User Guide

Use this guide to choose a workspace, write with AI, prepare a scientific paper, and manage your work. Start with the first walkthrough or jump to a task below.

1. Get started

Open Cothyra and use one of the sign-in options offered on the page. New accounts receive a one-time grant of 500 AI credits. Reading and writing are free; AI requests use credits.

Choose a workspace in the library: a book for chapters, a daily journal for dated notes, or a LaTeX project for a paper.
Open or create a document and write a few lines. In a book, try a heading, a paragraph, and an equation.
Open the assistant, choose a model, and ask a specific question about the document. For example: “Explain the assumption in this paragraph before changing it.”
Review the answer or proposed changes. Continue editing, or undo a change you do not want.

On desktop, navigation, your document, and chat can sit side by side. On smaller screens, switch between the panels using the bottom navigation.

2. Choose and organize a workspace

Books: organize longer work into a table of contents and chapters. Keep outlines, research material, and working notes outside the manuscript in the notes area. You can also import a book from a Git repository using the library’s import flow.
Daily journals: create a journal, then choose Today to open or create today’s entry. Earlier entries are grouped by month. Opening a journal alone does not create an entry.
LaTeX projects: keep TeX sources, bibliography files, and figures together with a compiled PDF preview. See the LaTeX walkthrough.
Use the workspace’s Info settings to describe its purpose and audience. Link related workspaces when you want the assistant to consult them; see connections and related work.

3. Write and edit

Book chapters and daily entries use a rendered Markdown editor. Click into a block to edit it in place; the surrounding document stays readable.

Type / at the start of a line to open the block insert menu. Drag block handles to rearrange content, and use the outline to jump between headings.
Select text for formatting or an AI action such as Explain. In tables, click a cell to edit it and use row or column handles to rearrange the table.
Write inline math with $…$ and display math with $$…$$. Equation rendering in a Markdown chapter is separate from compiling a full LaTeX project.
Use citations such as [@key] with your book’s reference list. Footnotes, syntax-highlighted code, and task lists are also supported.
Paste or drop images into the page. Use drawing tools for pen sketches and editable vector diagrams; Mermaid and JavaScript render blocks can add diagrams and interactive figures. Some figures need libraries or network access, so do not assume every figure works offline.
Your edits and the assistant’s document edits share an undo history that survives reloads. Use Undo to step back through document changes. This does not reverse an external action such as publishing a link or pushing to GitHub.

4. Work with the AI assistant

Give the assistant a clear task and check the context beside the message before sending. “Explain this derivation” and “Rewrite this derivation in the chapter” request different actions.

You can ask app questions directly in chat, such as “How do I import from Overleaf?” The assistant can look up this guide and link to the relevant steps. Help explains the workflow; it does not change your settings for you.
Choose a model per conversation. Available models and rates are shown in the app; different sessions can use different models. Start a separate session for a different line of work, or branch from an earlier message to explore an alternative.
Expand context chips to inspect the document, selection, or location associated with your message. Use the context picker or # mentions to add material, and remove optional attachments you do not need.
The current-view chip distinguishes location information from the full document body. Unchecking its body does not remove the location marked “Always sent” or prevent the assistant from reading files through its tools.
Attach images when using a model that supports vision. The attachment controls indicate when the selected model cannot accept images.
Check Settings → Permissions to choose which tool categories require approval, including edits, deletion, reorganization, Git actions, and image generation. Approval behavior depends on these settings; not every action always prompts.
Inspect proposed changes and tool results as the assistant works. Use Stop to interrupt an active response, then review any edits already made.

5. Research, citations, and study

Ask the assistant to search for sources, compare findings, or check a claim. Research tools can search the web and scholarly sources such as arXiv, OpenAlex, Crossref, and Wikipedia.
Ask for citations and a reference entry alongside an explanation. Open the cited source and check that it supports the claim before relying on it in a paper.
In chat, type / to see the skills available for the current workspace. Book skills include research, verification, expansion, quizzes, and review by a panel of models. The chat skill menu is separate from the editor’s block insert menu.
For a focused study session, select a passage, ask for an explanation, then ask for questions that test your understanding. Save the explanation or study notes where you want them in the workspace.
Research and multi-model reviews may make several AI calls. Check Usage to understand the cost of a longer task.

6. Write a LaTeX paper

A LaTeX project has its own source editor, PDF preview, and assistant. Use it for papers, theses, and technical reports that need a TeX build; use the book editor when you prefer rendered Markdown.

In the library, create a LaTeX project. Start from a template, import a ZIP (including an Overleaf project download), or import a Git repository.
Open the main TeX file. In the project’s Info settings, check the main file, bibliography setting, and engine: XeLaTeX, pdfLaTeX, or LuaLaTeX.
Edit the source with completions. Choose Compile/Recompile, or use Ctrl/Cmd+Enter in the source editor. Enable automatic compilation if you want builds to follow edits.
Inspect the PDF and build status. Open the errors or log panel when compilation fails; error entries link to the source. A PDF may still be visible from an older successful build, so check for a stale-output warning.
Use the source editor’s PDF navigation action to locate the current line in the output. Double-click a position in the PDF to jump back to its source through SyncTeX.
Ask the assistant to help revise the source or investigate a compile error. It can compile and, with a suitable model, inspect rendered pages. Review the result and build status before downloading.
Download the PDF or the project archive. Keep the source archive when you need to continue editing or submit source files.

