Cohort planner

Work backwards from the mice your experiment needs to the mice your colony has to produce including the generations it takes to get the breeders you need, how much it costs, how long it will take, and how many surplus animals you'll generate.

Experimental Animals

40 animals

Animals per group

Groups

Timepoints or cohorts

Sex needed

Genetics

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One row per locus. For each one: what your colony holds today, the genotypes the breeding pair will carry at that locus, and what the pups have to be to be usable. The gap between the first two is what the setup generations below are for.

All of these alleles are already carried by the same mouse

Colony Assumptions

edit to match your strain

Pups weaned per litter

Litters per pair (lifetime)

Weeks between litters

Pre-weaning loss (%)

Loss after weaning (%)

Age at first mating (wks)

Age at experiment start (wks)

Weeks on study

Breeding pairs to run 0 = fewest that will do

Running more pairs at once does not change how many pups you need — it changes how they arrive. Many pairs deliver the cohort in one wave, close in age, in exchange for holding more breeding cages at the same time. Few pairs hold fewer cages and deliver the same animals across several litters, months apart in age.

Cost

per diems vary — use yours

Per diem ($/cage/day)

Genotyping ($/sample)

Mice per holding cage

Imported mouse ($ each)

Import lead time (wks)

To get one usable mouse you breed

19 pups born

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How this number is calculated

Pups born → survive to weaning → carry the required genotype at every locus → are the required sex → survive to the start of the study.

Each locus is treated as segregating independently. If two of your loci are linked, the real genotype fraction is lower than this one.

Breeding Timeline

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Animal Estimates

Category	Animals	Why they are needed
Total to request	—	—

Estimated Cost

estimates, not quotes

—per diem, genotyping and imports

—breeding cages at peak

—today → full cohort on study

Line	Cost	Basis
Total	—	excludes labour, procedures and consumables

Draft justification

for the protocol narrative

The plan is the easy part

Use SqueakBase to keep track of your colony in real time

Start free

Alleles are assumed to segregate independently; linked loci yield fewer usable pups than shown. Institutions differ on whether pre-weaning deaths, retired breeders and imported founders count against your approved number. Check your own IACUC's counting rules before submitting. This app runs locally, no information is transmitted.