> ## Documentation Index
> Fetch the complete documentation index at: https://docs.biomni.phylo.bio/llms.txt
> Use this file to discover all available pages before exploring further.
# Resources
> Databases, tools, and packages available in Biomni Lab
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
Don't see a tool or database you need? Request it:
1. Click the **Help** button in the sidebar
2. Select **Live Chat** or **Join Slack** to connect with other researchers and our team
3. Describe the tool/database and your use case
4. Our team evaluates requests weekly
Popular requests are prioritized for addition.