The Zeteyn Manual

Everything you need to go from a blank project to a submission-ready manuscript. No prior experience with research software required.

Five-Minute Quickstart

These five steps will take you from an empty workspace to a draft with a cited source and an AI conversation that you can return to. Everything else in Zeteyn builds on these five actions.

1. 1
   Upload a PDF

   Drag any PDF into the Evidence Vault (the right panel). Zeteyn indexes it in the background. You can keep working while it processes. Once indexed, the AI can search it and you can read it in the built-in PDF viewer.

2. 2
   Save a snippet from the PDF

   Open the PDF in the Reader panel. Highlight a sentence. Drag it onto the Editor in the centre. A small menu appears asking what role this evidence plays — Supporting, Methodology, etc. Select one. The snippet is now a hard-linked citation: clicking it in future will scroll the PDF to that exact sentence.

3. 3
   Write something in the Editor

   Click in the Editor (centre panel) and type a sentence or paste existing notes. The editor works like a word processor. Press / to see a list of things you can insert — equations, diagrams, code cells, and more.

4. 4
   Ask the AI a question

   The Chat panel is on the right side of the screen. Make sure the mode at the top says Brainstorm. Type a question about your draft or your uploaded PDF. The AI has read everything in your Evidence Vault and will answer using your own sources, not generic knowledge. To ask about a specific sentence, select it in the Editor first, then type your question.

5. 5
   Save the exchange to your Thought Log

   After the AI replies, look for the [+] button at the bottom of the exchange. Click it. The conversation is saved to your Thought Log — a permanent record of your reasoning that the AI can search in future sessions. Your thinking does not disappear when you close the tab.

Understanding the Layout

Zeteyn uses a four-panel workspace. You can resize or hide any panel. Here is what each one does.

Five AI Modes

The Chat panel has a mode selector at the top. The mode you choose changes how the AI approaches your request — not just what it says, but what tools it uses, what it prioritises, and what it produces. Choose the mode that matches what you are trying to accomplish right now.

Switching modes mid-session

You can switch modes at any point. A common arc: Brainstorm to develop an argument → Edit to write it up → Challenge to find weaknesses → Respond once actual reviewer comments arrive.

Talking to the AI

The AI understands plain language. You do not need special syntax. Just describe what you want. A few things that help:

• Select text first, then ask. If you want the AI to help with a specific sentence or paragraph, select it in the Editor before typing your message. The AI will know you are referring to that selection.
• Be specific about what kind of help you want. "Improve this" is less useful than "make this argument more concise without removing the claim about sample size."
• The AI will ask for clarification if needed. If your request could mean more than one thing, the AI will describe its interpretation and ask you to confirm before acting.
• The AI never changes your manuscript without showing you first. Any proposed edit appears as a preview. You decide whether to accept it.

Floor buttons: [+] and [+↑]

Each AI exchange is called a "floor." At the bottom of each floor you will see:

• [+] — Save this specific exchange to your Thought Log
• [+↑] — Save all exchanges from the beginning of the session up to and including this one
• The checkbox on the left of each floor lets you select multiple floors; the [+] button then saves all selected floors at once

What the AI can see

By default, in every session the AI has access to:

• Your Research Anchor — your core research question, confirmed findings, and constraints (from RESEARCH_ANCHOR.md)
• The current conversation history (recent exchanges in full; older ones as summaries)
• Your Evidence Vault, which it searches on request
• Your manuscript, which it reads freshly each time in Edit mode

It does not have access to the internet unless you ask it to search ArXiv or another connected source.

Thought Log

The Thought Log is a permanent record of your reasoning. Unlike your conversation history — which compresses over time — the Thought Log is persistent across sessions and fully searchable.

To view your Thought Log, click the log file in the Left Sidebar or click the [↗] icon in the conversation header. It opens in the Viewer panel alongside your Editor.

What belongs in the Thought Log

Save exchanges where you worked something out — a decision about methodology, a finding you confirmed, a direction you ruled out. The AI can search your Thought Log in future sessions, so saving "why you decided against approach X" is as useful as saving "what you concluded about approach Y."

Research Anchor

The Research Anchor (RESEARCH_ANCHOR.md in your project root) is a special file that the AI reads at the start of every session. It keeps the AI oriented around your core research question even as conversation histories grow and compress.

