Biomni provides access to a curated collection of biomedical databases, analysis tools, and software packages. Browse the Resources panel in the sidebar to explore what’s available.
Databases
Curated biomedical databases for reference data and annotations:
| Database | Description | Use Cases |
|---|
| UniProt | Protein sequences and functional annotations | Protein lookup, sequence retrieval, functional annotation |
| NCBI Gene | Gene-centric information across species | Gene IDs, symbols, descriptions, orthologs |
| PDB | Protein 3D structures | Structure retrieval, visualization, docking prep |
| KEGG | Pathway and genome information | Pathway mapping, enrichment analysis |
| GO | Gene Ontology annotations | Functional classification, enrichment analysis |
| Ensembl | Genome browser and annotation | Genome coordinates, transcript info, variants |
| dbSNP | Single nucleotide polymorphisms | SNP lookup, variant annotation |
| ClinVar | Clinical variant interpretations | Pathogenicity, clinical significance |
| RefSeq | Reference sequences | Transcript and protein sequences |
| GEO | Gene expression datasets | Public expression data, sample metadata |
Database queries are cached for faster subsequent lookups. Results are refreshed weekly to ensure up-to-date information.
| Tool | Best For | Speed | Memory |
|---|
| STAR | RNA-seq alignment, splice-aware | Fast | High (30GB+) |
| Bowtie2 | DNA-seq, ChIP-seq | Fast | Low |
| BWA-MEM | DNA-seq, whole genome | Fast | Medium |
| HISAT2 | RNA-seq, low memory | Medium | Low |
| Minimap2 | Long reads (PacBio, ONT) | Very fast | Low |
When to Use Which Aligner
- RNA-seq: Use STAR for best splice junction detection, HISAT2 for lower memory
- DNA-seq/WGS: Use BWA-MEM for accuracy, Bowtie2 for speed
- ChIP-seq: Bowtie2 with default settings
- Long reads: Minimap2 for PacBio or Oxford Nanopore
Tools for identifying genetic variants:
| Tool | Variant Types | Use Case |
|---|
| GATK HaplotypeCaller | SNPs, indels | Germline variants, best practices pipeline |
| GATK Mutect2 | SNPs, indels | Somatic variants (tumor/normal) |
| BCFtools | SNPs, indels | Fast variant calling, manipulation |
| FreeBayes | SNPs, indels, MNPs | Haplotype-based calling |
| DeepVariant | SNPs, indels | Deep learning-based, high accuracy |
RNA-seq Analysis
Packages for gene expression analysis:
| Package | Language | Best For |
|---|
| DESeq2 | R | Differential expression, small sample sizes |
| edgeR | R | Differential expression, larger datasets |
| limma-voom | R | Microarray and RNA-seq |
| featureCounts | CLI | Read counting, fast |
| HTSeq | Python | Read counting, flexible |
| Salmon | CLI | Transcript quantification, fast |
| kallisto | CLI | Transcript quantification, pseudoalignment |
Single-Cell Analysis
Tools for single-cell RNA-seq:
| Tool | Language | Features |
|---|
| Seurat | R | Comprehensive scRNA-seq, integration |
| Scanpy | Python | Scalable analysis, visualization |
| Cell Ranger | CLI | 10x Genomics data processing |
| scVI | Python | Deep learning, batch correction |
| Monocle3 | R | Trajectory analysis, pseudotime |
Structural Biology
Tools for protein structure analysis:
| Tool | Description | GPU |
|---|
| AlphaFold | Protein structure prediction | Yes |
| ColabFold | Fast AlphaFold with MSA server | Yes |
| PyMOL | Molecular visualization | No |
| AutoDock Vina | Molecular docking | No |
| RoseTTAFold | Structure prediction | Yes |
GPU-accelerated tools run on HPC infrastructure. Structure predictions for large proteins may take 30-60 minutes.
Visualization
Packages for creating figures and plots:
| Package | Language | Best For |
|---|
| ggplot2 | R | Publication-ready plots, grammar of graphics |
| matplotlib | Python | General purpose, customizable |
| seaborn | Python | Statistical visualizations |
| plotly | R/Python | Interactive plots |
| ComplexHeatmap | R | Advanced heatmaps, annotations |
Reference Genomes
Pre-indexed reference genomes available:
| Organism | Assemblies |
|---|
| Human | GRCh38 (hg38), GRCh37 (hg19) |
| Mouse | GRCm39 (mm39), GRCm38 (mm10) |
| Rat | mRatBN7.2 |
| Zebrafish | GRCz11 |
| Drosophila | BDGP6 |
| C. elegans | WBcel235 |
| Yeast | R64 |
| E. coli | K-12 MG1655 |
For organisms not listed, you can provide your own reference FASTA file. Biomni will index it automatically.
Requesting New Resources
Don’t see a tool you need? Request it:
- Click the chat icon in the bottom-right corner
- Describe the tool and your use case
- Our team evaluates requests weekly
Popular requests are prioritized for addition. 