Skip to main content
Find answers to common questions about using Biomni.

​
General

Biomni 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.
No. Biomni is designed to be accessible to researchers at all skill levels. You can describe what you want to accomplish in plain language, and Biomni will handle the technical details. However, having domain knowledge about your research area helps you ask better questions and interpret results.
Biomni 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

​
Trust & Accuracy

Yes. We do not share your data with other users or use it to train AI models. See our privacy policy for details.
Biomni 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.
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 to explain its reasoning or provide additional citations for any claim.

​
Files & Data

Biomni 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
The maximum file size is 10 GB per file. Contact support if you need to process larger files.
Files are stored for the duration of your subscription. You can download or delete files at any time. When you cancel your subscription, files are retained for 30 days before deletion.
Yes. Biomni supports gzip-compressed files (.gz) for sequences and other large files. This is recommended for FASTQ files to save upload time and storage space.

​
Analysis & Tools

Biomni 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 page for a complete list.
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 shows progress updates during long-running tasks.
Biomni can write and execute Python and R code for your analyses. If you have specific requirements, you can ask Biomni to implement custom analysis pipelines. However, you cannot upload and run arbitrary executable files for security reasons.
Biomni has pre-indexed reference genomes for common model organisms:
  • Human (GRCh38/hg38, GRCh37/hg19)
  • Mouse (GRCm39/mm39, GRCm38/mm10)
  • Rat, Zebrafish, Drosophila, C. elegans
  • And many more
You can also provide custom reference sequences.

​
Compute & Limits

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
Resource allocation scales based on your subscription plan and the complexity of the analysis.
The maximum file size is 5-10 GB per file. Need to process larger files? Contact [email protected] to discuss options.
Storage limits depend on your subscription plan:
  • Free trial: 10 GB total storage
  • Standard: 100 GB total storage
  • Enterprise: Custom storage allocation
You can free up space by deleting old files or downloading and archiving completed projects.
You can run multiple analyses in parallel, but there are fair-use limits:
  • Concurrent sessions: Up to 5 simultaneous running analyses
  • Daily compute: Based on subscription plan
  • Monthly usage: Based on subscription plan
Heavy computational tools (genome alignment, structure prediction) consume more resources than simple queries. Contact us for enterprise plans with higher limits.
  • 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.
  • Compute limit: New analyses will be queued until resources are available, or you can upgrade your plan.
You’ll receive notifications when approaching limits so you can plan accordingly.

​
Projects & Organization

  • 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.
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.
Yes. All results can be downloaded including:
  • Generated files (BAM, VCF, CSV, etc.)
  • Figures and visualizations
  • Analysis reports
  • Chat transcripts

​
Account & Billing

Contact our sales team at [email protected] for information about subscription plans and pricing.
Yes. New users can explore Biomni with a free trial. Contact us to get started.
Contact [email protected] to manage your subscription. Your data will be retained for 30 days after cancellation.

​
Troubleshooting

  • 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
  • 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 for detailed tips
  • 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 page for more information
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.

​
Still Have Questions?