Mouse Colony Planner

---

name: mouse-colony-planner

description: Calculate breeding timelines and cage requirements for transgenic mouse

colonies

version: 1.0.0

category: Wet Lab

tags: []

author: AIPOCH

license: MIT

status: Draft

risk_level: Medium

skill_type: Tool/Script

owner: AIPOCH

reviewer: ''

last_updated: '2026-02-06'

---

# Mouse Colony Planner

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

Functions

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

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

Prerequisites

# Python dependencies
pip install -r requirements.txt

Evaluation Criteria

Success Metrics

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

- Performance optimization

- Additional feature support