majiayu000 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
- heterozygote (Heterozygote breeding): Heterozygote x Wild type → 50% Heterozygotes
- homozygote (Homozygote breeding): Heterozygote x Heterozygote → 25% Homozygotes
- 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
- Basic Functionality: Standard input → Expected output
- Edge Case: Invalid input → Graceful error handling
- 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