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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 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’s capabilities.
Creating a Quick Task from the sidebar menu

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Using Workflow Templates

Workflow templates provide pre-built analysis workflows to help you get started quickly:
  1. Look for the suggested workflow templates displayed in the chat area
  2. Click on a template to see what it does
  3. Click Use Template to apply it to your task
  4. Provide the required input files when prompted
Workflow templates displayed in the chat interface
Workflow templates are created from successful analyses. You can save your own workflows as templates to reuse later.

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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: Choose from files you’ve already uploaded to Biomni
  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 begins processing. You’ll see:
  1. Planning phase: Biomni 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 prepares the computational environment. Subsequent requests in the same session start faster.

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The Execution Trace

As Biomni works, you’ll see a trace of its actions in the chat:
  • Thinking: Biomni’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 Panel System

Biomni uses a flexible panel layout to display your chat, results, and file previews.

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Opening the Right Panel

When Biomni generates results, you can open them in the right panel:
  1. Plan button: Click to view the analysis plan in the right panel
  2. Open in tab button: Click on any result to open it in a new tab
  3. Expand button: Click to view details in a larger view

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Tab Management

The right panel uses tabs to organize multiple views:
  • Click a tab to switch between views
  • Drag tabs to reorder them
  • Click the X to close a tab
  • Multiple results can be open simultaneously

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Resizing Panels

Drag the divider between the chat and right panel to adjust the layout:

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Viewing and Downloading Results

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Viewing Results

Results appear in multiple places:
  1. In the chat: Inline previews of generated files and visualizations
  2. In the right panel: Full-size views when you click “Open in tab”
  3. In the Results sidebar: 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
Result file actions showing view, download, and find source options
From the Results tab in the right panel, you can also:
  • Download all: Download everything as a ZIP file
  • Execution trace: Download execution_trace.ipynb—a Jupyter notebook with all code and outputs from your session
The execution trace notebook is useful for reproducing your analysis outside of Biomni or sharing your workflow with collaborators.

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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 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 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 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 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 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

File Management

Organize your uploads and results

Resources

Explore available tools and databases

FAQ

Common questions and answers