Research Mode (Cafes)

Overview

Research Mode ("Cafes") is a standalone research feature where you create independent research workspaces, gather material from multiple sources, and curate findings for use in your Scribes. Available to all tiers — Free users can access Research Cafes using their token balance.

Getting Started

1. Click Research in the navigation bar
2. Click + New Cafe to create a research workspace
3. Name your Cafe (e.g., "Climate Research", "AI Startups")
4. Start searching and gathering research

Research Sources

AI Web Search

Type a search query with the AI Web toggle selected. The AI searches the web, synthesizes findings, and presents a formatted response with inline citation links and a numbered Sources section at the bottom. Cost: a small portion of your allowance per search (varies by model). The per-action estimate is shown before you confirm.

Web search works with all models — not just Perplexity Sonar. The AI receives real-time web results regardless of which model you select.

Academic Papers

Click the Academic dropdown to choose from three academic search sources:

• OpenAlex — Search 250M+ works across all disciplines. Includes citation counts. Free, open-access metadata.
• arXiv — Search preprints in physics, mathematics, computer science, and related fields. Includes direct PDF links.
• PubMed — Search 35M+ biomedical and life sciences articles from the NCBI database.

Which database should I use?

Results show paper title, authors, year, citation count (where available), and abstract. Each paper card shows relevant links (DOI, arXiv ID, or PMID). You can:

• Analyze — Send the paper to AI for analysis (Key Findings, Methodology, Compare, ELI5, or custom prompt)
• Add Raw — Save the paper's abstract directly to your Cafe without AI processing
• Dismiss — Remove individual papers from results

The Analyze and Add Raw flows work identically regardless of which academic source you use.

YouTube Transcripts

Paste a YouTube URL and the search bar auto-detects it, showing a "YouTube Transcript" badge. Before extraction, a modal lets you choose:

• Content only — Extract just the transcript
• Summarize, Key Points, Fact Check, Topics & Structure — Extract and analyze in one step
• Custom prompt — Ask anything about the video

You can select multiple options at once.

URL Scraping

Paste any article URL (including www. addresses) and the search bar auto-detects it, showing a "Scrape URL" badge. Same modal options as YouTube — extract content only, or extract and analyze.

Add Multiple Sources at Once (Batch Import)

Pasting two or more sources into the search bar at once triggers the batch import modal automatically — no separate button to find. The bar's placeholder reads "AI web search, YouTube URL, article link — or paste multiple sources at once" as a reminder.

How it works:

1. In the search bar, paste a list of links and/or queries — newline-separated, comma-separated, or just whitespace-separated.
2. As soon as the parser detects 2+ items, the "Add multiple sources at once" modal opens, pre-populated with what you pasted.
3. Each item shows its detected type (Web Search / YouTube / Article / OpenAlex / arXiv / PubMed) with an icon and a per-item token cost. The footer shows the total source count and total cost estimate.
4. Click Run all — items are dispatched to the correct backends with a concurrency cap of 3 (so we don't burst-rate-limit Apify or OpenRouter) and a 1.5s stagger between launches.
5. Each row updates live: Pending → In progress → Done ✓ / Failed ✗. A retry counter appears next to in-progress rows when transient failures (502/503/timeout/Apify/network) trigger an automatic retry.
6. After the batch completes, a summary banner shows how many succeeded, how many failed, how many tokens were charged. Failed items can be retried with one click; sibling successes are not re-run.

Mixed input examples:

Type-hint prefixes (case-insensitive — useful when you want to force a specific backend instead of relying on auto-detect):

• arxiv: pubmed: openalex: academic: — academic backends
• web: search: — force web search (handy when a query happens to look like a domain)
• youtube: yt: — force YouTube (rarely needed; auto-detect handles the common YouTube URL forms)
• url: scrape: — force URL scraping

A line that starts with one of these prefixes is treated as a single item even if it contains spaces (e.g. arxiv: deep RL for robotics is one query, not three).

Tier limits:

If you paste more than the cap, the extras are dropped and an amber "Capped at N items per batch" hint appears. The modal still runs the items it kept.

Failure isolation and retries:

• One bad URL (404, 502, Apify timeout) does not stop sibling items.
• Each item retries up to 3 attempts automatically on transient failures (5xx, 429, timeout, network, Apify-shaped errors). 4xx errors and "no papers found" fail immediately.
• The summary banner is colour-coded: green (all succeeded), amber (partial), red (none succeeded). Failed items can be re-run via the Retry button — successes are skipped.
• The modal blocks accidental dismiss (Escape, click-outside) only while the run is in flight so you don't lose progress mid-batch. After the run completes, you can close it normally.

Cancelling mid-batch: click Cancel. In-flight items are allowed to complete (the server has already done the work and may have already billed for them); pending items are dropped at no charge.

Cost: the same per-item fees as the single-input bar — see the Token Costs table below. The total at the bottom of the modal is the sum of every parsed item's per-type fee, computed before you click Run all.

