Frequently Asked Questions#

General Questions#

What is PhaseLab?#

PhaseLab is a phase-coherence analysis framework for quantum, biological, and dynamical systems. It provides tools for CRISPR guide RNA design, circadian clock modeling, and quantum coherence validation.

What is the GO/NO-GO threshold?#

The GO/NO-GO threshold is e^-2 (approximately 0.135). Systems with coherence R > e^-2 are classified as “GO” (coherent, reliable), while those below are “NO-GO” (decoherent, unreliable).

This threshold emerges from information-theoretic considerations in the Informational Relativity framework.

What’s the difference between heuristic and quantum coherence modes?#

Heuristic mode (default):

  • Fast (~0.1ms per guide)

  • Uses Hamiltonian coefficient variance as proxy

  • R values cluster around 0.68-0.69

  • Good for screening, use as tie-breaker

Quantum mode:

  • Slow (~100-500ms per guide)

  • Runs actual VQE simulation

  • R values range 0.84-0.97 (matches hardware)

  • Use for research-grade analysis

CRISPR Questions#

Which CRISPR modality should I use?#

Modality

Use Case

Typical R Range

CRISPRa

Gene activation

0.84-0.97

CRISPRi

Gene repression

0.84-0.97

Knockout

Gene disruption

0.80-0.95

Prime edit

Precise edits

0.75-0.92

Base edit

Single nucleotide changes

0.78-0.94

How do I interpret the combined_score?#

The combined score (0-1) integrates:

  • GC content (40-70% optimal)

  • Thermodynamic stability

  • Position relative to TSS

  • Chromatin accessibility

  • Off-target specificity

  • Coherence (heuristic or quantum)

Higher scores indicate better candidates.

What are evidence levels?#

  • Level A: Hardware-validated on IBM Quantum (strongest)

  • Level B: VQE-simulated with quantum mode

  • Level C: Heuristic only (weakest)

Prefer guides with Level A or B evidence for experimental validation.

Quantum Questions#

Do I need IBM Quantum access?#

No. PhaseLab works fully with:

  • Heuristic mode (fast, no quantum needed)

  • Quantum simulation mode (local VQE)

  • ATLAS-Q backend (if installed)

IBM Quantum is only needed for hardware validation (Level A evidence).

What is ATLAS-Q?#

ATLAS-Q is a GPU-accelerated quantum tensor network simulator. When available, it provides:

  • 5x variance reduction via IR measurement grouping

  • Faster coherence computation

  • Better accuracy

Install with: pip install atlas-quantum

How do I set up IBM Quantum?#

from qiskit_ibm_runtime import QiskitRuntimeService

QiskitRuntimeService.save_account(
    channel="ibm_quantum",
    token="your-token-here"
)

Get your token at quantum.ibm.com.

Troubleshooting#

ImportError: No module named ‘phaselab’#

Ensure you’re in the correct Python environment:

python -m pip install phaselab
python -c "import phaselab; print(phaselab.__version__)"

ATLAS-Q not detected#

from phaselab.quantum import is_atlas_q_available
print(is_atlas_q_available())  # Should be True

If False, install ATLAS-Q:

pip install atlas-quantum

Quantum mode is slow#

Quantum mode runs VQE simulation (~100-500ms per guide). For screening:

  1. Use heuristic mode for initial filtering

  2. Apply quantum mode only to top candidates

# Screen with heuristic
guides = design_guides(seq, tss, config=Config(coherence_mode="heuristic"))

# Validate top 10 with quantum
top_10 = guides.head(10)
quantum_r = compute_coherence_batch(top_10['sequence'].tolist(), mode="quantum")

Getting Help#