": "E.coli" |
| }, |
| "⇌children": { |
| "⇌domains": { |
| "⧖depth": 2, |
| "🜏pattern": "protein_domain_architecture", |
| "∴seed": { |
| "fold_type": "beta_barrel", |
| "chromophore": "GFP_derived" |
| }, |
| "⇌children": { |
| "⇌n_terminal": { |
| "⧖depth": 3, |
| "🜏pattern": "domain_instance", |
| "☍anchor": "#/patterns/recursive_biocircuit_0x3bc2" |
| }, |
| "⇌chromophore_region": { |
| "⧖depth": 3, |
| "🜏pattern": "functional_motif", |
| "∴seed": { |
| "sequence": "SYG", |
| "modification": "autocatalytic" |
| } |
| }, |
| "⇌c_terminal": { |
| "⧖depth": 3, |
| "🜏pattern": "domain_instance", |
| "☍anchor": "#/patterns/recursive_biocircuit_0x3bc2" |
| } |
| } |
| } |
| } |
| }, |
| "⇌feedback_loop": { |
| "⧖depth": 1, |
| "🜏pattern": "regulatory_cascade", |
| "∴seed": { |
| "topology": "negative_feedback", |
| "delay": "transcriptional" |
| }, |
| "⇌children": { |
| "⇌sensor_module": { |
| "⧖depth": 2, |
| "🜏pattern": "signal_integration", |
| "☍anchor": "#/content/⇌children/⇌promoter_module" |
| }, |
| "⇌actuator_module": { |
| "⧖depth": 2, |
| "🜏pattern": "response_element", |
| "∴seed": { |
| "mechanism": "repression", |
| "kinetics": "hill_coefficient_2" |
| } |
| } |
| } |
| }, |
| "⇌characterization_data": { |
| "⧖depth": 1, |
| "🜏pattern": "experimental_results", |
| "∴seed": { |
| "assay_type": "flow_cytometry", |
| "conditions": "standard_growth" |
| }, |
| "⇌children": { |
| "⇌time_series": { |
| "⧖depth": 2, |
| "🜏pattern": "oscillation_data", |
| "∴seed": { |
| "period": "120_minutes", |
| "amplitude": "4_fold", |
| "damping": "minimal" |
| } |
| }, |
| "⇌dose_response": { |
| "⧖depth": 2, |
| "🜏pattern": "transfer_function", |
| "∴seed": { |
| "hill_coefficient": 2.1, |
| "ec50": "10_uM", |
| "dynamic_range": "100_fold" |
| } |
| } |
| } |
| } |
| } |
| } |
| } |
|
|
