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Biomni is an AI-powered research assistant designed specifically for biomedical and life sciences research. It combines the power of large language models with specialized bioinformatics tools, curated databases, and computational resources to help you analyze data, run experiments, and accelerate your research.

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What is Biomni?

Biomni acts as your intelligent lab assistant that can:
  • Understand your research goals and break them down into actionable analysis steps
  • Execute complex bioinformatics pipelines using industry-standard tools
  • Access and query biological databases to retrieve relevant information
  • Generate visualizations and reports from your data
  • Learn from your preferences to provide personalized recommendations
Unlike general-purpose AI assistants, Biomni is built from the ground up for biomedical research, with access to specialized tools and the ability to run real computational analyses on your data.

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What Can Biomni Do?

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Genomic Analysis

  • Sequence alignment: Align FASTQ reads to reference genomes using tools like Bowtie2, BWA, and STAR
  • Variant calling: Identify SNPs, indels, and structural variants with GATK and BCFtools
  • Gene expression analysis: Perform differential expression analysis with DESeq2 and edgeR
  • Genome assembly: Assemble sequencing reads into contigs and scaffolds
  • Quality control: Assess read quality with FastQC and MultiQC

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Protein & Structural Biology

  • Structure prediction: Predict 3D protein structures using AlphaFold
  • Sequence analysis: Search protein databases, identify domains, and predict function
  • Molecular docking: Model protein-ligand interactions
  • Pathway analysis: Map genes to biological pathways using KEGG and Gene Ontology

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Data Analysis & Visualization

  • Statistical analysis: Perform t-tests, ANOVA, regression, and other statistical tests
  • Machine learning: Build predictive models with scikit-learn
  • Publication-ready figures: Generate plots with ggplot2, matplotlib, and seaborn
  • Single-cell analysis: Process and analyze scRNA-seq data with Seurat and Scanpy

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Literature & Knowledge

  • Database queries: Search UniProt, NCBI, PDB, Ensembl, and other biological databases
  • Literature search: Find and summarize relevant research papers
  • Gene/protein information: Retrieve annotations, functions, and relationships

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File Support

Biomni supports a wide range of file formats commonly used in bioinformatics:
CategorySupported Formats
SequencesFASTA, FASTQ, FASTQ.GZ, FASTA.GZ, FA, FQ
AlignmentsSAM, BAM, CRAM, BAI, CSI
VariantsVCF, BCF, GVCF, VCF.GZ
StructuresPDB, CIF, MMCIF, MOL, MOL2, SDF
AnnotationsGFF, GFF3, GTF, BED, BED12, BEDGRAPH
Tabular DataCSV, TSV, XLSX, XLS, TXT, PARQUET
ImagesPNG, JPG, JPEG, SVG, PDF, TIFF
OtherJSON, XML, YAML, ZIP, GZ, TAR.GZ

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Computational Resources

Biomni runs analyses on cloud infrastructure with access to:
  • CPU computing for standard bioinformatics tools
  • GPU acceleration for deep learning models like AlphaFold
  • High-memory nodes for large genome assemblies
  • Parallel processing for batch analyses
You don’t need to manage servers, install software, or configure environments—Biomni handles all the infrastructure so you can focus on your research.

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Getting Started

Ready to try Biomni? Here’s how to get started:
  1. Quickstart Guide - Create your first task and run an analysis
  2. How to Prompt - Learn how to communicate effectively with Biomni
  3. FAQ - Common questions and answers