Mouse Colony Planner

Calculate timelines and cage numbers required for transgenic mouse breeding to optimize breeding costs.

Functions

• Timeline Calculation: Calculate time required for each stage based on breeding scheme
• Cage Planning: Estimate cage numbers needed for experiments
• Cost Estimation: Calculate total breeding costs (cage fees, husbandry fees, genotyping fees, etc.)

Usage

Command Line

python scripts/main.py --scheme <breeding_scheme> --females <number_of_females> --males <number_of_males> [options]

Parameters

--scheme

heterozygote

homozygote

conditional

--females

--males

--gestation

--weaning

--sexual-maturity

--cage-capacity

--cage-cost

--genotyping-cost

--target-pups

Breeding Scheme Descriptions

1. heterozygote (Heterozygote breeding): Heterozygote x Wild type → 50% Heterozygotes
2. homozygote (Homozygote breeding): Heterozygote x Heterozygote → 25% Homozygotes
3. conditional (Conditional knockout): Requires two-step breeding, introducing Cre/loxp system

Examples

# Heterozygote breeding scheme, starting with 10 females and 5 males, target to obtain 10 heterozygote offspring
python scripts/main.py --scheme heterozygote --females 10 --males 5 --target-pups 10

# Homozygote breeding, custom cycle parameters
python scripts/main.py --scheme homozygote --females 20 --males 10 --target-pups 20 --gestation 21 --weaning 21

# Conditional knockout scheme
python scripts/main.py --scheme conditional --females 15 --males 15 --target-pups 15

Output

• Timeline for each stage
• Cage numbers required at each stage
• Estimated total cost
• Breeding flowchart

Risk Assessment

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

# Python dependencies
pip install -r requirements.txt

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