life-science-ai-prompts/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.yml

---
title: "Awesome Computational Biology - machine-readable resource list"
task: ""
lineage_type: import
upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/c6f07d90/data/resources.yml
upstream_sha: c6f07d90
imported_at: 2026-08-31
prompt_class: catalogue
upstream_changes: accepted
author: upstream
validated: false
---

# Awesome Computational Biology - machine-readable resource list
# Fields
#   id          : unique slug (required)
#   name        : display name (required)
#   type        : category, e.g. database | tool | model | benchmark | api (required)
#   url         : canonical URL (required)
#   description : one-line description (required)
#   license     : SPDX identifier or free-text (optional)
#   api         : true | false - whether a programmatic API is available (default: false)
#   updated     : last-known update date as string YYYY-MM-DD (optional)
#   tasks       : list of ML/bio tasks (optional)
#   modalities  : list of data modalities (optional)
#   tags        : additional free-form tags (optional)
#   organism    : list of organisms covered (optional)
#   paper       : DOI or URL to primary publication (optional)

resources:
  - id: chembl_web_services
    name: "ChEMBL Web Services"
    type: api
    url: https://www.ebi.ac.uk/chembl/ws
    description: "REST API for bioactive molecules, targets, and bioassays."
    tags: [api]
    tasks: []
    modalities: []
    organism: []
    api: true

  - id: clinicaltrials_gov_api
    name: "ClinicalTrials.gov API"
    type: api
    url: https://clinicaltrials.gov/api/gui
    description: "API for querying clinical trial metadata and results."
    tags: [api]
    tasks: []
    modalities: []
    organism: []
    api: true

  - id: ensembl_rest_api
    name: "Ensembl REST API"
    type: api
    url: https://rest.ensembl.org/
    description: "API for genomic annotations, variants, genes, and comparative genomics."
    tags: [api]
    tasks: []
    modalities: []
    organism: []
    api: true

  - id: kegg_rest_api
    name: "KEGG REST API"
    type: api
    url: https://www.kegg.jp/kegg/rest/keggapi.html
    description: "API for accessing KEGG pathways, compounds, genes, and reactions."
    tags: [api]
    tasks: []
    modalities: []
    organism: []
    api: true

  - id: ncbi_e_utilities
    name: "NCBI E-utilities"
    type: api
    url: https://www.ncbi.nlm.nih.gov/books/NBK25501/
    description: "Unified APIs for accessing NCBI databases (Gene, GEO, SRA, PubChem, etc)."
    tags: [api]
    tasks: []
    modalities: []
    organism: []
    api: true

  - id: open_targets_platform_api
    name: "Open Targets Platform API"
    type: api
    url: https://platform.opentargets.org/api
    description: "API for target–disease associations integrating genetics, genomics, and drug data."
    tags: [api]
    tasks: []
    modalities: []
    organism: []
    api: true

  - id: pubmed_e_utilities_esearch_efetch
    name: "PubMed E-utilities (esearch/efetch)"
    type: api
    url: https://www.nlm.nih.gov/dataguide/edirect/esearch.html
    description: "APIs for searching and retrieving biomedical literature from PubMed."
    tags: [api]
    tasks: []
    modalities: []
    organism: []
    api: true

  - id: uniprot_rest_api
    name: "UniProt REST API"
    type: api
    url: https://www.uniprot.org/help/api
    description: "Programmatic access to protein sequence and functional annotation data."
    tags: [api]
    tasks: []
    modalities: []
    organism: []
    api: true

  - id: 1000_genomes_project
    name: "1000 Genomes Project"
    type: benchmark
    url: https://www.internationalgenome.org/
    description: "Reference panel of human genetic variation from 2,504 individuals across 26 populations."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: bace
    name: "BACE"
    type: benchmark
    url: https://www.kaggle.com/datasets/gokturkkoch/bace
    description: "Binary classification and regression dataset for β-secretase 1 (BACE-1) inhibitor binding affinity."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: beat_aml
    name: "BEAT AML"
    type: benchmark
    url: https://biodev.github.io/BeatAML2/
    description: "Functional ex vivo drug sensitivity measurements paired with genomics for acute myeloid leukemia."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: bento
    name: "Bento"
    type: benchmark
    url: https://github.com/LigandPro/Bento
    description: "Protein-ligand docking benchmark covering rigid, flexible, de novo, blind, induced-fit, and covalent docking tasks."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: bindingdb_curated_sets
    name: "BindingDB Curated Sets"
    type: benchmark
    url: https://www.bindingdb.org/rwd/bind/chemsearch/marvin/SDFdownload.jsp?all_download=yes
    description: "Curated binding affinity datasets for protein–ligand interaction benchmarking."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: cancer_therapeutics_response_portal_ctrp
    name: "Cancer Therapeutics Response Portal (CTRP)"
    type: benchmark
    url: https://portals.broadinstitute.org/ctrp/
    description: "Drug sensitivity profiles across ~900 cancer cell lines for >400 compounds."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: clintox
    name: "ClinTox"
    type: benchmark
    url: https://tdcommons.ai/single_pred_tasks/tox/#clintox
    description: "Clinical toxicity dataset contrasting FDA-approved drugs with those that failed clinical trials due to toxicity."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: cptac_clinical_proteomic_tumor_analysis_consortium
    name: "CPTAC (Clinical Proteomic Tumor Analysis Consortium)"
    type: benchmark
    url: https://proteomics.cancer.gov/programs/cptac
    description: "Multi-omic proteogenomic datasets for multiple cancer types linking proteomics with genomics."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: crossdocked2020
    name: "CrossDocked2020"
    type: benchmark
    url: https://arxiv.org/abs/2001.01037
    description: "Large-scale dataset for structure-based virtual screening."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: dud_e_directory_of_useful_decoys_enhanced
    name: "DUD-E (Directory of Useful Decoys, Enhanced)"
    type: benchmark
    url: http://dude.docking.org/
    description: "Structure-based virtual screening benchmark with active ligands and challenging decoy sets across diverse protein targets."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: flip_fitness_landscape_inference_for_proteins
    name: "FLIP (Fitness Landscape Inference for Proteins)"
    type: benchmark
    url: https://github.com/J-SNACKKB/FLIP
    description: "Benchmark collection of protein fitness landscape datasets for evaluating protein ML models."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: guacamol
    name: "GuacaMol"
    type: benchmark
    url: https://github.com/BenevolentAI/guacamol
    description: "Benchmark suite for generative molecular design models."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: hest_xenium_virtual_spatial_transcriptomics
    name: "HEST Xenium virtual spatial transcriptomics"
    type: benchmark
    url: https://huggingface.co/datasets/ratschlab/HEST_Xenium_virtual_spatial_transcriptomics
    description: "DeepSpot-M predicted transcriptome-wide ST for 59 HEST-1k 10x Xenium samples (~13.3M cells) (gated). Paper: [DeepSpot-M](https://www.medrxiv.org/content/10.64898/2026.06.19.26356060v1)."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: jump_cell_painting_datasets
    name: "JUMP Cell Painting Datasets"
    type: benchmark
    url: https://github.com/jump-cellpainting/datasets
    description: "Consortium-scale cell imaging perturbation datasets (chemical and genetic) for phenotypic profiling and drug discovery research."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: lincs_l1000
    name: "LINCS L1000"
    type: benchmark
    url: https://lincsproject.org/LINCS/tools/workflows/find-the-best-place-to-obtain-the-lincs-l1000-data
    description: "Gene expression profiles (978 landmark genes) for >20,000 chemical and genetic perturbations across cell lines."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: moleculenet
    name: "MoleculeNet"
    type: benchmark
    url: http://moleculenet.ai/
    description: "Benchmark datasets for molecular machine learning."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: moses
    name: "MOSES"
    type: benchmark
    url: https://github.com/molecularsets/moses
    description: "Benchmarking platform for molecular generation models."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: ogb_open_graph_benchmark
    name: "OGB (Open Graph Benchmark)"
    type: benchmark
    url: https://ogb.stanford.edu/
    description: "Large-scale graph ML benchmark suite including biological datasets such as ogbl-ppa (protein-protein associations) and ogbg-molhiv."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: openbiolink
    name: "OpenBioLink"
    type: benchmark
    url: https://github.com/OpenBioLink/OpenBioLink
    description: "Benchmark datasets for biological knowledge graph completion."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: pharmgkb
    name: "PharmGKB"
    type: benchmark
    url: https://www.pharmgkb.org/
    description: "Curated pharmacogenomics dataset linking genetic variants to drug response phenotypes across thousands of drugs."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: pk_db
    name: "PK-DB"
    type: benchmark
    url: https://pk-db.com/
    description: "Open database of experimental pharmacokinetics (PK) and ADME data from clinical and preclinical studies."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: prism
    name: "PRISM"
    type: benchmark
    url: https://depmap.org/portal/prism/
    description: "Cancer drug sensitivity profiling of >4,500 drugs across >900 cancer cell lines using pooled-cell-line barcoding."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: proteingym
    name: "ProteinGym"
    type: benchmark
    url: https://github.com/OATML-Markslab/ProteinGym
    description: "Large-scale benchmark of deep mutational scanning assays for evaluating protein fitness landscape models."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: qm9
    name: "QM9"
    type: benchmark
    url: https://figshare.com/collections/Quantum_chemistry_structures_and_properties_of_134_kilo_molecules/978904
    description: "Quantum chemistry properties for 134K stable small organic molecules computed at DFT level."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: scib_single_cell_integration_benchmarks
    name: "scIB (Single-cell Integration Benchmarks)"
    type: benchmark
    url: https://github.com/theislab/scib
    description: "Comprehensive benchmarking framework for single-cell data integration methods."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: scperturb
    name: "scPerturb"
    type: benchmark
    url: https://github.com/sanderlab/scPerturb
    description: "Curated and continuously updated single-cell perturbation data resource spanning CRISPR and drug perturbation studies."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: sider_side_effect_resource
    name: "SIDER (Side Effect Resource)"
    type: benchmark
    url: http://sideeffects.embl.de/
    description: "Database of 1,430 approved drugs with their recorded adverse drug reactions across 27 system-organ classes."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: tabula_muris
    name: "Tabula Muris"
    type: benchmark
    url: https://tabula-muris.ds.czbiohub.org/
    description: "Comprehensive single-cell atlas of 20 mouse organs and tissues, enabling cross-tissue and cross-species comparisons."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: tabula_sapiens
    name: "Tabula Sapiens"
    type: benchmark
    url: https://tabula-sapiens-portal.ds.czbiohub.org/
    description: "Comprehensive human single-cell atlas of ~500K cells from 24 organs and tissues across multiple donors."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: tape_tasks_assessing_protein_embeddings
    name: "TAPE (Tasks Assessing Protein Embeddings)"
    type: benchmark
    url: https://github.com/songlab-cal/tape
    description: "Benchmark suite of five biologically meaningful semi-supervised learning tasks for evaluating protein representations."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: tcga_virtual_spatial_transcriptomics_atlas
    name: "TCGA virtual spatial transcriptomics atlas"
    type: benchmark
    url: https://huggingface.co/datasets/ratschlab/TCGA_virtual_spatial_transcriptomics_atlas
    description: "DeepSpot-M predicted transcriptome-wide ST for TCGA H&E (FF + FFPE; 28,664 slides / 32 cancer types; gated). Paper: [DeepSpot-M](https://www.medrxiv.org/content/10.64898/2026.06.19.26356060v1)."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: the_cancer_genome_atlas_tcga
    name: "The Cancer Genome Atlas (TCGA)"
    type: benchmark
    url: https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga
    description: "Comprehensive multi-omics (genomics, transcriptomics, proteomics, methylation) dataset for 33 cancer types across ~11,000 patients."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: therapeutics_data_commons_tdc
    name: "Therapeutics Data Commons (TDC)"
    type: benchmark
    url: https://tdcommons.ai/
    description: "Unified benchmark suite covering ADMET, drug-target interaction, drug response, and more."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: tox21
    name: "Tox21"
    type: benchmark
    url: https://tripod.nih.gov/tox21/challenge/
    description: "12,707 compounds tested in 12 nuclear receptor and stress-response pathway biochemical assays for toxicity prediction."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: uk_biobank
    name: "UK Biobank"
    type: benchmark
    url: https://www.ukbiobank.ac.uk/
    description: "Large-scale biomedical database of ~500K participants with genetic, imaging, and health data for population genetics and disease studies."
    tags: [benchmarks-and-datasets]
    tasks: []
    modalities: []
    organism: []
    api: false

