SqueakBase connects directly to Claude as a custom connector. Once it is set up, Claude answers questions from your live colony data instead of guessing:
You: Which litters wean in the next three days, and do I have cage space for the pups?
Claude: Three — L-2026-041 (7 pups, weans Tuesday), L-2026-044 (5 pups, Wednesday)…
The connection is read-only. Claude takes on the overhead of running a large colony, but you make the decisions. Less time keeping track of your colony, more time at the bench.
Setup takes about five minutes.
What you need
- A SqueakBase account — any plan, including free.
- Claude on the web or the desktop app
- A paid Claude plan that supports custom connectors.
Step 1: Copy the SqueakBase connector address
In SqueakBase, go to Settings → Connected Apps or copy paste the following address: https://api.squeakbase.com/mcp.
Step 2: Add SqueakBase to Claude
On claude.ai or the desktop app: Settings → Connectors → Add custom connector, name it SqueakBase, paste the address, click Add.
Step 3: Sign in and choose the scope
Claude opens a SqueakBase sign-in page. That page is served by SqueakBase; Your password is never shared with Claude or Anthropic. Sign in as usual, then choose what the connection may see:
- My data only: the mice, cages and litters you own. The default, and the right choice for most people.
- My lab's data: everything shared with your lab. Only offered if you belong to one.
Click Approve. That choice is locked into the connection itself and cannot be widened later by Claude.
What it can and cannot do
Read-only. Claude watches and reports; you decide and record. There are eight tools and every one is a lookup:
| Tool | What it returns |
|---|---|
colony_overview |
Headline counts — mice by sex, cages, breeding cages, litters, pregnancies, births due |
search_mice |
Mice filtered by ID, tag, sex, strain, genotype, cage or age |
get_mouse |
Full information about one mouse |
list_cages |
Cages, capacity, occupants |
get_cage |
Full information about one cage |
list_litters |
Litters, pup counts, days until weaning |
list_pregnancies |
Active pregnancies, due dates, checks owed |
list_strains |
The strains in your colony |
Nothing creates, edits, archives or deletes. Ask Claude to move a mouse and it will tell you to do it in the app.
Only what you can already see. The connection runs as you, under the same permissions as your login. If you approved My data only, your labmates' animals are invisible to it even though you share a lab.
Every tool call is recorded in your account's activity log, and Settings → Connected Apps shows each connection's scope and when it was last used.
What to ask it
Monday morning triage
What needs my attention in the colony this week?
Claude starts with the headline counts, then drills in: litters at or past weaning age, births due in the next seven days, and breeding pairs sitting at day 10–12 with no pregnancy check recorded. You get a short list with cage numbers, not a dashboard to read.
Weaning without overflowing a cage
Which litters wean in the next three days, and where will the pups go?
It pulls litters by days-until-weaning — using the weaning age set in your settings, not a hardcoded 21 — then compares each cage's capacity against its current occupants. The answer names the litters, the pup counts, and the cages that will be over.
Building an experimental cohort
I need 12 Cre-positive females between 8 and 12 weeks old. What do I have, and what's coming?
One filtered search on age, sex and genotype, plus the litters that will reach that age window. You get mouse IDs, cages and dates of birth — and an honest count of how short you are.
Pregnancy checks you forgot
Any breeding pairs I should be palpating right now?
Every active pregnancy carries a flag when it is 10–12 days past the breeding start date with no check recorded. This is the question that catches the pair you set up three weeks ago and stopped thinking about.
Litter performance
Compare initial pup counts to weaned counts for litters born since June. Anything look off?
Both numbers sit on the litter record, so Claude can do the arithmetic across the whole set and point at the outliers — losses concentrated in one strain, or one breeding cage.
The lab meeting update
Draft my colony update for lab meeting: what's new, what needs attention, what's coming.
Births in the last seven days, upcoming weanings, due dates, cages near capacity — written as prose you can paste.
Follow-ups are where it earns its keep. Claude already has the data loaded, so "which of those are in the same room?" or "now sort them by age" costs another sentence, not another query.
Getting better answers
Put the filter in the question. "Which females are over 6 months and still in breeding cages?" becomes one targeted query. "List all my mice and tell me which are old" drags your colony into the conversation and asks Claude to sift it — slower, less accurate, and heavier on your Claude usage limits.
Archived animals are hidden by default. Searches return active mice. If you want culled or deceased animals in the picture, say so.
Ask it to show its work before you act. For anything you would actually do — culling, ordering, scheduling — follow up with "which mice specifically, and what did you filter on?" The IDs and criteria come back, and a misread is obvious.
Turning it off
Settings → Connected Apps lists every connected app with a Disconnect button. Disconnecting takes effect on that connector's very next request — there is no delay to wait out — and you can reconnect any time by adding it again.
Worth a glance now and then. An entry you do not recognise, or a "last used" date that does not match when you were actually working, is the thing to catch.
Troubleshooting
| Problem | What it usually is |
|---|---|
| No option to add a connector | Custom connectors need a paid Claude plan. On Team or Enterprise, your workspace admin controls whether members can add them. |
| Sign-in page rejects your password | It is your SqueakBase password. If you signed up with Apple and never set one, use Forgot password first. Several failed attempts lock the account briefly, as in the app. |
| Claude sees no mice | Either you approved My data only and the animals belong to labmates, or the connection is gone — check Connected Apps. |
| Answers look stale | The connector reads live from the server. But SqueakBase is offline-first: changes made on a phone while offline are invisible to everyone until that device syncs. |
Anything else — contact@squeakbase.com, and mention which Claude app you were using.
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