You can edit it directly or ask the AI to update it: "Add our finding about sample size to the Research Anchor." It contains:

• Your core research question
• Confirmed findings (with their source references)
• Methodological constraints
• Disproven hypotheses (the "Context Blacklist" — the AI won't repeat these mistakes)

Checkpoint & Rollback

Zeteyn automatically saves a checkpoint before every significant edit — a manuscript change, a Thought Log insertion, a bulk replacement. If you accept an AI suggestion and then change your mind, you can roll back to exactly the state before that edit.

Where to find checkpoints

Look at the right edge of the Chat panel. You will see a vertical strip of small dots, one per conversation floor. Checkpoint markers appear as diamond shapes — distinct from the regular floor dots. Hover over any diamond to see when it was created and what triggered it.

Rolling back

Manual checkpoints

You can also save a checkpoint at any time. Click the [...] menu in the conversation header and select Save Checkpoint. You can add a label like "before restructuring introduction." Useful before a large edit session you might want to undo entirely.

Evidence Vault

The Evidence Vault is your indexed library of sources. Everything you add to it is searchable by the AI and linkable from your manuscript. Think of it as the verified foundation your writing stands on.

Adding sources

• Drag a PDF into the Vault panel. Zeteyn indexes it automatically.
• Paste a URL into the Editor or Chat. Zeteyn captures and indexes it.
• Paste BibTeX anywhere. Zeteyn detects it and creates a citation entry automatically.
• Connect Zotero (see Zotero Integration) to sync your existing library.
• Ask the AI: "Search ArXiv for recent papers on [topic]." Any paper you save from the results goes into the Vault.

Source Cards

When the AI references a paper in its response, it shows a Source Card — a small block with the paper title, author, and year. Two buttons appear on each card:

• Save to Vault — downloads and indexes the paper if not already in your Vault
• Open in Reader — opens the paper in the Viewer panel alongside your Editor

Snippets

A snippet is a piece of text from a source — a sentence, a table, a passage — that you have saved and linked to its origin. Every snippet remembers exactly which PDF it came from and which page.

To create a snippet: open a PDF in the Reader, highlight text, and drag it onto the Editor. You will be asked to categorise it (Supporting, Methodology, Counterargument, etc.). The snippet appears in your manuscript as a citation that links back to the source.

PDF Reader

The Reader panel opens any PDF from your Vault alongside your Editor. The two panels are connected: a snippet you drag from Reader to Editor creates a permanent link — click the citation in your manuscript and the Reader scrolls to that exact sentence.

To verify any citation later: click the citation marker in your manuscript. The Reader opens the source PDF at the exact sentence. No more hunting through reference lists.

Snippets & Citations

Snippets are the granular unit of evidence in Zeteyn. They live in your Evidence Vault, each one linked to a specific location in a source document.

Inspiration snippets

Not all useful fragments come from sources you have uploaded. If you encounter a thought you want to keep but cannot yet attribute, use Save as Inspiration (available in the Chat right-click menu and the Editor right-click menu). Inspiration snippets are saved without a source link — a note to yourself rather than a citation. You can add a source link later.

Automatic detection

Zeteyn detects certain formats when you paste them and asks what you want to do:

• BibTeX block → automatic citation entry in your Vault
• SMILES notation (e.g. C1=CC=CC=C1) → opens the 3D molecule viewer
• URL to an academic paper → captured and indexed, asks if you want to add to Vault

Zotero Integration

If you already have a Zotero library, you do not need to re-upload anything. Connect Zotero once and your full library syncs into the Evidence Vault — including your annotations.

Your Zotero library is now available in the Evidence Vault. The AI can reference your annotations, and you can open any Zotero paper in the Reader panel.

The Editor

The Editor is where your manuscript lives. It works like a familiar word processor, with a few additions specific to research writing.

Modules

Your manuscript is divided into modules — sections like Introduction, Methods, Discussion. Each module is a separate file in the manuscript/ folder of your project. The Left Sidebar lists them in order. You can reorder, split, or merge modules from the sidebar.

The status bar

At the bottom of the Editor, a floating status bar shows your word count (total, current module, and selected text), the current language, and the connection status. It disappears when you start typing and reappears on hover.

