Colony size calculator

Method

The tool follows, line by line, The Jackson Laboratory’s worksheet: the need per week, multiplied by the sex, cross and margin factors, then divided by the pups one female weans per week.

A monthly need counts 4 weeks, as on the worksheet. It is divided by the smaller of the age range and the frequency: animals born the same week mean producing the whole month’s need in one week.

Animals and cages are rounded up. Line 12 keeps its full precision; the paper worksheet rounds it to the hundredth, which can give slightly fewer females.

Non-productive pairs are taken off the litters per female, as in the JAX manual (15%: litters × 0.85). The safety margin is line 7: 10% gives a factor of 1.1.

Replacement females (lines 14 to 16) only when the breeders have the genotype of the animals used (hom × hom, or het × hom with both sexes) and the age range covers the frequency. Otherwise, the pups not used serve as breeders.

In trios, two females per cage, with the same productivity per female as in pairs, as in the JAX examples.

Limits

• The calculation is deterministic: averages in, averages out, with no statistical margin.
• Productivity depends strongly on the strain: use your own colony’s figures. As the NC3Rs puts it, neonate mortality can vary considerably between strains.
• The worksheet counts pups at weaning: losses after weaning are not in it.
• The JAX worksheet is less accurate for colonies carrying sublethal genes or with variable penetrance.
• On small cohorts, Mendelian ratios are unreliable (NC3Rs): plan a contingency.
• Het × het counts the homozygotes (25%); the worksheet has no line for breeding the heterozygotes.

Sources

• The Jackson Laboratory, Breeding Colony Size Planning Worksheet: the formula, lines 1 to 16.
• The Jackson Laboratory, Breeding Strategies for Maintaining Colonies of Laboratory Mice (2009): the A2 example, non-productive pairs taken off the litters (appendix A5), trios; copy hosted by the University of California, Irvine.
• The Jackson Laboratory, Guidelines for Sizing Experimental Mouse Colonies (webinar, 2017): the age range in the replacement rule (lines 14 to 16); copy hosted by National Cheng Kung University.
• NC3Rs, How to plan a colony: productivity by strain, non-productive matings, Mendelian ratios on small cohorts.
• The Jackson Laboratory, Colony Planning: the page that links to the worksheet.