Stochastic Breeding Planning Tools

This website offers two interactive tools designed to help researchers plan mouse breeding more efficiently, reducing surplus and adhering to the 3Rs principle.

Select a planning approach based on your experimental needs

Calculator Cohort Breeding

Cohort‑based breeding is a time‑synchronized production strategy. A defined number of breeding pairs are mated simultaneously to generate experimental cohorts of mice with specified genotype, sex, and age within a narrow time window (e.g. >30‑day interval). It is ideal for Mendelian crosses, genotype-specific knockout models, and sex-specific experimental designs.

Our tool uses probabilistic modeling to calculate the minimum number of breedings needed to reach your target cohort size, based on fertility rates, litter size distribution, and Mendelian inheritance.

Calculator Colony Breeding

Colony‑based (continuous production) breeding operates as a rolling breeding model: a stable group of breeders produces pups continuously over time, supplying both experimental needs and replacements for aging breeders. It is ideal for long-term needs, strains requiring continuous maintenance, and flexible experimental timeline. Frequently, the Breeding Colony Size Planning Work Sheet by The Jackson Laboratory is used for the planning of breeding colonies. We provide here an Excel instead of the original PDF version of this worksheet.

Our tool helps manage dynamic breeder populations and predicts output based on litter size, productivity, fertility, and shelf-life to prevent surplus.

Breeding genetically modified animals is governed by biological uncertainty. Even with tight controls, outcomes are probabilistic rather than fixed. This randomness must be accounted for in any responsible breeding plan.

Sources of Stochasticity:

1. Mendelian Segregation - Gamete formation and fertilization follow probabilistic rules. For example, mating two heterozygotes (Aa × Aa) yields a 25% chance of homozygous mutants (aa) per offspring, but actual litter outcomes vary due to random sampling
2. Fertility Variability - Breeding pairs sometimes fail to produce any litters. Also, ertility rates depend on strain, age, and environment, creating unpredictable variation.
3. Litter Size Fluctuation - While a strain may have an average litter size (e.g., 6–8 pups), actual litter follows a statistical (Poisson) distribution
4. Sex Ratio Deviation - Although the expected sex ratio is generally ~50:50, random variation leads to imbalances
5. Inter‑Litter Interval – Especially in colony breeding, time between litters (~3 weeks) is not absolutely fixed, yielding variability in overall output.

Each of these factors contributes to random variation in breeding results, making deterministic planning unreliable, often leading to either shortages or surplus euthanasia. Our tools model these stochastic processes mathematically using probability distributions for fertility, litter size, and genotype to provide robust predictions with defined confidence levels (e.g., 90% chance of success).

1. Milchevskaya, V., Bugnon, P., ten Buren, E. B. J., & Tresch, A. (2023). Group size planning for breedings of gene-modified mice and other organisms following Mendelian inheritance. Laboratory Animals, 52(4), 183–188. https://doi.org/10.1038/s41684-023-01213-1
2. GV-SOLAS Working Group. (2024). Breeding planning of genetically modified mice: Guidelines for animal facilities and researchers. German Society for Laboratory Animal Science (GV-SOLAS). https://www.gv-solas.de/wp-content/uploads/2024/12/Breeding-planning_2024.pdf
3. NC3Rs. (2024). Colony management scenarios and strategies. National Centre for the Replacement, Refinement and Reduction of Animals in Research. https://nc3rs.org.uk/3rs-resources/breeding-and-colony-management/colony-management-scenarios-and-strategies
4. University of North Carolina at Chapel Hill. (2020). Mouse breeding and colony management. UNC Research. https://research.unc.edu/wp-content/uploads/2020/08/Mouse-Breeding-and-Colony-Management-2020.pdf
5. The Jackson Laboratory. (2016, April). How to prevent mouse breeding costs from destroying your research budget. The Jackson Laboratory. https://www.jax.org/news-and-insights/jax-blog/2016/april/how-to-prevent-mouse-breeding-costs-from-destroying-your-research-budget
6. Taconic Biosciences. (2024). Breed your own rodent models: Best practices and cost considerations. Taconic Biosciences. https://www.taconic.com/resources/breed-your-own-rodent-models
7. NC3Rs. (2024). Breeding and colony management overview. National Centre for the Replacement, Refinement and Reduction of Animals in Research. https://nc3rs.org.uk/our-portfolio/breeding-and-colony-management