Biomni Lab provides access to 60+ biomedical databases, HPC-accelerated analysis tools, and curated software packages. Browse the Resources panel in the sidebar to explore what’s available.
Databases
Protein Structures
| Database | Description |
|---|
| PDB | Protein Data Bank - experimental 3D structures |
| AlphaFold DB | Predicted protein structures for 200M+ proteins |
| UniProt | Protein sequences, function, and annotations |
| InterPro | Protein families, domains, and functional sites |
Genomics & Variants
| Database | Description |
|---|
| Ensembl | Genome browser, gene annotations, and comparative genomics |
| NCBI Gene | Gene-centric information across species |
| GEO | Gene Expression Omnibus - public expression datasets |
| dbSNP | Single nucleotide polymorphisms database |
| ClinVar | Clinical variant interpretations and pathogenicity |
| gnomAD | Genome/exome aggregation database - population variants |
| GTEx | Genotype-Tissue Expression - tissue-specific expression |
| RefSeq | Reference sequences for genomes, transcripts, proteins |
| 1000 Genomes | Human genetic variation from global populations |
| TOPMed | Trans-Omics for Precision Medicine variants |
| UK Biobank | Large-scale biomedical database (requires access) |
| ClinGen | Clinical genome resource for variant curation |
| LOVD | Locus-specific variant databases |
| HGMD | Human Gene Mutation Database |
Literature
| Database | Description |
|---|
| PubMed | Biomedical literature citations and abstracts |
Pathways & Ontologies
| Database | Description |
|---|
| KEGG | Pathway maps, genome, and disease information |
| Reactome | Curated pathway database |
| Gene Ontology | Standardized gene and protein function annotations |
| MSigDB | Molecular Signatures Database - gene sets for GSEA |
Cancer
| Database | Description |
|---|
| COSMIC | Catalogue of Somatic Mutations in Cancer |
| TCGA | The Cancer Genome Atlas - multi-omics cancer data |
| cBioPortal | Cancer genomics data visualization and analysis |
| DepMap | Cancer dependency map - gene essentiality |
Drugs & Compounds
| Database | Description |
|---|
| ChEMBL | Bioactivity data for drug-like molecules |
| PubChem | Chemical structures and biological activities |
| BindingDB | Protein-ligand binding affinities |
| ClinicalTrials.gov | Registry of clinical studies |
| DrugBank | Drug and drug target information |
| DGIdb | Drug-gene interaction database |
| PharmGKB | Pharmacogenomics knowledge base |
| TTD | Therapeutic Target Database |
Single Cell
| Database | Description |
|---|
| CZI Cell Census | Chan Zuckerberg Initiative single-cell atlas |
| Human Cell Atlas | Reference maps of all human cells |
| CellMarker 2.0 | Cell type marker genes |
Disease & Phenotype
| Database | Description |
|---|
| DisGeNET | Gene-disease associations |
| OMIM | Online Mendelian Inheritance in Man |
| GWAS Catalog | Published genome-wide association studies |
| OpenTargets | Drug target identification and validation |
| HPO | Human Phenotype Ontology |
| Orphanet | Rare disease information |
| MalaCards | Human disease database |
Protein Interactions & Networks
| Database | Description |
|---|
| STRING | Protein-protein interaction networks |
| BioGRID | Biological interaction repository |
| Human Protein Atlas | Protein expression across tissues and cells |
| PrimeKG | Precision medicine knowledge graph |
RNA & Regulatory
| Database | Description |
|---|
| miRTarBase | microRNA-target interactions |
| ENCODE | Encyclopedia of DNA Elements - regulatory data |
| JASPAR | Transcription factor binding profiles |
| ReMap | Regulatory atlas of DNA-binding proteins |
| RNAcentral | Non-coding RNA sequences |
| lncRNAdb | Long non-coding RNA database |
Additional Resources
| Database | Description |
|---|
| Addgene | Plasmid repository |
| PRIDE | Proteomics data repository |
| MouseMine | Mouse genome informatics |
| TxGNN | Therapeutic target prediction |
| ZINC | Purchasable compounds for virtual screening |
| ChEBI | Chemical Entities of Biological Interest |
| Pfam | Protein domain families |
| PROSITE | Protein domains and motifs |
| IntAct | Molecular interaction database |
| Metabolomics Workbench | Metabolomics data repository |
Database queries are cached for faster subsequent lookups. Results are refreshed regularly to ensure up-to-date information.
