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note.md is a native, macOS‑first academic research workspace that integrates a PDF reader, reference manager, Markdown note editor, and writing environment into a single window. All data is stored locally on the user’s Mac as plain text Markdown files, and all AI functions run entirely on-device—no content is uploaded, and no model training takes place—ensuring privacy and accessibility for up to ten years.

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Replace Zotero and Obsidian with one Mac app | note.md
01 / OVERVIEW

What is note.md?

note.md is specifically crafted for rigorous academic projects at Harvard, MIT, Stanford, Oxford, Cambridge, ETH Zurich, and similar institutions, earning the nickname “Academic IDE.” It puts an end to the long-standing fragmentation of researchers relying on four separate tools—Zotero, Obsidian, a PDF reader, and a standalone note‑taking app. Users can read papers, highlight key passages, write bi‑linked Markdown notes, insert BibTeX or APA citations derived from PDF metadata with a single click, and have each citation permanently anchored to its original highlight. Its on‑device AI supports deep workflows such as semantic search, evidence scanning (/scan), and matrix extraction—all running offline, enabling full‑text retrieval, claim validation, and knowledge graph construction without any internet connection.

02 / CAPABILITIES

Key features

  • Side-by-side dual‑pane reading: PDFs and the Markdown note editor are seamlessly juxtaposed, supporting highlighting, bookmarks, annotations, and one-click citation insertion—all in a unified workflow; every citation automatically links back to the specific highlighted passage and note timestamp within the original PDF.

  • Smart citation system: Generates BibTeX or APA‑style citations directly from PDF metadata, with each inserted citation双向 linked back to its corresponding highlight, ensuring that even months later, users can still click to jump straight to the original source.

03 / AUDIENCE & USE CASES

Use cases and audience

Designed for macOS researchers at prestigious institutions such as Harvard, MIT, Stanford, Oxford, Cambridge, ETH Zurich, and others who require an integrated local toolset combining PDF reading, reference management, bi-directional linked notes, and academic writing.

  • Read and annotate research papers: In a side‑by‑side interface of PDF reader and note editor, highlight key ideas, add bookmarks and annotations, and insert citations with one click—replacing Preview, Zotero, and standalone note‑taking apps.
  • Conduct a literature review: Classify papers into a real-world literature database, have the local AI populate an editable matrix, then perform semantic searches across all paragraphs. The AI provides suggestions, which the user reviews, revises, and uses to draft the review, with each claim still linked back to its original source.
  • Write your first academic paper: Use block-based Markdown authoring, inserting citations, source images, and evidence scan results via slash commands such as /cite, /link, /wiki, and /pdf, automatically constructing a knowledge graph.
Input

PDF papers (including embedded metadata), user‑entered bibliographic information, Markdown‑format notes, and local AI processing requests triggered by slash commands like /cite or /scan.

Output

Markdown note files with bi-directional links, BibTeX or APA‑style citations anchored to highlighted passages in PDFs, locally generated knowledge graphs (with Neo4j‑compatible exports), semantic search results, matrix extraction tables, and evidence‑scanning outputs identifying supporting, contradictory, or neutral passages.

Frequently asked questions

Can note.md be used offline?

Yes. note.md is a locally-first app: notes, PDFs, indexing, and all AI features run directly on your Mac, allowing you to read, write, search, and perform local AI workflows such as execution/scan or matrix extraction—all without an internet connection. You only need to download several gigabytes of language models during the initial AI setup.

Will note.md use my notes to train its AI model?

No. Your notes never leave your device. At note.md, all AI processing occurs locally on your device—there are no cloud servers collecting your content, no telemetry uploading articles or text data, and your data is never used for model training.

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