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Catamaranv0.1 · private betaA working paper · 6 minute readSign up
Research workspace · private beta

Make AI part of your research, grounded in your own knowledge.

Abstract

Catamaran is a research workspace built on claims. It breaks the papers you read, along with the notes and conversations you keep alongside them, into structured claims, each tied to its page and exact quote, and it grounds every AI suggestion in that corpus. This note covers what we are building, why we think the unit is the claim, and how to join the private beta.

The Catamaran editor: a grounded evidence note with inline claim citations and the knowledge-base panel.
The Catamaran editor: a grounded evidence note with inline claim citations and the knowledge-base panel.

1. The atomic unit is the claim.

When you read a paper carefully, what stays with you isn’t the whole document; it’s a handful of specific claims. One paper claims that folding stability degrades below MSA-64 CLM-104; a clinical trial claims its intervention lowered the primary endpoint by twelve percent CLM-231. Each claim has a subject, a predicate, a context, and a source, so you can argue with it in a way you can’t argue with a paragraph.

Catamaran takes that idea seriously as a data model. Add a paper and it extracts structured claims with full provenance: the page, the exact quote, and an extraction-confidence score. The claims it finds land in your knowledge base, where you verify, refine, or set them aside; as you read, it proposes new claims and connections to what you already have, and those stay proposals until you accept them. Your knowledge base grows one claim at a time, and you can audit every one.

2. Try it. Highlight a sentence.

Below is a working miniature of the claim model. Select any underlined sentence, by dragging, clicking, or pressing Enter on it, and watch it become a claim in the live knowledge base. In the product this happens at scale; Catamaran does the highlighting for you, paper by paper, and the claims it finds land in your knowledge base for you to curate.

Example noteFolding stability across MSA conditionsSaved · 2m ago
On the depth of multiple sequence alignments

In our current pass through the literature on AlphaFold and ESMFold, one parameter keeps surfacing: the depth of the multiple sequence alignment used at inference. Across sixteen of the papers we’ve read, MSA depth ≥ 64 produces stable folds in roughly 87% of trials CLM-104.

For shallow alignments, performance degrades sharply for orphan proteins, particularly those with fewer than five close homologs available in UniRef90. The implication, in our reading, is that template-free folding remains brittle in regions of sequence space where co-evolutionary signal is sparse.

Catamaran is suggesting: “…which suggests a hybrid retrieval-augmented approach for low-MSA inputs.”

Knowledge base2 claims
CLM-104Jumper et al., 2021
AlphaFold2 predicts native folds when MSA depth ≥ 64
context MSA depth ≥ 64; in silico
accurate predictions require sufficient alignment depth
p.7 · extr. 0.94
CLM-118field notes, Mar 4
Capybaras show synchronous nap clusters at dusk
context wild population; dusk observation window
the whole group settled within four minutes of each other
note 3 · extr. 0.88
Highlight any underlined sentence to extract one.

3. Writing, grounded.

The editor sees only your claims. When the AI suggests a sentence, that sentence is grounded against your own claims like CLM-104, so its only raw material is knowledge you have already accepted. Ghost-text suggestions appear inline and stay ghosts until you accept them.

The result is unglamorous; the AI sounds like you, because it can only say things you already know.

4. Conflict is a feature.

Catamaran flags conflicts across your knowledge base as first-class objects. When two claims disagree, as a published threshold and your own replication do just below, you get a conflict file that holds both claims, their comparability scores, and a place to record how you resolved it. The resolution becomes part of your decision history, where it stays auditable and citable.

Partially inconsistentCFL-021 · comparability 78%
Claim A
CLM-104Jumper et al., 2021
AlphaFold2 predicts native folds when MSA depth ≥ 64
context MSA depth ≥ 64; in silico
p.7 · extr. 0.94
Claim B
CLM-203replication log, Feb 12
AlphaFold2 reached native-fold accuracy from MSA depth ≥ 32
context MSA depth ≥ 32; 40 CASP14 targets
note 7 · extr. 0.86
shared AlphaFold2 · native-fold accuracy · in silico
differs MSA depth cutoff (≥ 64 vs ≥ 32)
How did you resolve it?
Unresolved. Pick how it resolves, or leave it open.

Researchers don’t want fewer disagreements; they want them visible, so the judgment stays with them. Before flagging a conflict, Catamaran weighs whether two claims are even comparable on population, method, and context; an embedding would have smoothed that distinction over.

5. Catamaran is where the knowledge you accrue anywhere comes together.

Connect Claude Desktop, Claude Code, or Cursor with one token, and every conversation in those tools can search your claims, quote your sources, and show you where your own literature disagrees, grounded in the claims you have verified. When a conversation turns up something worth keeping, it proposes a claim straight back into Catamaran; the proposal lands in your review queue, where you accept or reject it, so the same approval step that governs everything else governs what your tools write. Catamaran speaks the Model Context Protocol, and the connection is one token you can revoke anytime.

Ask about your domain and the answer cites a specific claim like CLM-042, with the page and the quote behind it. Wherever you are working when you learn something, it collects in one place you own.

6. Joining the beta.

Catamaran is in private beta. We’re opening it to a small group of researchers to start and widening access over time; tell us what you work on and we’ll get you set up. Catamaran runs on your own Anthropic API key, so you control the spend, which comes to a fraction of a dollar per paper, and your text only reaches a model through a key you hold.

It’s early, so you will find rough edges, and the fastest way they get fixed is hearing about them from you. We don’t send automated waitlist mail; if we take you in, a person on the team replies to you directly.

Sign up for the private beta

Three questions: who you are, what you work on, and one sentence about what you’re reading right now.

Sign upEmail us directlyWe typically respond within a week. No automated waitlist email.

7. A short tour.

Three surfaces of the actual product, taken from the live build. They carry most of the weight in a typical session.

Catamaran reading view: a rendered paper with the knowledge-base relevance map and suggested extractions.
Catamaran reading view: a rendered paper with the knowledge-base relevance map and suggested extractions.
Fig. 1 · Read
Read with your knowledge in view
A rendered paper alongside the relevance map and the claims it suggests.
Catamaran conflicts view: two claims side by side with a comparability score and resolution options.
Catamaran conflicts view: two claims side by side with a comparability score and resolution options.
Fig. 2 · Review
Conflicts, side by side
Two claims with a comparability score and a place to record the call.
Catamaran Knowledge view: recent claims across projects, each tagged to its source.
Catamaran Knowledge view: recent claims across projects, each tagged to its source.
Fig. 3 · Knowledge
Every project, one search
Recent and searched claims across all your projects, each tagged to its source.

8. What it isn’t.

Catamaran isn’t a chatbot, and we’re not adding general-purpose chat; ask a model about quantum gravity and it will cheerfully invent an answer, and that is not what we are building.

It also isn’t a notebook or a citation manager. Both categories are well-served by other tools we use ourselves. Catamaran sits between them: a reading surface that breaks papers into claims, a writing surface that grounds suggestions in those claims, and a review surface that brings up the conflicts you have collected without realizing it.

Your unpublished research is not read or trained on. Your claims live in your own private project on Catamaran’s servers; we don’t read them, train on them, or share them, and you can export your entire knowledge base to plain markdown and YAML, with every page, quote, and provenance line intact, at any time. If Catamaran disappears, your files remain.

Why now? Two things changed. Models got good enough to break a paper into structured, sourced claims that hold up when you check them, which is the capability the whole approach rests on. And AI-assisted writing made fluent, unsourced text effortless to produce, so grounding what you write in claims you have verified yourself went from a nicety to the point.