Synthetic Bio Circuit Designer#

Design and simulate gene circuits for synthetic biology.

Usage#

bash

python scripts/main.py --type toggle --p1 P1 --p2 P2
python scripts/main.py --type oscillator

Circuit Types#

• Toggle switch: Bistable genetic switch
• Oscillator: Repressilator circuit

Output#

• Circuit design
• Component list
• Expected behavior

Risk Assessment#

Risk IndicatorAssessmentLevelCode ExecutionPython/R scripts executed locallyMediumNetwork AccessNo external API callsLowFile System AccessRead input files, write output filesMediumInstruction TamperingStandard prompt guidelinesLowData ExposureOutput files saved to workspaceLow

Security Checklist#

• No hardcoded credentials or API keys
• No unauthorized file system access (../)
• Output does not expose sensitive information
• Prompt injection protections in place
• Input file paths validated (no ../ traversal)
• Output directory restricted to workspace
• Script execution in sandboxed environment
• Error messages sanitized (no stack traces exposed)
• Dependencies audited

Prerequisites#

No additional Python packages required.

Evaluation Criteria#

Success Metrics#

• Successfully executes main functionality
• Output meets quality standards
• Handles edge cases gracefully
• Performance is acceptable

Test Cases#

1. Basic Functionality: Standard input → Expected output
2. Edge Case: Invalid input → Graceful error handling
3. Performance: Large dataset → Acceptable processing time

Lifecycle Status#

• Current Stage: Draft

• Next Review Date: 2026-03-06

• Known Issues: None

• Planned Improvements:

  • Performance optimization
  • Additional feature support