aipoch/mouse-colony-planner

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

| Parameter | Description | Default | |------|------|--------| | --scheme | Breeding scheme: heterozygote, homozygote, conditional | Required | | --females | Starting number of females | Required | | --males | Starting number of males | Required | | --gestation | Gestation period (days) | 21 | | --weaning | Weaning age (days) | 21 | | --sexual-maturity | Sexual maturity age (days) | 42 | | --cage-capacity | Maximum cage capacity | 5 | | --cage-cost | Cage cost per day (CNY) | 3.0 | | --genotyping-cost | Genotyping cost per mouse (CNY) | 15.0 | | --target-pups | Target number of specific genotype mice | 10 |

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

| Risk Indicator | Assessment | Level | |----------------|------------|-------| | Code Execution | Python/R scripts executed locally | Medium | | Network Access | No external API calls | Low | | File System Access | Read input files, write output files | Medium | | Instruction Tampering | Standard prompt guidelines | Low | | Data Exposure | Output files saved to workspace | Low |

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