Read the literature.
See how it connects.

Synaptate is a desktop workspace for scientists. Annotate papers, pull highlights onto a canvas, and build claims backed by the evidence that supports — or refutes — them.

Download for Windows See how it works

Free while in beta. Your library stays on your machine.

Works offline Your files stay yours No account required

You've read forty papers. Now what?

Your highlights are trapped in forty separate PDFs. Your notes don't remember which paper they came from. When your advisor asks "what actually supports this?", you go hunting through folders.

Reference managers organize your citations. They don't help you think.

read · connect · synthesize

Three moves, one workspace

Read

A real scientific PDF reader — highlights, ink, sticky notes, figure extraction. Genes, proteins, and accession numbers are detected as you read, and abbreviations are collected into a glossary automatically.

Connect

Send any highlight or note to a project canvas. Draw the relationships yourself — label an edge "supports," "contradicts," "replicates" — and watch the argument take shape.

Synthesize

Build claim nodes that tally their own evidence. Compare papers side by side in a matrix of the attributes you define. Export it when you're ready to write.

The claim board

Every claim, with its receipts

Make a claim. Connect the papers, notes, and highlights that support it and the ones that don't — label each link "supports" or "refutes." The connections turn green and red so a weak claim looks weak at a glance.

This is the part no reference manager does. It's the difference between having read the literature and understanding it.

The Synaptate canvas: paper, note, highlight, and claim cards connected by green 'supports' and red 'refutes' links, with a figure region and minimap

The reader

Built for papers, not documents

Highlight, ink, and annotate directly on the page, with your annotations listed beside it. Landscape figures and scanned PDFs are handled properly, and a floating tool dock keeps every markup tool within reach.

The Synaptate reader: a PDF page with a highlighted passage, the Annotations panel listing highlights, and the tool dock

Science-native

It speaks your field's language

Genes, proteins, chemicals, and accession numbers are detected as you read and link out to UniProt, NCBI Gene, PubChem, and RRID. Abbreviations are harvested into a per-paper glossary automatically — so you stop scrolling back to find what "RNP" or "FAME" meant.

The glossary panel listing detected abbreviations and their expansions, such as FAME, GC-MS, RFLP, RNP, and TAGs

Structures

See the molecule, next to the paper

Type a PDB ID and Synaptate renders the 3D protein structure right beside the text — rotate, zoom, and switch between cartoon, stick, and sphere views. Structures are pulled from the RCSB Protein Data Bank.

The 3D structure viewer showing protein 1CRN in cartoon representation alongside the paper text

Private by design

Your work stays on your machine

Synaptate is a desktop application with a local database. No cloud account, no upload, no training on your library. Your PDFs sit in a folder you can open yourself — and if you ever stop using Synaptate, everything you highlighted is still yours.

It doesn't summarize the literature for you either. The connections are the ones you drew — which is why you can defend them.

Where Synaptate fits

It doesn't replace your reference manager — it's the step after it.

	Synaptate	Reference managers	AI research tools	Visual note apps
PDF reading & annotation	✓	✓	partial	partial
Science-native entities & glossary	✓	—	—	—
Manual claim / evidence board	✓	—	—	partial
Evidence matrix	✓	—	partial	—
Works offline · data stays local	✓	partial	—	partial
Automatic AI summaries	—	partial	✓	—

Questions

Which platforms does it run on?

Windows today. macOS and Linux are planned — the app is built on a cross-platform stack.

What does it cost?

Free while in beta. Pricing for the full release will be announced before it ships — beta users will get plenty of notice.

Do I need an account?

No. There's no sign-up and nothing to log into. You download the app and start reading.

Does it replace Zotero or EndNote?

No — it's the step after. Keep your reference manager for citations; use Synaptate to read, connect, and synthesize.

Where are my files stored?

In a local folder on your machine, alongside a local database. Nothing is uploaded.

Does it use AI on my papers?

No. Entity detection and glossary building are local, deterministic algorithms — not a language model reading your library.

Can I export my work?

Yes — notes as Markdown, the matrix as CSV or Markdown, and annotations as XFDF or flattened PDF.

Read the literature.See how it connects.