Resources

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.

Tools

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

Biomni Package Tools

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

R

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

CLI Tools

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

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Features

Support

Databases

Protein Structures

Genomics & Variants

Literature

Pathways & Ontologies

Cancer

Drugs & Compounds

Single Cell

Disease & Phenotype

Protein Interactions & Networks

RNA & Regulatory

Additional Resources

Tools

Structure Prediction (HPC-Accelerated)

Genome Assembly

Alignment

Variant Calling

Biomni Package Tools

Packages

Python

R

CLI Tools

Reference Genomes

Requesting New Resources

​Databases

​Protein Structures

​Genomics & Variants

​Literature

​Pathways & Ontologies

​Cancer

​Drugs & Compounds

​Single Cell

​Disease & Phenotype

​Protein Interactions & Networks

​RNA & Regulatory

​Additional Resources

​Tools

​Structure Prediction (HPC-Accelerated)

​Genome Assembly

​Alignment

​Variant Calling

​Biomni Package Tools

​Packages

​Python

​R

​CLI Tools

​Reference Genomes

​Requesting New Resources

Databases

Protein Structures

Genomics & Variants

Literature

Pathways & Ontologies

Cancer

Drugs & Compounds

Single Cell

Disease & Phenotype

Protein Interactions & Networks

RNA & Regulatory

Additional Resources

Tools

Structure Prediction (HPC-Accelerated)

Genome Assembly

Alignment

Variant Calling

Biomni Package Tools

Packages

Python

R

CLI Tools

Reference Genomes

Requesting New Resources