Frequently Asked Questions

Transparent Lab is a private research library in the cloud, powered by AI and designed specifically for biomedical and scientific research. Upload papers you already have access to, and the system indexes the knowledge they contain within your private space. Ask complex questions and receive evidence-based answers with proper citations—every claim traces back to specific passages in your own library.

Create an account, complete your research profile (this helps personalize your experience), upload your first document (PDF or EPUB), and start asking questions. The system will search your library, find relevant passages, and synthesize answers with proper citations.

We support PDF files (the most common format for scientific papers), EPUB files (e-books, theses, longer reports), and HTML from open-access URLs (PubMed Central, bioRxiv, etc.).

Absolutely. While optimized for scientific literature, you can upload research papers, textbooks, theses, technical reports, review articles, grant proposals, and any text-based document you want to query.

Citations appear as [1.1], [1.2], [2.1], etc. The first number indicates which document, the second indicates which passage within that document. Click any citation to see the exact source text and navigate to that location.

Yes. When you ask a question, the system searches for relevant text passages and relevant figures based on their captions. Matching figures appear alongside your answer, so you can see the original data visualization without hunting through PDFs.

@deepdive activates comprehensive source analysis for thorough, well-evidenced answers. @short provides brief, to-the-point answers for quick fact lookups. @explore searches external scientific databases (OpenAlex or PubMed) to discover papers beyond your library.

When you upload papers, the system identifies important entities (genes, proteins, drugs, diseases) and enriches them with data from authoritative databases: UniProt, PubChem, MeSH, and NCBI. This context appears alongside your answers.

The document is processed entirely within your private library. The system extracts text (including multi-column layouts), identifies metadata (title, authors, DOI), extracts tables and figures, creates a searchable index, and generates a structured summary with key findings, methods, and important entities. This typically takes 1-3 minutes.

Use hashtags. Type # followed by a tag name when viewing a document (e.g., #neuroscience, #clinical-trial, #methods-reference). Then filter your questions to specific documents using the same hashtags in your queries.

Yes. The system handles documents of all sizes, including review articles, book chapters, theses, and technical manuals. For very long documents, it uses intelligent chunking that processes in sections while preserving context and coherence.

Navigate to the main paper, click "Add Supplement," and upload the supplementary PDF. The supplement content becomes searchable alongside the main paper, so you won't miss details tucked away in supplementary materials.

Groups allow research teams to collaborate within a shared private library. Share documents, pool quotas, and ask questions across your team's combined collection. Only team members can access the group's documents—the same privacy isolation applies at the team level.

Go to Settings > Team and click "Create Team." You'll become the group owner with the ability to invite others. Enter email addresses to send invitation links valid for 7 days.

Yes, team members can leave at any time through Settings > Team > Leave Group. Note that documents you uploaded remain with the group. Group owners must transfer ownership before leaving.

Only you. Every user gets an isolated private library—your documents are never visible to other users, and there is no shared corpus across accounts. If you're in a group, team members can see the group's shared documents, but no one outside the group can. We don't aggregate, pool, or access your content.

No. Your documents and conversations are processed within your private space and are never used to train any AI models. We don't use your content for any purpose beyond providing the service to you.

Yes. You can delete individual documents at any time, clear your chat history, export your data, or delete your account entirely. When you delete a document, its content and all derived data (index entries, extracted figures, summaries) are removed from your library.

Basic (free): 10 documents/month, 5 messages/day, 500 MB storage. Individual ($10/month): 50 documents/month, 20 messages/day, 2 GB storage, book processing, deep analysis. Group Leader ($50/month): 500 documents/month, 200 messages/day, 20 GB storage, shared library, team invitations.

You'll see a notification when approaching limits. Upload limits reset on the 1st of each month. Message limits reset daily at midnight UTC. For storage limits, delete unused documents or upgrade your tier.

Visit Settings > Account to see documents uploaded this month, messages sent today, storage used, and remaining quotas.