Tutorials

Step-by-step guides for learning PhaseLab.

• Spatial Coherence Analysis (v1.0.0)
  • The Core Insight
  • Basic Example
  • Understanding the Output
  • Stability Classes
  • Loading Real Data
  • Configuring Analysis
  • The Key Insight
  • Next Steps
• Protein Mutational Scanning
  • Overview
  • Basic Example
  • Finding Essential Domains
  • Per-Residue Coherence Profile
  • Loading Real DMS Data
  • Mapping to Structure
  • Interpretation Guide
  • Use Cases
  • Next Steps
• Binding Landscape Analysis
  • Overview
  • Basic Example
  • Finding Binding Hot Spots
  • IC50 and Other Metrics
  • Drug Discovery Application
  • Reaction Optimization
  • HTS Screening Analysis
  • Interpretation
  • Next Steps
• SMS Therapeutic Pipeline
  • Overview
  • Quick Start
  • Understanding Results
  • Individual Trials
  • Falsification Tests
  • Claim Levels
  • Configuration Options
  • Full Example
  • Next Steps
• CRISPR Guide Design
  • Overview
  • CRISPRa Guide Design
  • CRISPRi Guide Design
  • Knockout Guide Design
  • Prime Editing
  • Base Editing
  • Multi-Guide Sets
  • Enhancer Targeting
  • Scoring Functions
  • Complete Pipeline Example
  • Next Steps
• Circadian Clock Modeling
  • Smith-Magenis Syndrome
  • Basic Clock Simulation
  • Custom Clock Parameters
  • Time Series Output
  • Therapeutic Dose-Response
  • Kuramoto Oscillators
  • Multi-Tissue Modeling
  • Chronotherapy Optimization
  • Integration with CRISPR Design
  • Next Steps
• Quantum Hardware Validation
  • Overview
  • Setup
  • Simulator Testing
  • Hardware Validation
  • IR Measurement Grouping
  • Error Mitigation
  • VQE Coherence
  • Hardware Results Analysis
  • Complete Validation Pipeline
  • Expected Hardware Results
  • Troubleshooting
  • Next Steps
• Coherence Basics
  • What is Coherence?
  • The GO/NO-GO Threshold
  • Computing Coherence
  • Classification
  • Circular Statistics
  • Physical Interpretation
  • Next Steps
• Coherence Modes (v0.6.1)
  • Overview
  • Heuristic Mode (Default)
  • Quantum Mode
  • Checking Method Details
  • Full Results with Details
  • Batch Processing
  • Z-Score for Relative Ranking
  • Evidence Levels
  • Best Practices
  • Next Steps

Core Tutorials (v1.0.0)

Spatial Coherence Analysis

The core v1.0.0 methodology - spatial coherence of response landscapes.

Spatial Coherence Analysis (v1.0.0)

Protein Mutational Scanning

Apply spatial coherence to deep mutational scanning (DMS) data.

Protein Mutational Scanning

Binding Landscape Analysis

Analyze protein-ligand and protein-protein binding data.

Binding Landscape Analysis

SMS Therapeutic Pipeline

Complete Smith-Magenis Syndrome gene therapy assessment.

SMS Therapeutic Pipeline

Additional Tutorials

CRISPR Guide Design

Design guide RNAs with phase-coherence validation.

CRISPR Guide Design

Circadian Clock Modeling

Model SMS circadian disruption and gene therapy effects.

Circadian Clock Modeling

Quantum Hardware Validation

Validate guides on IBM Quantum hardware (research use).

Quantum Hardware Validation

Legacy Tutorials

Note

The tutorials below cover pre-v1.0.0 concepts. Guide-sequence coherence has been deprecated in favor of spatial coherence analysis.

Coherence Basics (Legacy)

Fundamentals of IR coherence metrics.

Coherence Basics

Coherence Modes (Legacy)

Understanding heuristic vs quantum coherence computation.

Coherence Modes (v0.6.1)