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 ```bash 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 ```bash # 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 ```bash # 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