  - id: 10x_genomics_dataset
    name: "10x Genomics Dataset"
    type: database
    url: https://www.10xgenomics.com/resources/datasets
    description: "Collection of single-cell datasets."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: alphafold_protein_structure_database
    name: "AlphaFold Protein Structure Database"
    type: database
    url: https://alphafold.ebi.ac.uk/api-docs
    description: "3D protein structure predictions."
    tags: [protein]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: bindingdb
    name: "BindingDB"
    type: database
    url: https://www.bindingdb.org/rwd/bind/index.jsp
    description: "Compounds and target database."
    tags: [chemical-protein-interaction, interaction]
    tasks: []
    modalities: [Protein, Small Molecule]
    organism: []
    api: false

  - id: biocyc
    name: "BioCyc"
    type: database
    url: https://biocyc.org/
    description: "Collection of pathway/genome databases across thousands of organisms."
    tags: [pathway]
    tasks: []
    modalities: [Pathway]
    organism: []
    api: false

  - id: biogrid
    name: "BioGRID"
    type: database
    url: https://thebiogrid.org/
    description: "Protein, genetic, and chemical interactions."
    tags: [interaction, protein-protein-interaction]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: cancer_cell_line_encyclopedia
    name: "Cancer Cell Line Encyclopedia"
    type: database
    url: https://sites.broadinstitute.org/ccle/
    description: "Database of ~1000 cancer cell lines."
    tags: [drug-cell-line-response, interaction]
    tasks: []
    modalities: [Gene Expression, Small Molecule]
    organism: []
    api: false

  - id: catalogue_of_somatic_mutations_in_cancer_cosmic
    name: "Catalogue Of Somatic Mutations In Cancer (COSMIC)"
    type: database
    url: https://cancer.sanger.ac.uk/cosmic
    description: "Resource on somatic mutations in cancers."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: cath_database
    name: "CATH database"
    type: database
    url: https://www.cathdb.info/
    description: "Hierarchical classification of protein domain structures."
    tags: [protein]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: cbioportal
    name: "cBioPortal"
    type: database
    url: https://www.cbioportal.org/
    description: "Cancer genomics database; aggregating many patient datasets."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: cellminer_cross_database_cellminercdb
    name: "CellMiner Cross Database (CellMinerCDB)"
    type: database
    url: https://discover.nci.nih.gov/cellminercdb/
    description: "Integrates multiple cancer cell line databases."
    tags: [drug-cell-line-response, interaction]
    tasks: []
    modalities: [Gene Expression, Small Molecule]
    organism: []
    api: false

  - id: chebi
    name: "ChEBI"
    type: database
    url: https://www.ebi.ac.uk/chebi/
    description: "Database focused on small chemical compounds."
    tags: [compound]
    tasks: []
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: chembl
    name: "ChEMBL"
    type: database
    url: https://www.ebi.ac.uk/chembl/
    description: "Bioactive molecules with drug-like properties."
    tags: [compound]
    tasks: []
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: chemspider
    name: "ChemSpider"
    type: database
    url: http://www.chemspider.com/
    description: "Chemical structure database."
    tags: [compound]
    tasks: []
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: clinicaltrials_gov
    name: "ClinicalTrials.gov"
    type: database
    url: https://clinicaltrials.gov/
    description: "Privately and publicly funded clinical studies."
    tags: [clinical-trial]
    tasks: []
    modalities: [Clinical]
    organism: []
    api: false

  - id: comparative_toxicogenomics_database
    name: "Comparative Toxicogenomics Database"
    type: database
    url: http://ctdbase.org/
    description: "Chemical-gene interactions, chemical-disease and gene-disease associations, chemical-phenotype associations."
    tags: [drug-gene-interaction, interaction]
    tasks: []
    modalities: [Gene, Small Molecule]
    organism: []
    api: false

  - id: critical_assessment_of_structure_prediction_casp
    name: "Critical Assessment of Structure Prediction (CASP)"
    type: database
    url: https://predictioncenter.org/
    description: "Assessing methods for protein structure prediction."
    tags: [protein]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: cz_cellxgene
    name: "CZ CELLxGENE"
    type: database
    url: https://cellxgene.cziscience.com/
    description: "Single-cell dataset repository and interactive explorer from the Chan Zuckerberg Initiative."
    tags: [scrna]
    tasks: []
    modalities: [Single Cell]
    organism: []
    api: false

  - id: davis_kinase_inhibitors_db
    name: "Davis kinase inhibitors DB"
    type: database
    url: http://staff.cs.utu.fi/~aijrinas/dti/
    description: "Experimental kinase inhibitor binding affinity dataset for protein–ligand interaction research."
    tags: [chemical-protein-interaction, interaction]
    tasks: []
    modalities: [Protein, Small Molecule]
    organism: []
    api: false

  - id: dependency_map_depmap
    name: "Dependency Map (DepMap)"
    type: database
    url: https://depmap.org/portal/
    description: "CRISPR-Cas9 screens in cancer cell lines."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: dgidb
    name: "DGIdb"
    type: database
    url: https://www.dgidb.org/
    description: "Drug-gene interactions and the druggable genome."
    tags: [drug-gene-interaction, interaction]
    tasks: []
    modalities: [Gene, Small Molecule]
    organism: []
    api: false

  - id: diseases
    name: "DISEASES"
    type: database
    url: https://diseases.jensenlab.org/
    description: "Gene–disease association database integrating evidence from text mining, curated databases, and experimental data."
    tags: [disease]
    tasks: []
    modalities: [Disease]
    organism: []
    api: false

  - id: disgenet
    name: "DisGeNET"
    type: database
    url: https://www.disgenet.org/
    description: "Database of gene-disease associations integrating expert-curated and GWAS data."
    tags: [disease]
    tasks: []
    modalities: [Disease]
    organism: []
    api: false

  - id: drkg
    name: "DRKG"
    type: database
    url: https://github.com/gnn4dr/DRKG
    description: "Large-scale biological knowledge graph for drug discovery."
    tags: [interaction, knowledge-graph]
    tasks: []
    modalities: [Knowledge Graph]
    organism: []
    api: false

  - id: drug_mechanism_database_drugmechdb
    name: "Drug Mechanism Database (DrugMechDB)"
    type: database
    url: https://github.com/SuLab/DrugMechDB/tree/2.0.1
    description: "Mechanisms of action from drug to disease."
    tags: [interaction, knowledge-graph]
    tasks: []
    modalities: [Knowledge Graph]
    organism: []
    api: false

  - id: drug_repurposing_hub
    name: "Drug Repurposing Hub"
    type: database
    url: https://repo-hub.broadinstitute.org/repurposing#download-data
    description: "Collections of drug repurposing data (drug, MoA, target, etc)."
    tags: [compound]
    tasks: []
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: drugbank
    name: "DrugBank"
    type: database
    url: https://go.drugbank.com/
    description: "Database of drugs and targets (University of Alberta)."
    tags: [disease]
    tasks: []
    modalities: [Disease]
    organism: []
    api: false

  - id: drugcentral
    name: "DrugCentral"
    type: database
    url: http://drugcentral.org/
    description: "Online drug compendium with drug mode of action and indication information."
    tags: [compound]
    tasks: []
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: drugtargetcommons
    name: "DrugTargetCommons"
    type: database
    url: https://drugtargetcommons.fimm.fi/
    description: "Community platform for curating and integrating experimental bioactivity data across drugs and targets."
    tags: [compound]
    tasks: []
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: encode
    name: "ENCODE"
    type: database
    url: https://www.encodeproject.org/
    description: "Encyclopedia of DNA Elements; regulatory and functional genomic elements across the genome."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: ensembl
    name: "Ensembl"
    type: database
    url: https://www.ensembl.org/
    description: "Genome browser and annotation database for vertebrate and other eukaryotic genomes."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: eu_drug_regulating_authorities_clinical_trials_db_eudract
    name: "EU Drug Regulating Authorities Clinical Trials DB (EudraCT)"
    type: database
    url: https://eudract.ema.europa.eu/
    description: "European clinical trial database."
    tags: [clinical-trial]
    tasks: []
    modalities: [Clinical]
    organism: []
    api: false

  - id: fantom5
    name: "FANTOM5"
    type: database
    url: https://fantom.gsc.riken.jp/5/
    description: "Functional annotation of mammalian genome; comprehensive atlas of active enhancers, promoters, and transcription start sites across human and mouse cell types."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: genbank
    name: "GenBank"
    type: database
    url: https://www.ncbi.nlm.nih.gov/genbank/
    description: "NCBI's database of genetic sequences."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: gene_expression_omnibus
    name: "Gene Expression Omnibus"
    type: database
    url: https://www.ncbi.nlm.nih.gov/geo/
    description: "Public functional genomics database."
    tags: [scrna]
    tasks: []
    modalities: [Single Cell]
    organism: []
    api: false