A book can also be exported to LaTeX without becoming a LaTeX workspace. These are separate workflows: exporting converts the book; a LaTeX project lets you work directly with TeX files.

7. Listen and ask by voice

Use the chapter’s headphones control to start narration. Choose Verbatim for the written text, Faithful for a version smoothed for listening, or Summary for a shorter account.
Choose voices, engines, and narration preferences in Settings → Voice. Playback speed is adjustable. Voice synthesis and generating a narration script are separate steps; a free voice does not necessarily make every AI step free.
Mathematical notation is converted into spoken explanations. Follow the text when you need to check exact symbols or equations.
Use voice input to ask a question while listening. Microphone permission and speech support depend on your browser and selected input engine.
The mini-player lets you control playback while moving around the app. Keep your attention on your surroundings when listening away from your desk.

Use Export to choose the current page or whole book and download PDF, Word (.docx), or LaTeX. Review the format options before exporting. You can also print.
Check the exported file before sharing it. Interactive figures become a static result in print-oriented formats; a PDF cannot preserve dragging or other browser interactions.
LaTeX projects offer their own PDF and source-project downloads in the preview pane.
Use sharing controls for a workspace, an individual file, or a chat session where available. Check the scope of the public link before sending it; public readers do not need an account.
Settings → Sharing lists your public links and lets you manage them. Revoke a link when you no longer want that material publicly accessible.
For a complete account export, use Settings → Account.

9. Connect tools and related work

In Settings → Connections, inspect the services available on your installation. Connect only the account and scope you need; you can disconnect later. A connected account does not imply that every action offered by that service is available in the assistant.
With GitHub connected and the appropriate repository permissions, the assistant can help push source files to a repository. Review the destination and Git approval settings first.
Link related workspaces from the current workspace’s Info settings. This gives the assistant a way to consult related material without copying everything into one document.
Advanced users can register a bridge in Connections to expose tools from a machine or network they control. Follow the setup instructions shown there, enable the intended tools, and attach the bridge to the workspace that needs it. The bridge must be online for those tools to work.
After connecting Google Drive, open the file explorer in any workspace. Expand Google Drive to browse folders, or search your Drive by text. Click a file for a read-only preview; PDF files open in the built-in viewer (up to 50 MB); use Open in Google Drive for other formats. Google Docs and Slides export as text; Sheets preview the first sheet as CSV. Text previews are limited to 10 MB and 100,000 characters. You can also ask the assistant “Find my Google Drive notes about X” or “Summarize this Google Drive document” with its link. Files remain in Drive; this connection does not edit or delete them.
Connect a Zotero API key with personal-library read access in Settings → Connections. In the file explorer, expand Zotero alongside Linked workspaces, Connected bridges, and Google Drive. Browse collections, search titles/authors/years, and open references to read metadata and abstracts or show BibTeX. In chat, ask “Find my Zotero references about X” or “Get BibTeX for this reference.” Open a reference and select a PDF attachment to view it in the app (up to 50 MB). Standalone PDF attachments open directly. PDFs must be synced to Zotero Storage; local linked files and WebDAV-only files are unavailable through this connection. Group libraries are not included. Chat tools currently read reference metadata, not PDF contents.

10. Credits and usage

Reading and writing are free. AI work uses credits at the rates shown in the app. A credit represents $0.01; the actual cost depends on the model, usage, and the tools involved.
The 500 signup credits are a one-time grant. Some premium models require purchased credits; the model picker indicates restrictions.
Open Settings → Billing to check your balance and payment records. When purchasing is enabled, Add credits opens checkout. Review the price and any taxes there.
Settings → Usage shows spending and token usage by time, model, and workspace. A research task, narration request, or multi-agent turn may contain several billable calls.
For refunds, use the available payment controls or contact support. The Refund Policy contains the applicable terms.

11. Settings, sync, and your data

Settings contains appearance, editor, language, voice, AI, and permissions preferences. Workspace-specific Info settings describe that workspace; account settings apply more broadly.
Documents save as you work. Cached content can remain usable during a connection interruption, but AI, server compilation, and uncached files need a connection. Browser storage is not a substitute for a backup.
Watch save or sync indicators. If a conflict appears, inspect the choices before keeping your version or the server’s. Avoid clearing browser storage while changes are still unsynced.
Settings → Account → Download my data creates an archive of your account data and library files. Keep a downloaded copy before a major migration or account deletion.
Settings → Account also contains Delete account. Read the confirmation and the Privacy Policy for deletion and retention details.
AI requests send the relevant prompt, context, and tool results to the selected model’s provider. Context chips help you inspect a message, but are not an access restriction on workspace tools.

12. Troubleshooting and help

The assistant is using the wrong material: expand the message’s context chips, check the open document and attached files, and state the intended scope. Start a separate conversation when the topic changes.
A request is waiting: look for a tool-approval prompt. For a model or credit error, check the selected model and Billing before retrying.
The PDF is unchanged: check whether compilation succeeded, whether the preview is stale, and whether the correct main file and engine are selected. Open the build errors or log.
Changes have not synced: restore the connection and inspect the save state or conflict notice. Keep a copy of unsynced text before refreshing or clearing storage.
Voice input or playback fails: check microphone permission, the chosen engine, and whether the browser requires a tap to start audio.
An export or public link looks wrong: confirm its scope and inspect the downloaded file or link in a signed-out browser.

Use the in-app feedback form or email [email protected]. Include what you were doing, what you expected, and the exact error text. For a LaTeX issue, include the engine and relevant build-log excerpt.