Structure Prediction (HPC-Accelerated)
| Tool | Description | GPU |
|---|
| AlphaFold | Protein structure prediction | Yes |
| Boltz-2 | Fast structure prediction | Yes |
| RFDiffusion | Protein design with diffusion models | Yes |
| ColabFold | Fast AlphaFold with MSA server | Yes |
| ESMFold | Language model-based structure prediction | Yes |
| OpenFold | Open-source AlphaFold implementation | Yes |
| RoseTTAFold | Alternative structure prediction | Yes |
Genome Assembly
| Tool | Description | Best For |
|---|
| Canu | Long-read assembly | PacBio, ONT |
| Flye | Fast long-read assembly | ONT, PacBio HiFi |
| SPAdes | Short-read assembly | Illumina |
| Trinity | Transcriptome assembly | RNA-seq |
| Hifiasm | HiFi read assembly | PacBio HiFi |
| wtdbg2 | Fast long-read assembly | Large genomes |
Alignment
| Tool | Best For | Speed |
|---|
| minimap2 | Long reads (PacBio, ONT) | Very fast |
| STAR | RNA-seq, splice-aware | Fast |
| bowtie2 | DNA-seq, ChIP-seq | Fast |
| BWA-MEM | DNA-seq, whole genome | Fast |
| HISAT2 | RNA-seq, low memory | Medium |
| Salmon | Transcript quantification | Very fast |
| kallisto | Transcript quantification | Very fast |
Variant Calling
| Tool | Variant Types | Use Case |
|---|
| BCFtools | SNPs, indels | Fast variant calling |
| Clair3 | SNPs, indels | Long-read variants |
| Sniffles | Structural variants | Long-read SV calling |
| GATK HaplotypeCaller | SNPs, indels | Germline variants |
| GATK Mutect2 | SNPs, indels | Somatic variants |
| DeepVariant | SNPs, indels | Deep learning-based |
| FreeBayes | SNPs, indels, MNPs | Haplotype-based |
| Tool | Description |
|---|
| Primer Design | Design PCR and sequencing primers |
| Cloning Assistant | Plan molecular cloning strategies |
| CRISPR Guide Design | Design sgRNAs for gene editing |
| Sequence Analysis | Analyze DNA/protein sequences |
GPU-accelerated tools run on HPC infrastructure. Structure predictions for large proteins may take 30-60 minutes.
Packages
Python
| Package | Description |
|---|
| scanpy | Single-cell analysis |
| biopython | Biological computation |
| rdkit | Cheminformatics |
| pandas | Data manipulation |
| numpy | Numerical computing |
| scipy | Scientific computing |
| scikit-learn | Machine learning |
| torch | Deep learning |
| tensorflow | Deep learning |
| matplotlib | Visualization |
| seaborn | Statistical visualization |
| plotly | Interactive plots |
| anndata | Annotated data matrices |
| pyBigWig | BigWig file handling |
| pysam | SAM/BAM file handling |
| Package | Description |
|---|
| DESeq2 | Differential expression analysis |
| edgeR | Differential expression |
| limma | Linear models for microarray |
| ggplot2 | Data visualization |
| Seurat | Single-cell analysis |
| clusterProfiler | Enrichment analysis |
| ComplexHeatmap | Advanced heatmaps |
| GenomicRanges | Genomic intervals |
| Biostrings | Biological sequences |
| BSgenome | Reference genomes |
| VariantAnnotation | VCF handling |
| Tool | Description |
|---|
| samtools | SAM/BAM manipulation |
| bedtools | BED file operations |
| bcftools | VCF/BCF manipulation |
| blast | Sequence alignment |
| gatk | Genome analysis toolkit |
| fastqc | Quality control |
| trimmomatic | Read trimming |
| cutadapt | Adapter removal |
| featureCounts | Read counting |
| htseq | Read counting |
| vcftools | VCF manipulation |
| tabix | Index TAB-delimited files |
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 Lab will index it automatically.
Requesting New Resources
Don’t see a tool or database you need? Request it:
- Click the Help button in the sidebar
- Select Live Chat or Join Slack to connect with other researchers and our team
- Describe the tool/database and your use case
- Our team evaluates requests weekly
Popular requests are prioritized for addition. 