  - id: genomics_of_drug_sensitivity_in_cancer_gdsc
    name: "Genomics of Drug Sensitivity in Cancer (GDSC)"
    type: database
    url: https://www.cancerrxgene.org/
    description: "Drug sensitivity for ~1000 human cancer cell lines and hundreds of compounds."
    tags: [benchmarks-and-datasets, drug-cell-line-response, interaction]
    tasks: []
    modalities: [Gene Expression, Small Molecule]
    organism: []
    api: false

  - id: gnomad
    name: "gnomAD"
    type: database
    url: https://gnomad.broadinstitute.org/
    description: "Genome Aggregation Database; genetic variation from large-scale sequencing projects."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: hetionet
    name: "Hetionet"
    type: database
    url: https://github.com/hetio/hetionet
    description: "Heterogeneous network integrating genes, diseases, drugs, pathways, and more."
    tags: [interaction, knowledge-graph]
    tasks: []
    modalities: [Knowledge Graph]
    organism: []
    api: false

  - id: hippie
    name: "HIPPIE"
    type: database
    url: http://cbdm-01.zdv.uni-mainz.de/~mschaefer/hippie/
    description: "Human protein-protein interaction database."
    tags: [interaction, protein-protein-interaction]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: hmdb_human_metabolome_database
    name: "HMDB (Human Metabolome Database)"
    type: database
    url: https://hmdb.ca/
    description: "Comprehensive database of small molecule metabolites found in the human body."
    tags: [compound]
    tasks: []
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: human_cell_atlas
    name: "Human Cell Atlas"
    type: database
    url: https://www.humancellatlas.org/
    description: "Open global atlas of all cells in the human body."
    tags: [scrna]
    tasks: []
    modalities: [Single Cell]
    organism: []
    api: false

  - id: human_genome_resources_at_ncbi
    name: "Human Genome Resources at NCBI"
    type: database
    url: https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml
    description: "Database for genomics, proteomics, transcriptomics, and systems biology."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: human_phenotype_ontology_hpo
    name: "Human Phenotype Ontology (HPO)"
    type: database
    url: https://hpo.jax.org/
    description: "Standardized vocabulary of phenotypic abnormalities in human disease, linking genes, variants, and clinical features."
    tags: [disease]
    tasks: []
    modalities: [Disease]
    organism: []
    api: false

  - id: icd10
    name: "ICD10"
    type: database
    url: https://icd.who.int/browse10/2019/en
    description: "International Classification of Diseases, 10th revision."
    tags: [clinical-trial]
    tasks: []
    modalities: [Clinical]
    organism: []
    api: false

  - id: intact
    name: "IntAct"
    type: database
    url: https://www.ebi.ac.uk/intact/home
    description: "Open-source molecular interaction database and analysis system from EMBL-EBI."
    tags: [interaction, protein-protein-interaction]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: interpro
    name: "InterPro"
    type: database
    url: https://www.ebi.ac.uk/interpro/
    description: "Protein families, domains, and functional sites database integrating 14 member databases including Pfam and PROSITE."
    tags: [protein]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: jaspar
    name: "JASPAR"
    type: database
    url: http://jaspar.genereg.net/
    description: "Database of transcription factor binding profiles."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: kegg_compound
    name: "KEGG COMPOUND"
    type: database
    url: https://www.genome.jp/kegg/compound/
    description: "Collection of small molecules and biopolymers."
    tags: [compound]
    tasks: []
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: kegg_drug
    name: "KEGG DRUG"
    type: database
    url: https://www.genome.jp/kegg/drug/
    description: "Comprehensive, approved drug information."
    tags: [disease]
    tasks: []
    modalities: [Disease]
    organism: []
    api: false

  - id: kegg_pathway
    name: "KEGG PATHWAY"
    type: database
    url: https://www.genome.jp/kegg/pathway.html
    description: "Collection of pathway maps."
    tags: [pathway]
    tasks: []
    modalities: [Pathway]
    organism: []
    api: false

  - id: kinase_inhibitor_bioactivity_data_kiba
    name: "Kinase Inhibitor Bioactivity Data (KIBA)"
    type: database
    url: https://janeliascicomp.github.io/KIBA/
    description: "Integrated bioactivity scores for kinase inhibitors combining Ki, Kd, and IC50 measurements."
    tags: [chemical-protein-interaction, interaction]
    tasks: []
    modalities: [Protein, Small Molecule]
    organism: []
    api: false

  - id: lipid_maps
    name: "LIPID MAPS"
    type: database
    url: https://www.lipidmaps.org/databases/lmsd/overview
    description: "Database of lipids."
    tags: [compound]
    tasks: []
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: massbank
    name: "MassBank"
    type: database
    url: http://www.massbank.jp/
    description: "Open source databases and tools for mass spectrometry reference spectra."
    tags: [mass-spectra]
    tasks: []
    modalities: [Mass Spectra]
    organism: []
    api: false

  - id: mgnify
    name: "MGnify"
    type: database
    url: https://www.ebi.ac.uk/metagenomics/
    description: "Resource for metagenomic and metatranscriptomic data."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: mimic_iv
    name: "MIMIC-IV"
    type: database
    url: https://mimic.mit.edu/
    description: "Freely accessible critical care database."
    tags: [clinical-trial]
    tasks: []
    modalities: [Clinical]
    organism: []
    api: false

  - id: mirbase
    name: "miRBase"
    type: database
    url: https://www.mirbase.org/
    description: "Reference repository for microRNA gene annotations, sequences, and experimentally validated targets."
    tags: [gene-regulatory-network, interaction]
    tasks: []
    modalities: [Gene Expression]
    organism: []
    api: false

  - id: mona_massbank_of_north_america
    name: "MoNA MassBank of North America"
    type: database
    url: https://mona.fiehnlab.ucdavis.edu/
    description: "Meta-database of metabolite mass spectra, metadata, and associated compounds."
    tags: [mass-spectra]
    tasks: []
    modalities: [Mass Spectra]
    organism: []
    api: false

  - id: msigdb_molecular_signatures_database
    name: "MSigDB (Molecular Signatures Database)"
    type: database
    url: https://www.gsea-msigdb.org/gsea/msigdb
    description: "Curated gene sets derived from pathways and biological processes."
    tags: [pathway]
    tasks: []
    modalities: [Pathway]
    organism: []
    api: false

  - id: nci60
    name: "NCI60"
    type: database
    url: https://dtp.cancer.gov/discovery_development/nci-60/
    description: "Focuses on 60 cancer cell lines and many drugs."
    tags: [benchmarks-and-datasets, drug-cell-line-response, interaction]
    tasks: []
    modalities: [Gene Expression, Small Molecule]
    organism: []
    api: false

  - id: nextprot
    name: "NeXtProt"
    type: database
    url: https://www.nextprot.org/
    description: "Expert knowledge base on human proteins with deep functional annotation, complementary to UniProt."
    tags: [protein]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: oadb_observed_antibody_space_database
    name: "OADB (Observed Antibody Space Database)"
    type: database
    url: http://opig.stats.ox.ac.uk/webapps/oas/
    description: "Database of antibody sequences from immune repertoire sequencing."
    tags: [protein]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: omim_online_mendelian_inheritance_in_man
    name: "OMIM (Online Mendelian Inheritance in Man)"
    type: database
    url: https://www.omim.org/
    description: "Comprehensive database of human genes and genetic disorders."
    tags: [disease]
    tasks: []
    modalities: [Disease]
    organism: []
    api: false

  - id: omnipath
    name: "OmniPath"
    type: database
    url: https://omnipathdb.org/
    description: "Comprehensive resource integrating protein interactions, signaling pathways, gene regulatory networks, and miRNA targets from over 100 databases."
    tags: [pathway]
    tasks: []
    modalities: [Pathway]
    organism: []
    api: false

  - id: oncokb
    name: "OncoKB"
    type: database
    url: https://www.oncokb.org/
    description: "Precision oncology knowledge base of cancer genes, variants, and therapeutic implications."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: open_targets_platform
    name: "Open Targets Platform"
    type: database
    url: https://platform.opentargets.org/
    description: "Systematic target identification and prioritization platform integrating genetics, genomics, and drug data for drug discovery."
    tags: [disease]
    tasks: []
    modalities: [Disease]
    organism: []
    api: false

  - id: pathwaycommons
    name: "PathwayCommons"
    type: database
    url: https://www.pathwaycommons.org/
    description: "Database of pathways and interactions."
    tags: [pathway]
    tasks: []
    modalities: [Pathway]
    organism: []
    api: false

  - id: pdbbind
    name: "PDBBind"
    type: database
    url: https://www.pdbbind-plus.org.cn/
    description: "Binding affinity data for biomolecular complexes."
    tags: [chemical-protein-interaction, interaction]
    tasks: []
    modalities: [Protein, Small Molecule]
    organism: []
    api: false

  - id: pfam
    name: "Pfam"
    type: database
    url: https://www.ebi.ac.uk/interpro/entry/pfam/
    description: "Database of protein families described by multiple sequence alignments and hidden Markov models."
    tags: [protein]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: primekg
    name: "PrimeKG"
    type: database
    url: https://github.com/mims-harvard/PrimeKG
    description: "Multi-modal precision medicine knowledge graph integrating clinical, genetic, and drug data."
    tags: [interaction, knowledge-graph]
    tasks: []
    modalities: [Knowledge Graph]
    organism: []
    api: false

  - id: protein_data_bank_pdb
    name: "PROTEIN DATA BANK (PDB)"
    type: database
    url: https://www.rcsb.org/
    description: "3D structures of proteins, nucleic acids, complexes."
    tags: [protein]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: pubchem
    name: "PubChem"
    type: database
    url: https://pubchem.ncbi.nlm.nih.gov/
    description: "One of the largest chemical databases (compounds, genes, and proteins)."
    tags: [compound]
    tasks: []
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: rcsb_protein_data_bank
    name: "RCSB Protein Data Bank"
    type: database
    url: https://www.rcsb.org/
    description: "Repository for structural data of biological molecules."
    tags: [protein]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: reactome
    name: "Reactome"
    type: database
    url: https://reactome.org/
    description: "Expert-curated, peer-reviewed pathway database with detailed reaction mechanisms."
    tags: [pathway]
    tasks: []
    modalities: [Pathway]
    organism: []
    api: false

  - id: regnetwork
    name: "RegNetwork"
    type: database
    url: http://www.regnetworkweb.org/
    description: "Database of gene regulatory networks covering transcription factor–target gene and miRNA–gene interaction data across multiple species."
    tags: [gene-regulatory-network, interaction]
    tasks: []
    modalities: [Gene Expression]
    organism: []
    api: false