Accepting AI suggestions

When the AI proposes an edit in Edit mode, a diff preview appears: additions highlighted, deletions marked. You can:

• Click Accept to apply all changes
• Click Discard to reject all changes
• Click individual changes in the diff to accept or reject them one by one

After accepting, the Editor scrolls to the first changed location, highlighted briefly. If you do not like the result, the Undo button on the toast notification rolls back to the checkpoint created just before the edit.

Command Palette

Press / anywhere in the Editor (at the start of a new line) to open the command palette. This inserts special content blocks into your manuscript.

You can also open the command palette with Ctrl Space.

Right-Click Menu

Select any text in the Editor or the Reader panel and right-click to see context-sensitive actions. These are the same actions you can request verbally from the AI — the menu is a vocabulary list, not the only way to trigger them.

Keyboard Shortcuts

Challenge Mode

Challenge mode reads your manuscript as a hostile peer reviewer would. It audits every claim, cross-checks your citations against what the cited papers actually say, constructs counterarguments, and produces a structured issue report. Use it before you submit — or before someone else does this to you.

Challenge mode also works on external papers. Load a paper into the Viewer panel, switch to Challenge, and ask Zeteyn to audit it. Useful for dissertation literature reviews, grant committee preparation, or systematic critique.

Respond Mode

When you receive reviewer or supervisor comments, Respond mode turns them into a structured checklist of manuscript changes and drafts your response letter alongside each revision.

Peer Review Mode

Peer Review mode is for producing a formal structured review of an external paper — the kind you would submit to a journal as a referee. It follows a four-step protocol and outputs in standard academic format.

The four-step protocol Peer Review runs: (1) full structural scan of the paper's argument arc, (2) statistical and methodological audit, (3) citation verification against known literature, (4) structured verdict with actionable recommendations.

Skills

A Skill is a set of instructions you give Zeteyn once, and it applies automatically to every session. Skills let you encode your journal's style guide, your lab's terminology, or your supervisor's known preferences — without repeating them every time.

Built-in Skills

Zeteyn comes with several Skills pre-installed and enabled by default:

• Statistical reporting — reminds the AI to flag incomplete statistics (missing sample sizes, confidence intervals)
• Citation format — applies your chosen style (APA, AMA, Vancouver, IEEE) to all citation suggestions
• Academic writing register — preserves appropriate hedging language and does not simplify technical terminology
• Manuscript structure guardian — warns before any restructuring that would break an argument chain

Creating your own Skills

Go to Settings → Skills → New Skill. The AI will ask you questions to build the Skill — what conventions does your journal require? What terminology does your lab use? What does your supervisor always flag? The Skill is saved as a file in your project's .zeteyn/skills/ folder and applied automatically in future sessions.

Data & Code Cells

Type /data in the Editor to insert a live Python code cell. It works like a Jupyter notebook cell embedded in your manuscript.

You can ask the AI to write or debug code in a cell: select the cell, switch to Edit mode, and describe what you need.

Molecules, Maps & Diagrams

3D Molecule Viewer

Type /molecule or paste a SMILES string anywhere in the Editor. A 3D molecular viewer appears inline. You can rotate and zoom the molecule. It exports as a high-resolution image in the final PDF.

TikZ Diagrams

Type /tikz to insert a TikZ diagram block. Write your TikZ code and it renders in real time. The output is a vector graphic — it scales perfectly for any journal page size.

Geospatial Maps

Type /map to insert an interactive map layer. Connect a data source or draw regions manually. Useful for studies with geographic dimensions.

Equations

Standard LaTeX equation syntax works inline and in display mode. Type $...$ for inline equations, $$...$$ for display equations. They render immediately as you type.

Remote Lab Connection

If your simulations or data processing runs on a lab server or HPC cluster, you can connect to it from Zeteyn and pull results directly into your project.

New simulation outputs appear in your Vault as soon as they are generated. You can then open them in the Viewer, reference them in a code cell, or insert them into your manuscript directly.

Showroom & Formatting

The Showroom is a preview of your manuscript in a specific journal's layout. It is not the editor — it is a read-only preview that shows you exactly how your manuscript will look when exported.

Switching templates does not change your manuscript content — only the presentation. You can switch between templates as many times as you like and export the same manuscript in multiple formats.

Export Options

Export your manuscript from the Showroom or from the File menu. Available formats: