> ## Documentation Index
> Fetch the complete documentation index at: https://docs.biomni.phylo.bio/llms.txt
> Use this file to discover all available pages before exploring further.

# FAQ

> Frequently asked questions about Biomni Lab

Find answers to common questions about using Biomni Lab.

## General

<AccordionGroup>
  <Accordion title="What is Biomni Lab?">
    Biomni Lab is an AI-powered research assistant designed for biomedical and life sciences research. It combines large language models with specialized bioinformatics tools, databases, and computational resources to help you analyze data and accelerate your research.
  </Accordion>

  <Accordion title="Do I need bioinformatics experience to use Biomni Lab?">
    No. Biomni Lab is designed to be accessible to researchers at all skill levels. You can describe what you want to accomplish in plain language, and Biomni Lab will handle the technical details. However, having domain knowledge about your research area helps you ask better questions and interpret results.
  </Accordion>

  <Accordion title="What types of research does Biomni Lab support?">
    Biomni Lab specializes in biomedical and life sciences research, including:

    * Genomics and transcriptomics
    * Proteomics and structural biology
    * Single-cell analysis
    * Pathway and network analysis
    * Biostatistics and machine learning
    * Literature and database searches
  </Accordion>
</AccordionGroup>

## Trust & Accuracy

<AccordionGroup>
  <Accordion title="Is my data secure?">
    Yes. We do not share your data with other users. See our privacy policy for details.
  </Accordion>

  <Accordion title="Can I trust Biomni Lab's results? How do you prevent AI hallucinations?">
    Biomni Lab is built with multiple safeguards to ensure accurate, reliable results:

    **Citations & References**

    * All database queries link directly to source records (UniProt, NCBI, PDB, etc.)
    * Literature references include DOIs and links to published papers
    * Tool parameters and methods are documented with official references

    **Review Mode**

    * Click the **Review** button at the top of any session to verify results
    * See all claims with their supporting evidence
    * Check data sources and identify assumptions

    **Hallucination Guardrails**

    * Claims are cross-referenced against authoritative databases
    * Uncertain results are flagged with confidence indicators
    * Input/output data is validated against expected formats
    * All steps are logged for reproducibility

    While these measures significantly reduce errors, we recommend verifying critical findings through independent sources—especially for clinical applications or publication-ready research.
  </Accordion>

  <Accordion title="How do I verify Biomni Lab's results?">
    Use the **Review** button at the top of any session to enter review mode. This shows:

    * All claims and statements with supporting evidence
    * Direct links to database records and literature
    * Data sources used in the analysis
    * Any assumptions or caveats

    You can also ask Biomni Lab to explain its reasoning or provide additional citations for any claim.
  </Accordion>
</AccordionGroup>

## Files & Data

<AccordionGroup>
  <Accordion title="What file formats does Biomni Lab support?">
    Biomni Lab supports common bioinformatics formats including:

    * **Sequences**: FASTA, FASTQ, FASTQ.GZ
    * **Alignments**: SAM, BAM, CRAM
    * **Variants**: VCF, BCF, GVCF
    * **Tabular**: CSV, TSV, XLSX, TXT
    * **Annotations**: GFF, GTF, BED
    * **Images**: PNG, JPG, SVG, PDF
  </Accordion>

  <Accordion title="What is the maximum file size I can upload?">
    The maximum file size is 10 GB per file. Contact support if you need to process larger files.
  </Accordion>

  <Accordion title="How long are my files stored?">
    Files are stored for the duration of your account and can be downloaded or deleted at any time.
  </Accordion>

  <Accordion title="Can I upload compressed files?">
    Yes. Biomni Lab supports gzip-compressed files (.gz) for sequences and other large files. This is recommended for FASTQ files to save upload time and storage space.
  </Accordion>
</AccordionGroup>

## Analysis & Tools

<AccordionGroup>
  <Accordion title="What bioinformatics tools are available?">
    Biomni Lab has access to many popular tools including:

    * **Alignment**: Bowtie2, BWA, STAR, HISAT2
    * **Variant calling**: GATK, BCFtools, FreeBayes
    * **RNA-seq**: DESeq2, edgeR, featureCounts
    * **Single-cell**: Seurat, Scanpy
    * **Structure**: AlphaFold
    * **Visualization**: ggplot2, matplotlib, seaborn

    See the [Resources](/features/resources) page for a complete list.
  </Accordion>

  <Accordion title="How long do analyses take?">
    Analysis time varies depending on:

    * Data size and complexity
    * Tools being used
    * Current system load

    Simple queries complete in seconds. Alignment of a typical RNA-seq sample takes 10-30 minutes. Large genome analyses may take several hours. Biomni Lab shows progress updates during long-running tasks.
  </Accordion>

  <Accordion title="Can I run custom scripts?">
    Biomni Lab can write and execute Python and R code for your analyses. If you have specific requirements, you can ask Biomni Lab to implement custom analysis pipelines. However, you cannot upload and run arbitrary executable files for security reasons.
  </Accordion>
</AccordionGroup>

## Compute & Limits

<AccordionGroup>
  <Accordion title="What are the compute resources available?">
    Each analysis session has access to:

    * **CPU**: Multi-core processing for parallel computations
    * **Memory**: Sufficient RAM for most bioinformatics workflows
    * **GPU**: Available for specific tools (marked with HPC badge) like AlphaFold and deep learning models
    * **Storage**: Temporary workspace for intermediate files during analysis

    Pro users get higher resource limits across the board. See the [Pricing FAQ](/pricing-faq) for details.
  </Accordion>

  <Accordion title="Are there limits on how many analyses I can run?">
    Yes. Usage is tracked based on the underlying LLM and compute resources consumed — not a simple message count. Each plan has a daily usage allowance that resets every day, and Pro users get 10x the daily allowance of Free users. You can also run multiple sessions concurrently (Free: up to 5, Pro: up to 10). You can check your current usage on the [Settings](https://biomni.phylo.bio/settings) page.
  </Accordion>

  <Accordion title="What happens if I hit a limit?">
    * **Daily usage limit**: Your tasks are queued until your usage resets the next day. See the [Pricing FAQ](/pricing-faq) for more details.
    * **File size limit**: Upload will fail with an error message. Try compressing the file or contact support.
    * **Storage limit**: You'll need to delete files before uploading more. Download important results first.
  </Accordion>
</AccordionGroup>

## Projects & Organization

<AccordionGroup>
  <Accordion title="What's the difference between a Quick Task and a Project?">
    * **Quick Task**: A standalone analysis session for one-off questions or explorations. Good for trying things out.
    * **Project**: An organized workspace for related analyses. Projects help you keep files, tasks, and results organized for ongoing research.
  </Accordion>

  <Accordion title="Can I collaborate with my team?">
    Yes. You can invite team members to your organization and share projects with them. Team members can view and contribute to shared projects while keeping personal work private.
  </Accordion>

  <Accordion title="Can I export my results?">
    Yes. All results can be downloaded including:

    * Generated files (BAM, VCF, CSV, etc.)
    * Figures and visualizations
    * Analysis reports
    * Chat transcripts
  </Accordion>
</AccordionGroup>

## Account & Billing

For detailed pricing, plan comparisons, academic discounts, and billing questions, see the **[Pricing FAQ](/pricing-faq)**.

<AccordionGroup>
  <Accordion title="How do I delete my account?">
    Contact [support@phylo.bio](mailto:support@phylo.bio) to manage your account. Your data will be retained for 30 days after cancellation.
  </Accordion>
</AccordionGroup>

## Troubleshooting

<AccordionGroup>
  <Accordion title="My analysis is taking too long. What should I do?">
    * Check that your input files are in the correct format
    * For large files, ensure they're compressed (.gz)
    * Consider breaking the analysis into smaller batches
    * Contact support if an analysis seems stuck
  </Accordion>

  <Accordion title="Biomni Lab doesn't understand my request. How can I improve it?">
    * Be more specific about what you want to accomplish
    * Mention your input files using @ references
    * Specify the tools or methods you want to use
    * Break complex requests into smaller steps
    * See [How to Prompt](/how-to-prompt) for detailed tips
  </Accordion>

  <Accordion title="I got an error. What should I do?">
    * Check the error message for specific issues (wrong file format, missing data, etc.)
    * Try rephrasing your request with more details
    * If the error persists, report it using the bug icon in the top-right corner
    * Check the [Bug Reporting](/support/bug-reporting) page for more information
  </Accordion>

  <Accordion title="My file upload failed. What went wrong?">
    Common causes:

    * File exceeds size limit
    * Unsupported file format
    * Network interruption
    * File is corrupted

    Try compressing large files, checking the format, and ensuring a stable connection.
  </Accordion>
</AccordionGroup>

## Still Have Questions?

* **[Join our Slack](https://join.slack.com/t/biomnigroup/shared_invite/zt-3p4aom0as-qiQGsPrISHQSCb8SJMquvw)** - Chat with the community and Biomni Lab team
* **[Contact Support](/support/customer-support)** - Get help from our support team
* **[Report a Bug](/support/bug-reporting)** - Let us know if something isn't working