  - id: rfam
    name: "Rfam"
    type: database
    url: https://rfam.org/
    description: "Database of RNA families with sequence alignments and consensus structures."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: rhea
    name: "Rhea"
    type: database
    url: https://www.rhea-db.org/
    description: "Database of chemical reactions."
    tags: [compound]
    tasks: []
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: roadmap_epigenomics
    name: "ROADMAP Epigenomics"
    type: database
    url: http://www.roadmapepigenomics.org/
    description: "Reference epigenome maps for 111 primary human cell types and tissues, including histone modifications, chromatin accessibility, and DNA methylation."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: sabdab
    name: "SAbDab"
    type: database
    url: https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab
    description: "Structural Antibody Database containing all antibody structures in the PDB."
    tags: [protein]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: signor_2_0
    name: "SIGNOR 2.0"
    type: database
    url: https://signor.uniroma2.it/
    description: "Database of causal signaling interactions and pathways, with signed and directed relationships between proteins."
    tags: [pathway]
    tasks: []
    modalities: [Pathway]
    organism: []
    api: false

  - id: single_cell_expression_atlas
    name: "Single Cell Expression Atlas"
    type: database
    url: https://www.ebi.ac.uk/gxa/sc/home
    description: "Public database for single-cell RNA."
    tags: [scrna]
    tasks: []
    modalities: [Single Cell]
    organism: []
    api: false

  - id: single_cell_portal
    name: "Single Cell PORTAL"
    type: database
    url: https://singlecell.broadinstitute.org/single_cell
    description: "Public database for single-cell RNA."
    tags: [scrna]
    tasks: []
    modalities: [Single Cell]
    organism: []
    api: false

  - id: snap
    name: "SNAP"
    type: database
    url: https://snap.stanford.edu/biodata/datasets/10002/10002-ChG-Miner.html
    description: "Dataset of drug-gene interactions."
    tags: [drug-gene-interaction, interaction]
    tasks: []
    modalities: [Gene, Small Molecule]
    organism: []
    api: false

  - id: stitch
    name: "STITCH"
    type: database
    url: http://stitch.embl.de/
    description: "Chemical-protein interactions."
    tags: [chemical-protein-interaction, interaction]
    tasks: []
    modalities: [Protein, Small Molecule]
    organism: []
    api: false

  - id: string
    name: "STRING"
    type: database
    url: https://string-db.org/
    description: "PPI networks for multiple organisms."
    tags: [interaction, protein-protein-interaction]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: the_genotype_tissue_expression_gtex
    name: "The Genotype-Tissue Expression (GTEx)"
    type: database
    url: https://gtexportal.org/home/
    description: "Human gene expression and regulation resource."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: the_human_protein_atlas
    name: "THE HUMAN PROTEIN ATLAS"
    type: database
    url: https://www.proteinatlas.org/
    description: "Comprehensive human protein database (cells, tissues, organs)."
    tags: [protein]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: therapeutic_target_database
    name: "Therapeutic Target Database"
    type: database
    url: https://idrblab.net/ttd/full-data-download
    description: "Drug-target, target-disease, and drug-disease datasets."
    tags: [compound]
    tasks: []
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: trrust_v2
    name: "TRRUST v2"
    type: database
    url: https://www.grnpedia.org/trrust/
    description: "Manually curated database of human and mouse transcriptional regulatory interactions between transcription factors and their target genes, expanded with literature-derived evidence."
    tags: [gene-regulatory-network, interaction]
    tasks: []
    modalities: [Gene Expression]
    organism: []
    api: false

  - id: ucsc_genome_browser
    name: "UCSC Genome Browser"
    type: database
    url: https://genome.ucsc.edu/
    description: "UCSC's genome browser."
    tags: [genome]
    tasks: []
    modalities: [Genomics]
    organism: []
    api: false

  - id: uniclust
    name: "Uniclust"
    type: database
    url: https://uniclust.mmseqs.com/
    description: "Clustered protein sequence databases."
    tags: [protein]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: uniprot
    name: "UniProt"
    type: database
    url: https://www.uniprot.org/
    description: "Functional information on proteins."
    tags: [protein]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: uniref
    name: "UniRef"
    type: database
    url: https://www.uniprot.org/uniref/
    description: "Non-redundant sequence database clustering UniProtKB entries at multiple sequence identity thresholds."
    tags: [protein]
    tasks: []
    modalities: [Protein]
    organism: []
    api: false

  - id: wikipathways
    name: "WikiPathways"
    type: database
    url: https://wikipathways.org/
    description: "Database of biological pathways."
    tags: [pathway]
    tasks: []
    modalities: [Pathway]
    organism: []
    api: false

  - id: zinc_ligand_discovery_database
    name: "ZINC ligand discovery database"
    type: database
    url: https://zinc.docking.org/
    description: "Free database of commercially-available compounds for virtual screening."
    tags: [compound]
    tasks: []
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: aestetik
    name: "AESTETIK"
    type: model
    url: https://github.com/ratschlab/aestetik
    description: "Autoencoder for spatial transcriptomics representation learning using topology and histology image knowledge."
    tags: [foundation-models, single-cell-foundation-models, spatial-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Spatial Transcriptomics]
    organism: []
    api: false

  - id: ai4chem_chemllm_7b_chat
    name: "AI4Chem/ChemLLM-7B-Chat"
    type: model
    url: https://huggingface.co/AI4Chem/ChemLLM-7B-Chat
    description: "LLM for chemical & molecular science."
    tags: [llm-for-biology]
    tasks: [Language Modeling]
    modalities: [Text]
    organism: []
    api: false

  - id: alphafold3
    name: "AlphaFold3"
    type: model
    url: https://github.com/google-deepmind/alphafold3
    description: "Predicts structures of proteins, nucleic acids, small molecules, and their complexes."
    tags: [foundation-models, protein-foundation-models, protein-structure-prediction-and-design]
    tasks: [Foundation Model, Protein Structure Prediction]
    modalities: [Protein]
    organism: []
    api: false

  - id: ankh
    name: "Ankh"
    type: model
    url: https://github.com/agemagician/Ankh
    description: "Efficient protein language model optimized for downstream prediction tasks including secondary structure, localization, and function annotation."
    tags: [foundation-models, pre-trained-embedding, protein-foundation-models]
    tasks: [Foundation Model]
    modalities: [Protein]
    organism: []
    api: false

  - id: babel
    name: "BABEL"
    type: model
    url: https://github.com/wukevin/babel
    description: "Cross-modality translation model enabling prediction between scRNA-seq and scATAC-seq profiles without requiring paired single-cell measurements."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
    organism: []
    api: false

  - id: basenji
    name: "Basenji"
    type: model
    url: https://github.com/calico/basenji
    description: "Sequential regulatory activity prediction from DNA sequences."
    tags: [foundation-models, genomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Genomics]
    organism: []
    api: false

  - id: biogpt
    name: "BioGPT"
    type: model
    url: https://github.com/microsoft/BioGPT
    description: "LLM for biomedical text generation."
    tags: [llm-for-biology]
    tasks: [Language Modeling]
    modalities: [Text]
    organism: []
    api: false

  - id: biomedclip
    name: "BiomedCLIP"
    type: model
    url: https://huggingface.co/microsoft/BiomedCLIP-PubMedBERT_256-vit_g_14
    description: "CLIP-based vision-language foundation model for biomedical images and text trained on PubMed figure–caption pairs."
    tags: [foundation-models, multi-modal-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Modal]
    organism: []
    api: false

  - id: biomedlm
    name: "BioMedLM"
    type: model
    url: https://huggingface.co/stanford-crfm/BioMedLM
    description: "2.7B parameter GPT-2-style language model trained exclusively on biomedical literature from PubMed for biomedical question answering and text generation."
    tags: [llm-for-biology]
    tasks: [Language Modeling]
    modalities: [Text]
    organism: []
    api: false

  - id: boltz_1
    name: "Boltz-1"
    type: model
    url: https://github.com/jwohlwend/boltz
    description: "Open-source all-atom biomolecular structure prediction model for proteins, nucleic acids, small molecules, and their complexes achieving AlphaFold3-level accuracy."
    tags: [foundation-models, protein-foundation-models, protein-structure-prediction-and-design]
    tasks: [Foundation Model, Protein Structure Prediction]
    modalities: [Protein]
    organism: []
    api: false

  - id: borzoi
    name: "Borzoi"
    type: model
    url: https://github.com/calico/borzoi
    description: "Extended successor to Enformer for predicting RNA-seq coverage from long genomic sequence windows (524 kb) with improved resolution."
    tags: [foundation-models, genomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Genomics]
    organism: []
    api: false

  - id: bulkformer
    name: "BulkFormer"
    type: model
    url: https://github.com/KangBoming/BulkFormer
    description: "Foundation model for bulk RNA-seq data; learns general transcriptomic representations."
    tags: [foundation-models, single-cell-foundation-models, transcriptomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Transcriptomics]
    organism: []
    api: false

  - id: caduceus
    name: "Caduceus"
    type: model
    url: https://github.com/kuleshov-group/caduceus
    description: "Bidirectional equivariant long-range DNA sequence model based on Mamba."
    tags: [foundation-models, genomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Genomics]
    organism: []
    api: false

  - id: cancerfoundation
    name: "CancerFoundation"
    type: model
    url: https://github.com/BoevaLab/CancerFoundation
    description: "Single-cell RNA-seq foundation model trained exclusively on a curated dataset of malignant cells to learn cancer-specific embeddings."
    tags: [foundation-models, single-cell-foundation-models, transcriptomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Transcriptomics]
    organism: []
    api: false

  - id: cassia
    name: "CASSIA"
    type: model
    url: https://github.com/ElliotXie/CASSIA
    description: "Multi-agent LLM for reference-free, interpretable cell-type annotation of single-cell RNA-seq data, with dedicated annotation, validation, scoring, and reporting agents."
    tags: [llm-for-biology]
    tasks: [Language Modeling]
    modalities: [Text]
    organism: []
    api: false

  - id: cellot
    name: "CellOT"
    type: model
    url: https://github.com/bunnech/cellot
    description: "Neural optimal transport framework for predicting single-cell responses to drug and genetic perturbations."
    tags: [drug-discovery, drug-perturbation]
    tasks: [Drug Discovery, Drug Perturbation]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: cellplm
    name: "CellPLM"
    type: model
    url: https://github.com/OmicsML/CellPLM
    description: "Cell pre-trained language model with inter-cell transformer architecture for diverse single-cell analysis tasks."
    tags: [foundation-models, single-cell-foundation-models, transcriptomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Transcriptomics]
    organism: []
    api: false