Ask AI (on any saved source)

Every saved research source has an Ask AI button. Click it to open the analysis modal and run AI analysis on any previously saved content — web search results, transcripts, scraped pages, uploaded documents, or imported notebook entries.

The Serving Tray

The right panel is your Serving Tray — a curated collection of the most useful snippets from your research.

Adding to the Tray

• Highlight text in any research result → floating toolbar appears → "Add to Tray"
• Add to Tray button on each source card adds the full content
• Import from Notebooks brings in highlights and notes from your Scribes

Managing Tray Items

• Drag to reorder items
• Click to expand/collapse (items show 5 lines by default)
• Edit notes on any item
• Delete with undo (5-second window to restore)

Source Provenance

Each tray item shows a small label indicating where it came from — for example, "Web: coffee brewing methods" or "YouTube: How espresso works". Items you created manually show "Manual note". This helps you track the origin of each snippet, especially when combining research from multiple sources. The same labels appear in the Workspace Cafe Trays tab and the import modal.

When you import tray items into a Scribe section, the source attribution line includes the original source query and URL (when available), formatted as: Source: {Cafe name} . {query} . {url}.

Editing Tray Item Text

Click any tray item's text to edit it inline. A textarea opens where you can modify the content directly. Press Ctrl+Enter (or Cmd+Enter on Mac) to save, or Escape to cancel without changes. Each tray item supports a generous character limit per note — long enough for substantial excerpts.

Adding Notes

Click the + button in the Serving Tray header to create a blank note. This is useful for pasting in content from external sources that aren't covered by the built-in search and scraping tools, or for writing your own observations and annotations alongside your research.

Combining Items

To merge multiple tray items into one:

1. Click the Select toggle in the Serving Tray header to enter selection mode
2. Use the checkboxes to select two or more items you want to combine
3. Click the Combine button that appears
4. The selected items are merged into a single item, separated by horizontal rules (---)
5. An Undo option appears for 5 seconds in case you want to reverse the merge

Combining is useful for assembling related excerpts from different sources into one consolidated reference.

Using Tray Content

Tray items are ready to use in your Scribes, Notebooks, or Workspace. In the Workspace, the Cafe Trays tab lets you browse and paste tray items directly into sections.

Choosing a Model

The model selector appears below the search bar, next to the cost estimate. Your selected model is used for all AI operations — web search, paper analysis, and Ask AI.

• Free + Pro are locked to the curated CoffeeScribe Model (no picker shown)
• Creator unlocks the full picker — CoffeeScribe Model recommended at the top, ~12 curated alternatives, then a collapsed advanced disclosure for the full 350+ catalogue (at your own risk)

Each result card shows which model was used, how many tokens were charged, and whether web sources were found. Different models produce different quality results — experiment to find what works best for your research topic.

Q&A Chat (Ask Your Cafe)

Once your Cafe has research sources or tray items, a chat bubble appears in the bottom-right corner. Click it to open the Q&A panel and ask natural-language questions across all your collected research.

How It Works

Your research is automatically processed into searchable chunks using local embeddings — no data leaves the server. When you ask a question, the system finds the most relevant passages from your sources and tray items, then sends them to the AI along with your question to generate a grounded answer.

The chat bubble appears as soon as you add your first source. While your sources are being processed for search, a spinner indicates that embeddings are in progress. You can still browse your research — the Q&A will be ready in a few seconds.

Asking Questions

1. Click the chat bubble (bottom-right)
2. Type your question and press Enter (or click Send)
3. The AI answers using only your Cafe's research, citing sources as numbered references like [1], [2]
4. Click any citation badge to scroll to the original source in your Cafe

Filtering Sources

By default, Q&A searches across all sources and tray items in your Cafe. To query only specific items:

1. Click the filter icon (funnel) in the Q&A chat header
2. Checkboxes appear on all sources and tray items
3. Select the items you want to include in your query
4. An indicator shows "Querying N of M sources"
5. Ask your question — the AI will only search the selected items

To return to querying everything, deselect all items or click the filter icon again. When no items are selected, Q&A automatically searches all sources.

Conversation Context

The chat maintains conversation history within a session. Follow-up questions can reference earlier answers — for example, "Tell me more about point 3" or "How does that compare to the other study?"

Click Clear Chat to permanently delete all Q&A history and start fresh. This cannot be undone.

Actions on Answers

Each answer has action buttons:

• Copy — Copies the answer with a full reference list appended
• +Tray — Save the answer to your Serving Tray
• +Source — Save as a new research source
• +Notebook — Save to your Notebooks as a free note
• Delete — Remove a single Q&A entry

Editable Source Titles

Double-click any research source title to rename it. This helps you organise your sources when the auto-generated titles aren't descriptive enough. Tray items can also have custom titles.

Embedding Costs

Each research source and tray item is automatically chunked and embedded when created. This is a small one-time cost per item, broken into chunks of a few thousand characters each. The per-action estimate is always shown before you confirm.

