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Working with Files, Folders, and Workspaces

Upload files, organize your workspace, and add sources from search. A complete guide to files and workspaces in Ubik.

•Ubik Team
Working with Files, Folders, and Workspaces

Ubik Studio is built around a simple idea: your research lives in folders on your computer. Workspaces are those folders—self-contained projects you can create, organize, and work from with Ubik's AI agents. This guide walks through what a workspace is, how to create one, how to add files, and how notes and annotations work so agents can help you effectively.

What Is a Workspace?

A workspace is a centralized hub for organizing your research. It holds everything for a project in one place: folders, documents, sources, and saved searches. Ubik treats it as a single context so agents know which sources to use when you prompt them.

Ubik Studio sidebar showing folders, documents, searches, quick actions, and Context Indexed status

What it contains:

  • FOLDERS — Your file hierarchy. Create folders, nest subfolders, and organize PDFs and documents however you like. Each folder can hold papers, drafts, and project-specific materials.
  • SOURCES — Individual documents you've added as references, such as research papers or articles.
  • DOCUMENTS — UDOCs (editable documents with citations) and other written outputs.
  • SEARCHES — Saved USRCH expeditions (academic and web searches) you can return to.

When content is ready for AI use, you'll see Context Indexed at the top—a green banner indicating that your workspace has been processed and agents can search, cite, and reason over it. Workspaces let you separate projects; agents use @ references to pull in only the relevant files and folders for each task.

Creating a Workspace

You can create a workspace in two ways: from an existing folder or from scratch.

Ubik Studio Workspaces view with + New dropdown showing Create Workspace and Import options

From the sidebar:

  1. Click + New at the top of the sidebar.
  2. Under CREATE WORKSPACE, choose:
    • From Folder — Open an existing folder on your computer as a workspace.
    • New Workspace — Start from scratch with an empty workspace.
  3. Under IMPORT, you can also bring content in directly:
    • Import from Computer — Select PDF files from your device.
    • Import from Zotero — Browse your Zotero library and add papers.

You can also drag and drop files, folders, or start chatting to create a workspace. Your saved workspaces appear in the sidebar with file counts and last-accessed times.

Set up your new workspace:

Set up your new workspace modal with Name, Folder, and Add Description

When creating a new workspace, a modal appears where you can:

  • Name — Give your workspace a clear name (e.g. "Untitled Strawberry"). The folder will match this name by default.
  • Folder — The location where the workspace will live on your computer.
  • + Add description — Optionally add a description for context.

Click Create Workspace when you're ready. You can rename or reorganize this workspace anytime.

Uploading Files and Folders

Getting documents into Ubik is straightforward:

  • Import from Computer — Click + New → Import from Computer to select PDF files from your device.
  • Import from Zotero — Click + New → Import from Zotero to browse and add papers from your Zotero library.
  • Drag and drop — Drag files or folders directly into the sidebar or main area.
  • From Folder — Open an existing folder as a workspace; all files inside become part of it.

Ubik supports PDF, DOCX, and Markdown, and we're adding more formats regularly. Once added, files are stored locally and become part of your workspace, accessible in the sidebar file-tree at any time. You can reference them using the @ symbol when prompting Ubik agents.

Sidebar file management: In the sidebar you can drag and drop files and folders, create new folders, and organize and rename items. The sidebar is the main place for managing everything in your workspace.

Examples: Notes and Annotations

Ubik supports both agent and human note-taking. Notes are tied to highlights and page references, making it easy to collect evidence and build arguments.

Document viewer with Notes and Figures tabs, highlighted text, and evidence note with page references

Agent note-taking: Ubik agents can add notes to PDFs—highlighting text, annotating passages, and linking summaries to specific quotes. Each note is tied to a highlight and page reference (e.g. pp. 1, 5, 7, 8). Notes can be categorized (e.g. "evidence: Task-Dependent Contamination Effects") and include citations. For more on how agents annotate, see How to Take Notes with Ubik Agents.

Human note-taking: You can also annotate manually. Select text, add your own notes, and highlight sections you care about. Ubik encourages a mix: agents handle bulk annotation, and you add judgment where it matters.

The Notes tab shows all notes for the current document, with counts (e.g. "Notes 5", "Figures 8"). The Figures tab surfaces extracted figures. Use All Notes in the sidebar for a global view across the workspace.

Adding Sources from Search

If you've found papers through Ubik's academic search (USRCH), you can save them straight into the active workspace. Papers download to your local folder and appear in the sidebar, where agents can reference them in chat. For more on search, see Search, Save, and Analyze Papers with USRCH.