  - id: chai_1
    name: "Chai-1"
    type: model
    url: https://github.com/chaidiscovery/chai-lab
    description: "Unified molecular structure prediction model covering proteins, nucleic acids, small molecules, and complexes."
    tags: [foundation-models, protein-foundation-models, protein-structure-prediction-and-design]
    tasks: [Foundation Model, Protein Structure Prediction]
    modalities: [Protein]
    organism: []
    api: false

  - id: chatdrug
    name: "ChatDrug"
    type: model
    url: https://github.com/chao1224/ChatDrug
    description: "LLM-based conversational pipeline for drug discovery, using natural language prompts for iterative drug editing and optimization."
    tags: [llm-for-biology]
    tasks: [Language Modeling]
    modalities: [Text]
    organism: []
    api: false

  - id: chemberta_2
    name: "ChemBERTa-2"
    type: model
    url: https://github.com/seyonechithrananda/bert-loves-chemistry
    description: "RoBERTa-based molecular language model pretrained on SMILES for small-molecule representation learning."
    tags: [compound-embedding, compound-foundation-models, foundation-models]
    tasks: [Foundation Model]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: chemcpa
    name: "chemCPA"
    type: model
    url: https://github.com/theislab/chemCPA
    description: "Compositional perturbation autoencoder for predicting single-cell transcriptional responses to unseen drug perturbations and dose combinations."
    tags: [drug-discovery, drug-perturbation]
    tasks: [Drug Discovery, Drug Perturbation]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: chief
    name: "CHIEF"
    type: model
    url: https://github.com/hms-dbmi/CHIEF
    description: "Clinical Histopathology Imaging Evaluation Foundation model integrating histology images and clinical context for pan-cancer analysis."
    tags: [foundation-models, multi-modal-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Modal]
    organism: []
    api: false

  - id: clawbio
    name: "ClawBio"
    type: model
    url: https://github.com/ClawBio/ClawBio
    description: "Bioinformatics-native AI agent skill library with local-first pharmacogenomics, ancestry PCA, semantic similarity, nutrigenomics, and metagenomics skills."
    tags: [llm-for-biology]
    tasks: [Language Modeling]
    modalities: [Text]
    organism: []
    api: false

  - id: cmonge
    name: "CMonge"
    type: model
    url: https://github.com/AI4SCR/conditional-monge-gap
    description: "Conditional optimal transport model for generalizable single-cell perturbation response prediction across drugs and doses."
    tags: [drug-discovery, drug-perturbation]
    tasks: [Drug Discovery, Drug Perturbation]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: concerto
    name: "Concerto"
    type: model
    url: https://github.com/melobio/Concerto-reproducibility
    description: "Contrastive self-supervised learning framework for single-cell multimodal data integration, batch correction, and reference-query mapping."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
    organism: []
    api: false

  - id: conch
    name: "CONCH"
    type: model
    url: https://github.com/mahmoodlab/CONCH
    description: "Vision-language foundation model for computational pathology trained with contrastive captioning on pathology image–text pairs."
    tags: [foundation-models, single-cell-foundation-models, spatial-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Spatial Transcriptomics]
    organism: []
    api: false

  - id: cyclecdr
    name: "cycleCDR"
    type: model
    url: https://github.com/hliulab/cycleCDR
    description: "Interpretable cycle-consistency framework for modeling cellular responses to drug perturbations."
    tags: [drug-discovery, drug-perturbation]
    tasks: [Drug Discovery, Drug Perturbation]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: deepaeg
    name: "DeepAEG"
    type: model
    url: https://github.com/zhejiangzhuque/DeepAEG
    description: "GNN embedding + attention mechanism."
    tags: [drug-discovery, drug-response-prediction]
    tasks: [Drug Discovery, Drug Response Prediction]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: deepdsc
    name: "DeepDSC"
    type: model
    url: https://ieeexplore-ieee-org.ezp2.lib.umn.edu/stamp/stamp.jsp?tp=&arnumber=8723620&tag=1
    description: "Autoencoder + fully connected NN."
    tags: [drug-discovery, drug-response-prediction]
    tasks: [Drug Discovery, Drug Response Prediction]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: deepdta
    name: "DeepDTA"
    type: model
    url: https://github.com/hkmztrk/DeepDTA
    description: "Deep learning model using CNNs on protein sequences and drug SMILES."
    tags: [drug-discovery, drug-target-interaction]
    tasks: [Drug Discovery, Drug Target Interaction]
    modalities: [Protein, Small Molecule]
    organism: []
    api: false

  - id: deeppurpose
    name: "DeepPurpose"
    type: model
    url: https://github.com/kexinhuang12345/DeepPurpose
    description: "Deep learning library for drug repurposing."
    tags: [drug-discovery, drug-repurposing]
    tasks: [Drug Discovery, Drug Repurposing]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: deepsea
    name: "DeepSEA"
    type: model
    url: http://deepsea.princeton.edu/
    description: "Deep learning framework for predicting chromatin effects of sequence alterations with single-nucleotide sensitivity across thousands of chromatin features."
    tags: [foundation-models, genomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Genomics]
    organism: []
    api: false

  - id: deepspot
    name: "DeepSpot"
    type: model
    url: https://github.com/ratschlab/DeepSpot
    description: "Deep learning model predicting spatial transcriptomics from H&E images at spot and single-cell resolution."
    tags: [foundation-models, single-cell-foundation-models, spatial-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Spatial Transcriptomics]
    organism: []
    api: false

  - id: deepspot_m
    name: "DeepSpot-M"
    type: model
    url: https://github.com/ratschlab/DeepSpotM
    description: "Multimodal foundation model for transcriptome-wide virtual spatial transcriptomics from histology."
    tags: [foundation-models, single-cell-foundation-models, spatial-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Spatial Transcriptomics]
    organism: []
    api: false

  - id: deepspot2cell
    name: "DeepSpot2Cell"
    type: model
    url: https://github.com/ratschlab/DeepSpot2Cell
    description: "Predicts virtual single-cell spatial transcriptomics from H&E using spot-level supervision (NeurIPS 2025 Imageomics)."
    tags: [foundation-models, single-cell-foundation-models, spatial-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Spatial Transcriptomics]
    organism: []
    api: false

  - id: dgdrp
    name: "DGDRP"
    type: model
    url: https://github.com/minwoopak/heteronet
    description: "Multi-view embedding neural network."
    tags: [drug-discovery, drug-response-prediction]
    tasks: [Drug Discovery, Drug Response Prediction]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: diffdock
    name: "DiffDock"
    type: model
    url: https://github.com/gcorso/DiffDock
    description: "Diffusion generative model for molecular docking, predicting the binding pose of small molecules to protein targets."
    tags: [drug-discovery, molecular-generation]
    tasks: [Drug Discovery, Molecular Generation]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: diffsbdd
    name: "DiffSBDD"
    type: model
    url: https://github.com/arneschneuing/DiffSBDD
    description: "Equivariant diffusion model for structure-based drug design that generates molecules and binding conformations for protein targets."
    tags: [drug-discovery, molecular-generation]
    tasks: [Drug Discovery, Molecular Generation]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: dnabert
    name: "DNABERT"
    type: model
    url: https://github.com/jerryji1993/DNABERT
    description: "Pre-trained bidirectional encoder for DNA sequence analysis."
    tags: [foundation-models, genomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Genomics]
    organism: []
    api: false

  - id: dnabert_2
    name: "DNABERT-2"
    type: model
    url: https://github.com/Zhihan1996/DNABERT_2
    description: "Improved genome foundation model with efficient tokenization."
    tags: [foundation-models, genomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Genomics]
    organism: []
    api: false

  - id: drgat
    name: "drGAT"
    type: model
    url: https://github.com/inoue0426/drGAT
    description: "Attention-based model for drug response prediction with gene explainability."
    tags: [drug-discovery, drug-response-prediction]
    tasks: [Drug Discovery, Drug Response Prediction]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: drugban
    name: "DrugBAN"
    type: model
    url: https://github.com/peizhenbai/DrugBAN
    description: "Bilinear attention network for interpretable DTI prediction."
    tags: [drug-discovery, drug-target-interaction]
    tasks: [Drug Discovery, Drug Target Interaction]
    modalities: [Protein, Small Molecule]
    organism: []
    api: false

  - id: druml
    name: "DRUML"
    type: model
    url: https://github.com/CutillasLab/DRUMLR
    description: "Ensemble machine learning framework combining standard ML with deep learning to systematically rank anti-cancer drugs from proteomics and RNA-seq data."
    tags: [drug-discovery, drug-response-prediction]
    tasks: [Drug Discovery, Drug Response Prediction]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: dtinet
    name: "DTINet"
    type: model
    url: https://github.com/luoyunan/DTINet
    description: "Network-based framework integrating heterogeneous biological data for DTI prediction."
    tags: [drug-discovery, drug-target-interaction]
    tasks: [Drug Discovery, Drug Target Interaction]
    modalities: [Protein, Small Molecule]
    organism: []
    api: false

  - id: enformer
    name: "Enformer"
    type: model
    url: https://github.com/deepmind/deepmind-research/tree/master/enformer
    description: "Transformer model predicting gene expression from DNA sequence."
    tags: [foundation-models, genomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Genomics]
    organism: []
    api: false

  - id: esm3
    name: "ESM3"
    type: model
    url: https://github.com/evolutionaryscale/esm
    description: "Multimodal protein language model that jointly reasons over sequence, structure, and function for generative protein design and engineering."
    tags: [foundation-models, protein-foundation-models, protein-structure-prediction-and-design]
    tasks: [Foundation Model, Protein Structure Prediction]
    modalities: [Protein]
    organism: []
    api: false

  - id: esmfold
    name: "ESMFold"
    type: model
    url: https://github.com/facebookresearch/esm
    description: "Fast protein structure prediction using language model embeddings."
    tags: [foundation-models, protein-foundation-models, protein-structure-prediction-and-design]
    tasks: [Foundation Model, Protein Structure Prediction]
    modalities: [Protein]
    organism: []
    api: false

  - id: evo
    name: "Evo"
    type: model
    url: https://github.com/evo-design/evo
    description: "Long-context genomic foundation model (up to 1M tokens)."
    tags: [foundation-models, genomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Genomics]
    organism: []
    api: false

  - id: evodiff
    name: "EvoDiff"
    type: model
    url: https://github.com/microsoft/evodiff
    description: "Discrete diffusion framework for protein sequence generation trained on evolutionary-scale data, supporting unconditional generation, disordered region design, and functional motif scaffolding. [ [paper-2023](https://www.biorxiv.org/content/10.1101/2023.09.11.556673v1) ]"
    tags: [foundation-models, protein-foundation-models, protein-structure-prediction-and-design]
    tasks: [Foundation Model, Protein Structure Prediction]
    modalities: [Protein]
    organism: []
    api: false