Model

Q&A uses Gemini 2.5 Flash — a model chosen specifically for its ability to follow strict instructions and answer only from provided context. This is separate from the model you select for web search and analysis.

Sharing a Cafe

You can share any Cafe with other Coffeescribe users via a read-only link.

Enabling Sharing

1. Open a Cafe and click Share in the toolbar
2. Toggle Enable sharing on
3. A share URL appears — click Copy to copy it to your clipboard
4. Send the link to anyone with a Coffeescribe account

What Viewers Can Do

Viewers who open your shared link can:

• Browse all your research sources and their content
• Read your Serving Tray items
• Ask Q&A questions about your research (using their own tokens, not yours)
• Copy text from sources and tray items

What Viewers Cannot Do

Viewers cannot search, add sources, modify tray items, delete anything, or save Q&A answers to your Cafe. All edit controls are hidden. Read-only access is enforced at the database level.

Q&A on Shared Cafes

Viewers can ask Q&A questions in your shared Cafe. Their questions use their token balance (not yours), and their Q&A history is session-only — it is not saved to your Cafe and disappears when they close the page.

Revoking Access

Toggle sharing off in the Share dialog to immediately disable the link. Anyone with the old link will be redirected away.

Regenerating the Link

Click Regenerate link to create a new share URL. The old link immediately stops working. A confirmation dialog warns you before regenerating.

Share Indicator

Shared Cafes show a small share icon next to the cafe name on the Research listing page, so you can easily see which Cafes are currently shared.

Auto Research

Let an AI agent research a topic for you across all available tools automatically.

How to Use It

1. Click the Auto button in your Cafe toolbar
2. Enter your research topic and any extra instructions
3. Select which output types you want (Key Findings, Best Quotes, Most Up-to-Date Info, Summarize Results, Contradictions & Gaps)
4. Choose your tools (Web Search, Academic, YouTube, URL Scraping — all enabled by default)
5. Pick a depth level and set a token budget, then click Start Research

The agent creates a research plan, executes it step by step, and synthesizes curated findings into your Serving Tray.

Depth Levels

Live Progress

While the agent runs, you see a live progress log showing each step (which tool, what query), running token cost, and a Stop button. Sources appear in your Cafe as they're found.

Agent-Generated Tray Items

After research completes, the agent synthesizes findings into tray items based on your selected output types. These are marked with a robot icon so you can distinguish them from your own curated items. You can edit, delete, or build on them like any tray item.

Budget Control

You set a token budget before starting. The agent stops when approaching your limit and synthesizes with whatever it has gathered. You can also click Stop at any time — sources already found are kept.

Auto Research is available for all tiers. Free and Pro use the curated CoffeeScribe Model; Creator users can choose a different model from the picker.

Other Features

Notebook Import

Click Import in the Cafe toolbar to bring in highlights and notes from any of your Scribes. Choose to import as Research Material (left panel) or directly to the Tray (right panel).

Document Upload

Click Upload to add PDF, DOCX, TXT, or MD files (up to 5 MB) as research sources.

Deleting Sources

Hover over any research source to see the delete button. Deletion includes a 5-second undo window.

Token Costs

All costs are deducted from your token balance. The per-action estimate is always shown before you confirm so you know what you're spending.

Availability

Tips

• Create multiple Cafes for different topics — one Cafe per research project
• Use Academic search for scholarly sources — try OpenAlex for broad coverage, arXiv for preprints, or PubMed for biomedical literature
• YouTube transcripts are great for extracting key points from lectures and interviews
• Combine sources — search the web, find papers, scrape articles, then curate the best bits on your Tray
• Ask AI on anything — the Ask AI button works on every saved source, so you can re-analyze content with different questions
• Multi-select presets — when analyzing YouTube or URLs, select multiple presets (Summarize + Key Points) to get several analyses at once
• Add Notes for external content — use the + button to paste in material from sources outside Coffeescribe (emails, documents, other tools)
• Combine related items — merge excerpts from different sources into a single consolidated reference before pasting into your Workspace
• Edit tray text freely — click any tray item to refine wording, trim irrelevant parts, or add your own annotations inline
• Ask your Cafe — once you have research, use the Q&A chat bubble to ask questions and get referenced answers grounded in your collected material
• Filter Q&A sources — click the funnel icon in the Q&A header to query only specific sources instead of your entire Cafe
• Save Q&A answers — save useful answers back to your Tray, as new sources, or to Notebooks for use in your Scribes
• Rename sources — double-click any source title to give it a more descriptive name
• Share your research — use the Share button to send a read-only link to collaborators. They can browse and ask Q&A questions using their own tokens
• Paste a reading list in one go — got a tab-soup or a notes-app dump of links? Paste the whole blob into the search bar and the batch import modal opens automatically (Free 5 / Pro & Creator 50 items per batch). Way faster than feeding them in one at a time.