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This guide walks you through creating your first task, understanding the interface, and working with results.

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Creating a Task

When you first log in, Biomni Lab opens a Quick Task by default so you can start working right away. You have two options for creating new analyses:
  1. Click the + Create button in the sidebar
  2. Select Quick Task
  3. You’ll be taken directly to a new chat session
Quick Tasks are ideal for one-off analyses or exploring Biomni Lab’s capabilities.
Creating a Quick Task from the sidebar menu

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Using Workflow Templates

Workflow templates provide pre-built analysis workflows curated by the Biomni Lab team:
  1. Click the + Workflow button in the chat input area, or look for suggested templates displayed in the chat
  2. Browse templates by category or search for specific workflows
  3. Click on a template to see what it does
  4. Click Use Template to apply it to your task
  5. Provide the required input files when prompted
Workflow templates with + Workflow button in chat input
Templates include optimized parameters for common use cases. You can ask Biomni Lab to adjust parameters after applying a template.

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Submitting a Request

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Writing Your Request

Type your analysis request in the chat input at the bottom of the screen. Be specific about:
  • What you want to accomplish
  • Which files to use (reference them with @)
  • Any specific tools or parameters

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Using @ Mentions

Reference files and resources directly in your message by typing @: 
Align @sample_R1.fastq.gz and @sample_R2.fastq.gz to the human
genome using @STAR, then quantify gene expression
When you type @, a dropdown menu appears with:
  • Files: Your uploaded files
  • Databases: Reference databases like UniProt, NCBI
  • Tools: Bioinformatics tools like BLAST, STAR
  • Packages: R/Python packages like DESeq2, Seurat
@ mention dropdown showing files, databases, tools, and packages

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Attaching Files

Click the paperclip icon to attach files to your request:
  1. Click the paperclip icon in the chat input
  2. Choose your source:
    • From Computer: Select files or folders from your local machine
    • From Biomni Lab: Choose from files you’ve already uploaded to Biomni Lab
  3. Files appear as attachments in your message
  4. Submit your request
You can upload entire folders at once—useful for paired-end reads or multi-sample datasets.

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Understanding the Response

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Startup Time

After submitting a request, Biomni Lab begins processing. You’ll see:
  1. Planning phase: Biomni Lab analyzes your request and creates an execution plan
  2. Initialization: Resources are allocated (this may take a few moments for complex analyses)
  3. Execution: The analysis runs with real-time progress updates
Initial startup may take 10-30 seconds as Biomni Lab prepares the computational environment. Subsequent requests in the same session start faster.

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The Execution Trace

As Biomni Lab works, you’ll see a trace of its actions in the chat:
  • Thinking: Biomni Lab’s reasoning about how to approach your request
  • Tool calls: Commands being executed (alignment, analysis, etc.)
  • Results: Output from each step
  • Status updates: Progress indicators for long-running operations
Execution trace showing thinking, tool calls, and results
Click on any trace step to expand it and see more details.

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Working with the Workspace Layout

Biomni Lab uses a three-panel layout to organize your work.

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The Three Panels

  • Chat Panel (Left): Your messages, Biomni Lab’s responses, and trace sections
  • Center Panel (Middle): File previews, artifacts, and expanded module views
  • Modules Column (Right): Plan, Results, and Notes stacked vertically

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Working with Modules

The right column contains three key modules:
  • Plan: View the analysis workflow steps and progress
  • Results: Browse and download generated files
  • Notes: Add session notes and documentation
Layout showing Plan, Results, and Notes modules
Click any module to expand it in the center panel for a larger view.
Use the Layout button in the chat header to toggle which modules are visible.

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Viewing and Downloading Results

Results appear in two places:
  1. In the chat: As openable artifacts you can click to expand
  2. In the Results module: All generated files from your session

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Working with Result Files

Each result file has several actions available:
  • View: Click on any file to open it in the right panel for a full preview
  • Download: Click the download icon to save the file to your computer
  • Find source: Click to jump to the trace step that created this file

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Follow-up Requests

Continue the conversation to refine your analysis:

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Iterating on Results

The volcano plot looks good, but can you:
- Increase the font size
- Add gene labels for the top 10 significant genes
- Change the color scheme to blue/red

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Building on Previous Analysis

Reference earlier results in your follow-up: 
Using the differentially expressed genes from the previous analysis,
run GO enrichment analysis for biological processes

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Suggested Follow-up Questions

After completing an analysis, Biomni Lab generates suggested follow-up questions to help you explore your results further. These appear as clickable suggestions below the response:
What are the top upregulated genes?Run GO enrichment analysisCreate a volcano plot
Click any suggestion to automatically add it to your chat input.

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Asking Questions

You can ask Biomni Lab to explain results or suggest next steps: 
What do these results mean? Which genes should I focus on for
further validation?

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Running Multiple Sessions in Parallel

You can run multiple analyses simultaneously:
  1. Open a new task: Click + Create > Quick Task while an analysis is running
  2. Switch between tasks: Use the Tasks panel in the sidebar to switch
  3. Monitor progress: Each task runs independently with its own progress
Running analyses in parallel is useful when you have multiple samples to process or want to try different approaches simultaneously.

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Accuracy & Verification

Biomni Lab includes multiple features to ensure accuracy and help you verify results.

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Review Mode

Click the Review button at the top of any session to enter review mode:
Review button at the top of a session
In review mode, you can:
  • See all claims and statements with their supporting evidence
  • Verify citations and references
  • Check data sources used in the analysis
  • Identify any assumptions made

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Citations & References

Biomni Lab provides citations for:
  • Database queries: Links to source records (UniProt, NCBI, PDB, etc.)
  • Literature references: DOIs and links to published papers
  • Tool documentation: References to official tool documentation
  • Statistical methods: Citations for analytical approaches used

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Hallucination Guardrails

Biomni Lab uses multiple safeguards to prevent AI hallucinations:
  • Source verification: Claims are cross-referenced against databases
  • Confidence indicators: Uncertain results are flagged
  • Data validation: Input and output data are validated against expected formats
  • Reproducible workflows: All steps are logged and can be reproduced
While these guardrails significantly reduce errors, always verify critical findings through independent sources, especially for clinical or publication-ready research.

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Next Steps

Now that you understand the basics:

How to Prompt

Learn tips for writing effective requests

Projects & Drive

Organize your work and files

Resources

Explore 60+ databases and tools

FAQ

Common questions and answers