  - id: evolutionary_scale_modeling_esm
    name: "Evolutionary Scale Modeling (ESM)"
    type: model
    url: https://github.com/facebookresearch/esm
    description: "Protein embeddings."
    tags: [foundation-models, pre-trained-embedding, protein-foundation-models]
    tasks: [Foundation Model]
    modalities: [Protein]
    organism: []
    api: false

  - id: gears
    name: "GEARS"
    type: model
    url: https://github.com/snap-stanford/GEARS
    description: "Graph-based model for predicting transcriptional responses to single and combinatorial genetic perturbations using biological priors."
    tags: [foundation-models, single-cell-foundation-models, transcriptomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Transcriptomics]
    organism: []
    api: false

  - id: genecompass
    name: "GeneCompass"
    type: model
    url: https://github.com/xCompass-AI/GeneCompass
    description: "Large-scale foundation model integrating DNA regulatory sequences and single-cell transcriptomics from 120M+ cells across multiple species for gene regulation prediction."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
    organism: []
    api: false

  - id: geneformer
    name: "Geneformer"
    type: model
    url: https://huggingface.co/ctheodoris/Geneformer
    description: "Context-aware, attention-based deep learning model pretrained on a large corpus of single-cell transcriptomes."
    tags: [foundation-models, single-cell-foundation-models, transcriptomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Transcriptomics]
    organism: []
    api: false

  - id: genegpt
    name: "GeneGPT"
    type: model
    url: https://github.com/ncbi/GeneGPT
    description: "LLM for biomedical information, integrated with various APIs."
    tags: [llm-for-biology]
    tasks: [Language Modeling]
    modalities: [Text]
    organism: []
    api: false

  - id: genept
    name: "GenePT"
    type: model
    url: https://github.com/yiqunchen/GenePT
    description: "Foundation LLM for single-cell data."
    tags: [llm-for-biology]
    tasks: [Language Modeling]
    modalities: [Text]
    organism: []
    api: false

  - id: gigapath
    name: "GigaPath"
    type: model
    url: https://github.com/prov-gigapath/prov-gigapath
    description: "Slide-level digital pathology foundation model pretrained on 1.3 billion pathology image tokens from whole-slide images."
    tags: [foundation-models, single-cell-foundation-models, spatial-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Spatial Transcriptomics]
    organism: []
    api: false

  - id: glue
    name: "GLUE"
    type: model
    url: https://github.com/gao-lab/GLUE
    description: "Graph-Linked Unified Embedding framework for unpaired single-cell multi-omics data integration across RNA, ATAC, methylation, and protein modalities."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
    organism: []
    api: false

  - id: gpn_genomic_pre_trained_network
    name: "GPN (Genomic Pre-trained Network)"
    type: model
    url: https://github.com/songlab-cal/gpn
    description: "Masked language model for DNA sequences enabling zero-shot variant effect prediction without requiring functional annotations."
    tags: [foundation-models, genomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Genomics]
    organism: []
    api: false

  - id: graphdta
    name: "GraphDTA"
    type: model
    url: https://github.com/thinng/GraphDTA
    description: "Graph neural network–based DTI prediction using molecular graphs."
    tags: [drug-discovery, drug-target-interaction]
    tasks: [Drug Discovery, Drug Target Interaction]
    modalities: [Protein, Small Molecule]
    organism: []
    api: false

  - id: grover
    name: "GROVER"
    type: model
    url: https://github.com/tencent-ailab/grover
    description: "Self-supervised graph transformer for large-scale molecular representation learning from unlabeled compounds."
    tags: [compound-embedding, compound-foundation-models, foundation-models]
    tasks: [Foundation Model]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: hidra
    name: "HiDRA"
    type: model
    url: https://github.com/bsml320/HiDRA
    description: "Hierarchical network model incorporating gene and pathway-level information for cancer drug response prediction."
    tags: [drug-discovery, drug-response-prediction]
    tasks: [Drug Discovery, Drug Response Prediction]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: hyenadna
    name: "HyenaDNA"
    type: model
    url: https://github.com/HazyResearch/hyena-dna
    description: "Long-range genomic foundation model handling sequences up to 1M tokens with sub-quadratic attention."
    tags: [foundation-models, genomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Genomics]
    organism: []
    api: false

  - id: jamie
    name: "JAMIE"
    type: model
    url: https://github.com/Oafish1/JAMIE
    description: "Joint variational autoencoder for multimodal single-cell data imputation and embedding."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
    organism: []
    api: false

  - id: jtvae
    name: "JTVAE"
    type: model
    url: https://github.com/wengong-jin/icml18-jtnn
    description: "Junction tree variational autoencoder for molecular graph generation that guarantees chemical validity via a hierarchical tree decomposition."
    tags: [drug-discovery, molecular-generation]
    tasks: [Drug Discovery, Molecular Generation]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: matcha
    name: "Matcha"
    type: model
    url: https://github.com/LigandPro/Matcha
    description: "Multi-stage Riemannian flow matching model for physically valid molecular docking with scoring, pose filtering, and benchmarks."
    tags: [drug-discovery, molecular-generation]
    tasks: [Drug Discovery, Molecular Generation]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: mcpinn
    name: "MCPINN"
    type: model
    url: https://github.com/mhlee0903/multi_channels_PINN
    description: "Drug discovery via compound-protein interaction and machine learning."
    tags: [compound-protein-interaction, drug-discovery]
    tasks: [Compound-Protein Interaction, Drug Discovery]
    modalities: [Protein, Small Molecule]
    organism: []
    api: false

  - id: midas
    name: "MIDAS"
    type: model
    url: https://github.com/labomics/midas
    description: "Mosaic integration and differential accessibility model for single-cell multi-omics that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
    organism: []
    api: false

  - id: mira
    name: "MIRA"
    type: model
    url: https://github.com/cistrome/MIRA
    description: "Probabilistic multimodal topic model jointly modeling single-cell transcriptomics and chromatin accessibility for regulatory network inference."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
    organism: []
    api: false

  - id: mofa
    name: "MOFA+"
    type: model
    url: https://github.com/bioFAM/MOFA2
    description: "Multi-Omics Factor Analysis framework identifying shared axes of variation across bulk and single-cell datasets including RNA, ATAC, proteomics, methylation, and copy number."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
    organism: []
    api: false

  - id: mofgcn
    name: "MOFGCN"
    type: model
    url: https://github.com/weiba/MOFGCN/tree/main
    description: "GCN + heterogeneous network."
    tags: [drug-discovery, drug-response-prediction]
    tasks: [Drug Discovery, Drug Response Prediction]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: mol2vec
    name: "Mol2Vec"
    type: model
    url: https://github.com/samoturk/mol2vec
    description: "Unsupervised molecular embedding method inspired by Word2Vec for learning vector representations of chemical substructures."
    tags: [compound-embedding, compound-foundation-models, foundation-models]
    tasks: [Foundation Model]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: molecular_transformer
    name: "Molecular Transformer"
    type: model
    url: https://github.com/pschwllr/MolecularTransformer
    description: "Sequence-to-sequence model for retrosynthesis prediction."
    tags: [drug-discovery, molecular-generation]
    tasks: [Drug Discovery, Molecular Generation]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: molformer
    name: "MolFormer"
    type: model
    url: https://github.com/IBM/molformer
    description: "Linear attention transformer pretrained on millions of SMILES strings for efficient molecular embeddings."
    tags: [compound-embedding, compound-foundation-models, foundation-models]
    tasks: [Foundation Model]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: molgpt
    name: "MolGPT"
    type: model
    url: https://github.com/devalab/molgpt
    description: "Transformer-based model for molecular generation."
    tags: [drug-discovery, molecular-generation]
    tasks: [Drug Discovery, Molecular Generation]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: molt5
    name: "MolT5"
    type: model
    url: https://github.com/blender-nlp/MolT5
    description: "Language model for molecular tasks bridging text and SMILES, enabling molecule captioning and text-driven molecule generation."
    tags: [llm-for-biology]
    tasks: [Language Modeling]
    modalities: [Text]
    organism: []
    api: false

  - id: moltrans
    name: "MolTrans"
    type: model
    url: https://github.com/kexinhuang12345/MolTrans
    description: "Transformer-based DTI model leveraging molecular substructures."
    tags: [drug-discovery, drug-target-interaction]
    tasks: [Drug Discovery, Drug Target Interaction]
    modalities: [Protein, Small Molecule]
    organism: []
    api: false

  - id: multigrate
    name: "Multigrate"
    type: model
    url: https://github.com/theislab/multigrate
    description: "Asymmetric multi-omics variational autoencoder for integrating single-cell data across RNA, ATAC, and protein modalities with missing-modality support."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
    organism: []
    api: false

  - id: multivi
    name: "MultiVI"
    type: model
    url: https://github.com/scverse/scvi-tools
    description: "Multi-modal variational autoencoder for integrating paired and unpaired single-cell RNA-seq and ATAC-seq measurements into a unified latent space."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
    organism: []
    api: false

  - id: musk
    name: "MUSK"
    type: model
    url: https://github.com/lilab-stanford/MUSK
    description: "Vision-language foundation model for precision oncology analyzing multimodal paired text and pathology image data for biomarker prediction and retrieval."
    tags: [foundation-models, multi-modal-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Modal]
    organism: []
    api: false

  - id: nbbayeslm
    name: "NbBayesLM"
    type: model
    url: https://github.com/FairuzShadmaniShishir/NbBayesLM
    description: "Bayesian neural network integrating protein language model embeddings and physicochemical features to predict nanobody thermostability with uncertainty estimates. [Paper](https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2026.1832968/full)"
    tags: [protein-property-prediction]
    tasks: [Protein Property Prediction]
    modalities: [Protein]
    organism: []
    api: false

  - id: neodti
    name: "NeoDTI"
    type: model
    url: https://github.com/FangpingWan/NeoDTI
    description: "Library for drug-target interaction prediction."
    tags: [drug-discovery, drug-target-interaction]
    tasks: [Drug Discovery, Drug Target Interaction]
    modalities: [Protein, Small Molecule]
    organism: []
    api: false

  - id: nicheformer
    name: "Nicheformer"
    type: model
    url: https://github.com/theislab/nicheformer
    description: "Foundation model for single-cell and spatial omics using a transformer architecture with positional embeddings to encode spatial cell information."
    tags: [foundation-models, single-cell-foundation-models, spatial-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Spatial Transcriptomics]
    organism: []
    api: false

