Examples

Working code examples for common use cases.

SMS Gene Therapy Pipeline

Complete pipeline for Smith-Magenis Syndrome RAI1 gene therapy design.

from phaselab.crispr import design_guides, compute_coherence_batch
from phaselab.circadian import simulate_sms_clock

# Design RAI1-targeting guides
rai1_promoter = """GCGCGCTCGCGCGCTCGCGCGAAGGAGAGCAAGAGCGCGACGGCTA..."""

guides = design_guides(rai1_promoter, tss_index=200)
go_guides = guides[guides['go_no_go'] == 'GO']

# Quantum validation
quantum_r = compute_coherence_batch(
    go_guides.head(10)['sequence'].tolist(),
    mode="quantum"
)

# Predict therapeutic outcomes
for guide, r in zip(go_guides.head(10)['sequence'], quantum_r):
    predicted_rai1 = 0.5 + 0.35 * r  # Efficacy model
    sim = simulate_sms_clock(rai1_level=predicted_rai1)
    print(f"{guide[:10]}... R={r:.3f} -> Period={sim['period']:.1f}h")

Cancer CRISPRa Workflow

Tumor suppressor reactivation via CRISPRa.

from phaselab.crispr import design_guides, design_enhancer_guides

# TP53 reactivation
tp53_promoter = """..."""

# Promoter-targeting guides
promoter_guides = design_guides(tp53_promoter, tss_index=500)

# Enhancer-targeting guides
enhancer_guides = design_enhancer_guides(
    tp53_promoter,
    enhancer_regions=[(1000, 1500)],
)

# Compare approaches
print(f"Promoter guides: {len(promoter_guides)}")
print(f"Enhancer guides: {len(enhancer_guides)}")

Chronotherapy Optimization

Optimize drug dosing schedules using circadian modeling.

from phaselab.circadian import optimize_dosing_schedule

schedule = optimize_dosing_schedule(
    target_gene='RAI1',
    delivery_method='AAV',
    tissue_targets=['SCN', 'liver'],
)

print(f"Optimal times: {schedule['dose_times']}")
print(f"Predicted coherence: {schedule['predicted_coherence']:.4f}")