Write with Clarity.Think in Layers.
Zotero + Obsidian + your PDF reader, in one Mac app
Write with Clarity.
Think in Layers.A local-first research workspace for Mac. For students and researchers who read papers, manage sources, take linked markdown notes, cite evidence, and turn literature into structured writing — without scattering their workflow across Zotero, Obsidian, PDF readers and writing apps.
Local AI helps you search what you’ve read. Your thinking stays yours.
Made for the rigor of programs like
HarvardMITStanfordOxfordCambridgeETH Zürich
What is note.md?
The academic IDE
All your PDFs, in one place
Drop in every paper for your thesis. Read, organize and tag them without leaving the app — no more Zotero tab open in the background.
Notes that become your paper
Take linked notes in markdown as you read. Watch them grow into the chapter you’re actually writing — no separate Obsidian vault to sync.
Citations that just work
Insert BibTeX or APA citations straight from a PDF’s metadata, with every cite linked back to the highlight it came from.
Yours, ten years from now.
Built for how researchers actually work
Local and Private Vault
Your notes never leave your machine. Your thoughts stay yours.
Real markdown + LaTeX
GitHub-flavored markdown, complex tables and LaTeX math, all in plain-text files you can open in any editor.
Your notes, linked
Connect ideas with bidirectional links and see the whole network in a visual graph view.
Feature
Reading Studio.
Read with intention, highlight key insights, and cite sources in your markdown notes with a single click.
auto\_stories
#### Side-by-Side Reading
View your PDF and your note editor in a seamless dual-pane interface.
format\_quote
#### Smart Citations
Automatically generate BibTeX or APA citations from PDF metadata.
Feature
Knowledge Management.
Import scientific papers and complex PDFs directly into your workspace. Fill the metadata, and export all your sources at once as a .bib file.
folder\_managed
#### Source Management
View all your PDFs and sources at once and structure them by topic.
database\_search
#### Automatic Indexing (Premium)
Automatically extract figures, charts, and tables from your PDFs and insert them into your articles.
Feature
Graph View.
See how your articles and sources are connected.
hub
#### Relations
View your sources and your notes together in one connected graph.
account\_tree
#### Neo4j Support
Export your graph in a Neo4j-friendly format.
Premium Feature
Semantic Search.
Search your workspace by meaning instead of exact phrasing, powered by local AI models that keep your data private.
manage\_search
#### Search by Meaning
Find relevant passages even when the wording in your query does not match the source text.
bolt
#### Time Saver
Skip manual hunting across files and jump straight to the material you actually need.
Workflows
Put it to work.
Real research workflows, end to end. Local AI helps you search and organize what you’ve read — you do the thinking.
Reading workflowRead and annotate research papersHighlight, bookmark, annotate, cite — all in one window, replacing Preview, Zotero and a separate notes app. Every citation in your draft links back to the exact passage and the note you wrote when you read it.See workflow →Research workflowRun a literature reviewSort papers into a real library, let local AI fill an editable matrix you control, then search every passage by meaning. The AI proposes; you review, correct, and write the synthesis — every claim still linked to its source.See workflow →Writing workflowWrite your first articleArticles are your project's knowledge vault. Block-based markdown with slash commands for citations, source images, evidence-scanning, and links that auto-build your knowledge graph as you write.See workflow →Knowledge workflowBuild a knowledge graphArticles on the left, sources on the right, mirroring your articles sidebar. Every /cite, /link, /wiki or /pdf you place in an article becomes an edge in the graph — your reading and writing build the network as you go.See workflow →
Under the Hood
How note.md actually works.
Technical deep-dives into the local AI behind every feature. No black boxes — chunk sizes, ranking math, model parameters, and failure modes, all documented.
01·Architecture
The local AI architecture behind note.mdHow on-device indexing, retrieval, and inference fit together to power semantic search, Matrix extraction, and Evidence Scan — without sending a single byte off your Mac.8 min readRead →02·Pipeline
Source indexing: turning PDFs into a local knowledge index10 min readRead →03·Pipeline
Hybrid semantic search: meaning + keywords, fused9 min readRead →04·Pipeline
Matrix extraction: filling research tables with local AI9 min readRead →05·Pipeline
Evidence Scan: finding support and contradictions for any claim10 min readRead →
Where your paper actually takes shape.
\- High-contrast serif typography
\- Absolute minimalism
\- Distraction-free toggle
The Philosophy of Intentional Design
"Simplicity is the ultimate sophistication."
When we design digital tools, we often forget that the primary goal is not the interaction with the tool itself, but the output it enables. note.md was built on the principle that the UI should dissolve the moment you begin to type.
By using markdown as the fundamental storage format, we ensure that your data is truly yours: portable, readable, and future-proof. No proprietary formats, no lock-in.
This is where the second brain comes in. It is not just about storage; it is about synthesis. When you link two concepts together, you are not just creating a path, you are creating a new perspective.
Common questions from researchers
What people ask before switching.
What's the best app for organising research papers on Mac?It depends what you want it to do. If you only need a citation manager, Zotero is the long-standing free option. If you only need notes, Obsidian or Notion are popular choices. note.md is built for the people who want all of it in one place — reading PDFs, taking linked notes, managing citations and writing — without juggling four apps or syncing libraries across them.
Is there a good Zotero alternative for Mac?Zotero is excellent at what it does — managing references — but it's a separate app from where you actually write. note.md keeps the reference manager, the PDF reader, the notes editor and the citation system in one window, with every citation in your draft linked back to the exact highlighted passage you took it from.
How do I keep my notes, sources and citations in one place?Use a single tool that holds all three rather than syncing between them. In note.md, your sources (PDFs) live in Knowledge Management, your notes are written as articles in the same project, and citations created with /cite stay anchored to specific bookmarks inside your PDFs — so months later you can still click any citation and land on the exact passage that justified it.
Can I use note.md without an internet connection?Yes. note.md is local-first: your notes, your PDFs, your indexes and all AI features run entirely on your Mac. You don't need an internet connection to read, write, search, or run local-AI workflows like /scan or matrix extraction.
Will note.md use my notes to train AI models?No. Your notes never leave your machine. All AI in note.md runs locally on-device — there is no cloud server collecting your content, no telemetry uploading the text of your articles or sources, and nothing of yours used for model training.
Does note.md work with my existing PDFs and Zotero library?Yes. Drop any PDF directly into Knowledge Management and note.md handles the rest — metadata extraction, optional indexing, and citation generation. There's no proprietary file format, and you can export your bibliography as a standard .bib file for use in LaTeX or import into another reference manager any time.
Pricing
Free to start. Premium unlocks local AI.
The full writing workspace is free, forever. Premium adds the local-AI workflows — semantic search, Matrix extraction, Evidence Scan. Students from $4.99/mo.
Focus on what matters.
Download note.md and stop scattering your work across Zotero, Obsidian, your PDF reader and a writing app. Private, local-first, and free to start.
Free on the App Store