  - id: nucleotide_transformer
    name: "Nucleotide Transformer"
    type: model
    url: https://github.com/instadeepai/nucleotide-transformer
    description: "Foundation model for genomic sequences across multiple species."
    tags: [foundation-models, genomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Genomics]
    organism: []
    api: false

  - id: omegafold
    name: "OmegaFold"
    type: model
    url: https://github.com/HeliXonProtein/OmegaFold
    description: "High-resolution de novo protein structure prediction from sequence."
    tags: [foundation-models, protein-foundation-models, protein-structure-prediction-and-design]
    tasks: [Foundation Model, Protein Structure Prediction]
    modalities: [Protein]
    organism: []
    api: false

  - id: openfold
    name: "OpenFold"
    type: model
    url: https://github.com/aqlaboratory/openfold
    description: "Trainable, memory-efficient open-source reproduction of AlphaFold2 enabling custom protein structure prediction workflows."
    tags: [foundation-models, protein-foundation-models, protein-structure-prediction-and-design]
    tasks: [Foundation Model, Protein Structure Prediction]
    modalities: [Protein]
    organism: []
    api: false

  - id: paccmannrl
    name: "PaccMannRL"
    type: model
    url: https://github.com/PaccMann/paccmann_generator
    description: "Reinforcement learning-based generative model for de novo hit-like anticancer molecule design from transcriptomic data."
    tags: [drug-discovery, molecular-generation]
    tasks: [Drug Discovery, Molecular Generation]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: pathomicfusion
    name: "PathomicFusion"
    type: model
    url: https://github.com/mahmoodlab/PathomicFusion
    description: "Integrated framework fusing histopathology and genomic features via CNN, GNN, and attention gating for cancer diagnosis and prognosis."
    tags: [foundation-models, multi-modal-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Modal]
    organism: []
    api: false

  - id: phikon
    name: "Phikon"
    type: model
    url: https://huggingface.co/owkin/phikon
    description: "ViT-based pathology foundation model pretrained with iBOT self-supervision on TCGA whole-slide images."
    tags: [foundation-models, single-cell-foundation-models, spatial-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Spatial Transcriptomics]
    organism: []
    api: false

  - id: plip
    name: "PLIP"
    type: model
    url: https://github.com/PathologyFoundation/plip
    description: "Vision-language foundation model for pathology trained with contrastive learning on pathology image–text pairs for image classification and text-to-image retrieval."
    tags: [foundation-models, multi-modal-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Modal]
    organism: []
    api: false

  - id: porpoise
    name: "PORPOISE"
    type: model
    url: https://github.com/mahmoodlab/PORPOISE
    description: "Pan-cancer integrative histology-genomic analysis framework using multimodal deep learning for patient stratification."
    tags: [foundation-models, multi-modal-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Modal]
    organism: []
    api: false

  - id: prnet
    name: "PRNet"
    type: model
    url: https://github.com/Perturbation-Response-Prediction/PRnet
    description: "Deep generative model for predicting transcriptional responses to novel chemical perturbations for drug discovery."
    tags: [drug-discovery, drug-perturbation]
    tasks: [Drug Discovery, Drug Perturbation]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: progen2
    name: "ProGen2"
    type: model
    url: https://github.com/salesforce/progen
    description: "Protein language model trained on diverse protein families for sequence generation and fitness prediction."
    tags: [foundation-models, pre-trained-embedding, protein-foundation-models]
    tasks: [Foundation Model]
    modalities: [Protein]
    organism: []
    api: false

  - id: proteinmpnn
    name: "ProteinMPNN"
    type: model
    url: https://github.com/dauparas/ProteinMPNN
    description: "Deep learning model for protein sequence design given backbone structure."
    tags: [foundation-models, protein-foundation-models, protein-structure-prediction-and-design]
    tasks: [Foundation Model, Protein Structure Prediction]
    modalities: [Protein]
    organism: []
    api: false

  - id: prottrans
    name: "ProtTrans"
    type: model
    url: https://github.com/agemagician/ProtTrans
    description: "Suite of protein language models (ProtBERT, ProtT5, ProtXLNet) trained on billions of protein sequences from UniRef and BFD."
    tags: [foundation-models, pre-trained-embedding, protein-foundation-models]
    tasks: [Foundation Model]
    modalities: [Protein]
    organism: []
    api: false

  - id: recover
    name: "RECOVER"
    type: model
    url: https://github.com/RECOVERcoalition/Recover
    description: "Machine learning framework for predicting synergistic drug combination responses across cell lines."
    tags: [drug-discovery, drug-response-prediction]
    tasks: [Drug Discovery, Drug Response Prediction]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: reinvent
    name: "REINVENT"
    type: model
    url: https://github.com/MolecularAI/Reinvent
    description: "Reinforcement learning for de novo drug design."
    tags: [drug-discovery, molecular-generation]
    tasks: [Drug Discovery, Molecular Generation]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: release
    name: "ReLeaSE"
    type: model
    url: https://github.com/isayev/ReLeaSE
    description: "Deep reinforcement learning framework for de novo drug design combining a generative and predictive model."
    tags: [drug-discovery, molecular-generation]
    tasks: [Drug Discovery, Molecular Generation]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: rfdiffusion
    name: "RFdiffusion"
    type: model
    url: https://github.com/RosettaCommons/RFdiffusion
    description: "Generative model for protein backbone design using diffusion."
    tags: [foundation-models, protein-foundation-models, protein-structure-prediction-and-design]
    tasks: [Foundation Model, Protein Structure Prediction]
    modalities: [Protein]
    organism: []
    api: false

  - id: rosettafold
    name: "RoseTTAFold"
    type: model
    url: https://github.com/RosettaCommons/RoseTTAFold
    description: "Three-track neural network for protein structure prediction."
    tags: [foundation-models, protein-foundation-models, protein-structure-prediction-and-design]
    tasks: [Foundation Model, Protein Structure Prediction]
    modalities: [Protein]
    organism: []
    api: false

  - id: saprot
    name: "SaProt"
    type: model
    url: https://github.com/westlake-reup/SaProt
    description: "Structure-aware protein language model using structure-aware tokens that encode both sequence and backbone geometry for improved function prediction."
    tags: [foundation-models, protein-foundation-models, protein-structure-prediction-and-design]
    tasks: [Foundation Model, Protein Structure Prediction]
    modalities: [Protein]
    organism: []
    api: false

  - id: saturn
    name: "SATURN"
    type: model
    url: https://github.com/snap-stanford/SATURN
    description: "Transformer-based model integrating gene expression and protein sequences via a protein language model to learn unified multi-species cell embeddings."
    tags: [foundation-models, single-cell-foundation-models, transcriptomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Transcriptomics]
    organism: []
    api: false

  - id: scarches
    name: "scArches"
    type: model
    url: https://github.com/theislab/scarches
    description: "Transfer learning framework for mapping new single-cell datasets onto pre-trained reference atlases across batches, conditions, and modalities."
    tags: [domain-alignment, foundation-models, single-cell-foundation-models]
    tasks: [Domain Alignment, Foundation Model]
    modalities: [Single Cell]
    organism: []
    api: false

  - id: scbert
    name: "scBERT"
    type: model
    url: https://github.com/TencentAILabHealthcare/scBERT
    description: "BERT-based foundation model pretrained on large-scale scRNA-seq data for cell type annotation."
    tags: [foundation-models, single-cell-foundation-models, transcriptomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Transcriptomics]
    organism: []
    api: false

  - id: scbutterfly
    name: "scButterfly"
    type: model
    url: https://github.com/BioX-NKU/scButterfly
    description: "Dual-aligned variational autoencoder for single-cell cross-modality translation between paired and unpaired multiomics data."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
    organism: []
    api: false

  - id: scfoundation
    name: "scFoundation"
    type: model
    url: https://github.com/biomap-research/scFoundation
    description: "Large-scale foundation model for single-cell gene expression, enabling multiple downstream tasks."
    tags: [foundation-models, single-cell-foundation-models, transcriptomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Transcriptomics]
    organism: []
    api: false

  - id: scgpt
    name: "scGPT"
    type: model
    url: https://github.com/bowang-lab/scGPT
    description: "Transformer-based foundation model pretrained on millions of single-cell profiles."
    tags: [foundation-models, single-cell-foundation-models, transcriptomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Transcriptomics]
    organism: []
    api: false

  - id: scgpt_spatial
    name: "scGPT-spatial"
    type: model
    url: https://github.com/bowang-lab/scGPT-spatial
    description: "Extension of scGPT for spatial transcriptomics with continual pretraining and a mixture-of-experts decoder for spatial gene expression analysis."
    tags: [foundation-models, single-cell-foundation-models, spatial-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Spatial Transcriptomics]
    organism: []
    api: false

  - id: scmulan
    name: "scMulan"
    type: model
    url: https://github.com/SuperBianC/scMulan
    description: "Single-cell multi-omic language model pretrained on ~10M cells spanning transcriptomics, epigenomics, and proteomics for cross-omics transfer tasks."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
    organism: []
    api: false

  - id: scpair
    name: "scPair"
    type: model
    url: https://github.com/quon-titative-biology/scPair
    description: "Bidirectional feedforward network for single-cell multimodal analysis with cross-modality prediction leveraging single-cell atlases."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
    organism: []
    api: false

  - id: scprint
    name: "scPRINT"
    type: model
    url: https://github.com/cantinilab/scPRINT
    description: "Pretrained on 50M cells for scRNA-seq denoising & zero imputation."
    tags: [llm-for-biology]
    tasks: [Language Modeling]
    modalities: [Text]
    organism: []
    api: false

  - id: sei
    name: "Sei"
    type: model
    url: https://github.com/FunctionLab/sei-framework
    description: "Sequence-to-function framework learning a genome-wide regulatory activity code from DNA sequences for variant effect prediction."
    tags: [foundation-models, genomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Genomics]
    organism: []
    api: false

  - id: spatialglue
    name: "SpatialGlue"
    type: model
    url: https://github.com/zhanglabtools/SpatialGlue
    description: "Graph attention network for spatial multi-omics integration jointly embedding spatial transcriptomics with chromatin accessibility or proteomics."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
    organism: []
    api: false

  - id: targetdiff
    name: "TargetDiff"
    type: model
    url: https://github.com/guanjq/targetdiff
    description: "3D equivariant diffusion model for structure-based drug design."
    tags: [drug-discovery, molecular-generation]
    tasks: [Drug Discovery, Molecular Generation]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: tgsa
    name: "TGSA"
    type: model
    url: https://github.com/violet-sto/TGSA
    description: "Tumor gene set and attention-based model leveraging biological pathway knowledge for drug response prediction."
    tags: [drug-discovery, drug-response-prediction]
    tasks: [Drug Discovery, Drug Response Prediction]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: toad
    name: "TOAD"
    type: model
    url: https://github.com/mahmoodlab/TOAD
    description: "Tumor Origin Assessment via Deep-learning; weakly-supervised multi-task model predicting cancer primary origin from H&E whole-slide images."
    tags: [foundation-models, multi-modal-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Modal]
    organism: []
    api: false

  - id: tosica
    name: "TOSICA"
    type: model
    url: https://github.com/JackieHanlaopo/TOSICA
    description: "Transformer-based framework for one-stop interpretable cell-type annotation supporting cross-dataset and cross-species transfer."
    tags: [domain-alignment, foundation-models, single-cell-foundation-models]
    tasks: [Domain Alignment, Foundation Model]
    modalities: [Single Cell]
    organism: []
    api: false

  - id: totalvi
    name: "totalVI"
    type: model
    url: https://github.com/scverse/scvi-tools
    description: "Probabilistic framework for joint analysis of paired scRNA-seq and protein (CITE-seq) data enabling multi-modal cell state representation across single-cell datasets."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
    organism: []
    api: false

  - id: transformercpi
    name: "TransformerCPI"
    type: model
    url: https://github.com/lifanchen-simm/transformerCPI
    description: "CPI prediction using Transformer."
    tags: [compound-protein-interaction, drug-discovery]
    tasks: [Compound-Protein Interaction, Drug Discovery]
    modalities: [Protein, Small Molecule]
    organism: []
    api: false

  - id: transigen
    name: "TranSiGen"
    type: model
    url: https://github.com/myzhengSIMM/TranSiGen
    description: "Dual-VAE architecture for ligand-based virtual screening, drug response prediction, and drug repurposing using chemical-induced transcriptional profiles."
    tags: [drug-discovery, drug-repurposing]
    tasks: [Drug Discovery, Drug Repurposing]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: uce
    name: "UCE"
    type: model
    url: https://github.com/snap-stanford/UCE
    description: "Universal Cell Embeddings: zero-shot single-cell embedding model trained on 36M cells across species, tissues, and assays without fine-tuning."
    tags: [foundation-models, single-cell-foundation-models, transcriptomics-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Transcriptomics]
    organism: []
    api: false

  - id: uni
    name: "UNI"
    type: model
    url: https://github.com/mahmoodlab/UNI
    description: "General-purpose self-supervised pathology foundation model trained on 100K+ whole-slide images for diverse computational pathology tasks."
    tags: [foundation-models, single-cell-foundation-models, spatial-foundation-models]
    tasks: [Foundation Model]
    modalities: [Single Cell, Spatial Transcriptomics]
    organism: []
    api: false

  - id: uni_mol
    name: "Uni-Mol"
    type: model
    url: https://github.com/deepmodeling/Uni-Mol
    description: "3D molecular pretraining framework for universal representation learning on molecules and protein pockets."
    tags: [compound-embedding, compound-foundation-models, foundation-models]
    tasks: [Foundation Model]
    modalities: [Small Molecule]
    organism: []
    api: false

  - id: unitednet
    name: "UnitedNet"
    type: model
    url: https://github.com/LiuLab-Bioelectronics-Harvard/UnitedNet
    description: "Interpretable multi-task deep neural network for single-cell multi-omics integration spanning transcriptomics, chromatin accessibility, and proteomics."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
    organism: []
    api: false

  - id: virchow
    name: "Virchow"
    type: model
    url: https://huggingface.co/paige-ai/Virchow
    description: "Million-slide digital pathology foundation model using a vision transformer and self-supervised distillation for tile-level pathology image representation."
    tags: [foundation-models, multi-modal-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Modal]
    organism: []
    api: false

  - id: autozyme
    name: "AutoZyme"
    type: toolkit
    url: https://github.com/ElliotXie/autozyme
    description: "Autonomous agentic framework that speeds up bioinformatics software (e.g. Scanpy, Seurat) on CPUs while preserving the original results."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: biopython
    name: "Biopython"
    type: toolkit
    url: https://biopython.org/
    description: "Collection of Python tools for biological computation including sequence analysis, structure parsing, and database access."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: casper
    name: "CaSpER"
    type: toolkit
    url: https://github.com/akdess/CaSpER
    description: "CNV identification and visualization by integrative analysis of single-cell or bulk RNA-seq data."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: cellcharter
    name: "CellCharter"
    type: toolkit
    url: https://github.com/CSOgroup/cellcharter
    description: "Identification and characterization of spatial cell niches from spatial transcriptomics using VAEs and Gaussian mixture models."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: cellchat
    name: "CellChat"
    type: toolkit
    url: https://github.com/sqjin/CellChat
    description: "Inference and analysis of cell-cell communication ligand-receptor networks from single-cell transcriptomics data."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: celltypist
    name: "CellTypist"
    type: toolkit
    url: https://github.com/Teichlab/celltypist
    description: "Automated cell type annotation for scRNA-seq."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: chatspatial
    name: "ChatSpatial"
    type: toolkit
    url: https://github.com/cafferychen777/ChatSpatial
    description: "MCP server for spatial transcriptomics analysis via natural language."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: chemistry_development_kit
    name: "Chemistry Development Kit"
    type: toolkit
    url: https://github.com/cdk/cdk
    description: "Cheminformatics software & machine learning tools."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: commot
    name: "COMMOT"
    type: toolkit
    url: https://github.com/zcang/COMMOT
    description: "Optimal transport-based framework for screening cell-cell communication in spatial transcriptomics."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: deepchem
    name: "DeepChem"
    type: toolkit
    url: https://github.com/deepchem/deepchem
    description: "Deep learning library for drug discovery, quantum chemistry, and materials science."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: deeptalk
    name: "DeepTalk"
    type: toolkit
    url: https://github.com/JiangBioLab/DeepTalk
    description: "Graph attention network for deciphering cell-cell communication from spatial transcriptomics."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: doubletfinder
    name: "DoubletFinder"
    type: toolkit
    url: https://github.com/chris-mcginnis-ucsf/DoubletFinder
    description: "Machine learning approach for detecting multiplet (doublet) artifacts in single-cell RNA-seq data."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: flashdeconv
    name: "FlashDeconv"
    type: toolkit
    url: https://github.com/cafferychen777/flashdeconv
    description: "High-performance spatial transcriptomics deconvolution (~1M spots in ~3 min)."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: gromacs
    name: "GROMACS"
    type: toolkit
    url: https://www.gromacs.org/
    description: "Molecular dynamics simulation package for biochemical molecules."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: harmony
    name: "Harmony"
    type: toolkit
    url: https://github.com/immunogenomics/harmony
    description: "Fast and scalable integration of single-cell data across datasets, conditions, technologies, and species."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: kallisto
    name: "kallisto"
    type: toolkit
    url: https://pachterlab.github.io/kallisto/
    description: "Near-optimal RNA-seq quantification using pseudoalignment for fast transcript abundance estimation."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: linger
    name: "LINGER"
    type: toolkit
    url: https://github.com/Durenlab/LINGER
    description: "Neural network for gene regulatory network inference from single-cell multiome (RNA+ATAC-seq) data with bulk data pretraining."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: mdanalysis
    name: "MDAnalysis"
    type: toolkit
    url: https://www.mdanalysis.org/
    description: "Python library for analyzing and altering molecular dynamics simulation trajectories."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: mogonet
    name: "MOGONET"
    type: toolkit
    url: https://github.com/txWang/MOGONET
    description: "Multi-omics graph convolutional network framework for patient classification and biomarker identification."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: monocle3
    name: "Monocle3"
    type: toolkit
    url: https://cole-trapnell-lab.github.io/monocle3/
    description: "Single-cell trajectory analysis tool for learning developmental trajectories and ordering cells in pseudotime."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: ncem
    name: "NCEM"
    type: toolkit
    url: https://github.com/theislab/ncem
    description: "GNN-based model for learning intercellular communication from spatial graphs of cells."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: numbat
    name: "Numbat"
    type: toolkit
    url: https://github.com/kharchenkolab/numbat
    description: "Haplotype-aware copy number variation inference from single-cell RNA-seq using hidden Markov models."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: openmm
    name: "OpenMM"
    type: toolkit
    url: https://openmm.org/
    description: "High-performance toolkit for molecular simulation and GPU-accelerated MD."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: rdkit
    name: "RDKit"
    type: toolkit
    url: https://github.com/rdkit/rdkit
    description: "Cheminformatics software & machine learning toolkit."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: scanpy
    name: "Scanpy"
    type: toolkit
    url: https://scanpy.readthedocs.io/en/stable/
    description: "Python library for scRNA-seq analysis."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: scenic
    name: "SCENIC"
    type: toolkit
    url: https://github.com/aertslab/SCENIC
    description: "Single-cell regulatory network inference and clustering linking transcription factors to co-expressed gene modules."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: scipenn
    name: "sciPENN"
    type: toolkit
    url: https://github.com/jlakkis/sciPENN
    description: "RNN-based method for simultaneous protein expression prediction, uncertainty estimation, and cell-type label transfer from CITE-seq and scRNA-seq data."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: scvelo
    name: "scVelo"
    type: toolkit
    url: https://github.com/theislab/scvelo
    description: "RNA velocity estimation for single-cell transcriptomics, inferring the direction and speed of cell differentiation."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: scvi_tools
    name: "scvi-tools"
    type: toolkit
    url: https://scvi-tools.org/
    description: "Probabilistic models for single-cell omics data analysis."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: seqbench
    name: "SeqBench"
    type: toolkit
    url: https://seqbench.com/
    description: "Web-based molecular biology sequence workbench for primer design, cloning simulation (Gibson, Golden Gate, restriction digest), CRISPR guide RNA design, and sequence analysis, with a public REST API, OpenAPI 3.1 spec, and MCP server."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: seurat
    name: "Seurat"
    type: toolkit
    url: https://satijalab.org/seurat/
    description: "R library for scRNA-seq analysis."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: squidpy
    name: "Squidpy"
    type: toolkit
    url: https://squidpy.readthedocs.io/
    description: "Python library for spatial single-cell analysis."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: stagate
    name: "STAGATE"
    type: toolkit
    url: https://github.com/RucDongLab/STAGATE
    description: "Adaptive graph attention auto-encoder for spatial domain identification in spatial transcriptomics."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: star
    name: "STAR"
    type: toolkit
    url: https://github.com/alexdobin/STAR
    description: "Ultrafast universal RNA-seq aligner with support for spliced alignment and single-cell quantification via STARsolo."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false

  - id: tigon
    name: "TIGON"
    type: toolkit
    url: https://github.com/yutongo/TIGON
    description: "Neural optimal transport method for reconstructing growth and dynamic trajectories from single-cell transcriptomics."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
    organism: []
    api: false