AI tools for biology, verified.

311 hand-checked tools across 16 categories, from single-cell, spatial omics, protein design, genomics, drug discovery, agents, cloud labs, imaging, datasets, sequencing, proteomics/metabolomics, CRISPR, RNA, microbiome, clinical LLMs and R&D platforms.

Recently released Oct 19 – Nov 2

Released Nov 2

Tiny 1.96M-parameter ProteinMPNN-style inverse-folding model (backbone to sequence) trained with structure-reward RL by Tencent's Hyra 2.0 agent; CPU/GPU, fixed-position design, fused Triton fast path.

Protein structure & designOpen sourcePermissive (commercial OK)#inverse-folding
Released Nov 2

650M-parameter protein language model trained by Tencent's Hyra 2.0 agent, with an INT8 engine embedding ~130k residues/s on one H20; ProteinGym zero-shot Spearman 0.409, tied with ESM-2 650M and ESM C 600M.

Protein structure & designOpen sourcePermissive (commercial OK)#protein-language-model
Released Oct 30

Cherimoya

Compact BPNet-family sequence-to-function model with an end-to-end CLI (peak calling, training, attribution, motif discovery); ships pretrained atlases CATv1 (accessibility) and BATv1 (17,145 TF-binding models).

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#sequence-to-function
Released Oct 30

GPT-Rosalind

OpenAI's life-sciences reasoning models for biology, genomics and drug discovery; GPT-6 Rosalind (Oct 2026) runs on GPT-6 Astra weights. Trusted access, plus an open Codex research plugin.

Bio LLM agents & copilotsContactProprietary (paid or negotiated license)#llm
Released Oct 27

Mol-1

Molence Bio's open all-atom structure prediction model, derived from Protenix, for protein, nucleic acid, ligand and ion complexes, tuned for antibody–antigen, protein–ligand and peptide accuracy, with fine-tuning code.

Protein structure & designOpen sourcePermissive (commercial OK)#structure
Released Oct 27

Ginkgo Datapoints' open arrayed DRUG-seq resource for virtual cell models: 26,000+ compounds profiled in THP-1 cells, including the 12,949-compound ReFRAME library.

Datasets & benchmarksOpen sourcePermissive (commercial OK)#perturbation
Released Oct 22

Carbon-X

Hugging Face's 14.8B DNA-and-English chat model built on Qwen3-14B: paste up to ~50 kbp of DNA and ask about variant effects, regulatory regions, organism group or sequence continuation, with explanations.

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#dna-model
Released Oct 22

Ant Group inclusionAI's open-weight healthcare MoE model (124B total, 5.1B active, 256K context) for medical reasoning, evidence synthesis and tool-using research agents; research use, not a medical device.

Clinical & biomedical LLMsOpen sourcePermissive (commercial OK)#llm
Released Oct 21

Pinal

Westlake University model that designs protein sequences from a natural-language description: a text-to-structure model (T2struc) proposes structure tokens, then SaProt-T writes the sequence.

Protein structure & designOpen sourcePermissive (commercial OK)#protein-design
Released Oct 20

BioEmu2

Foundation model for biomolecular structure and dynamics: structure prediction, equilibrium ensemble sampling and time-lagged trajectory generation for proteins, nucleic acids and ligands.

Protein structure & designOpen sourcePermissive (commercial OK)#dynamics
Released Oct 20

Chaperone

Baker lab harness that wires 50+ protein design, folding and analysis tools into reproducible SLURM pipelines and ships agent skills so coding agents can build and run design campaigns.

Bio LLM agents & copilotsOpen sourcePermissive (commercial OK)#agent
Released Oct 19

recAMPLIFY

Chandar Lab's recursive masked protein language model: a weight-tied recurrent core refines residue embeddings over several cycles, so you can spend more compute per sequence at inference without adding parameters.

Protein structure & designOpen sourcePermissive (commercial OK)#protein-language-model
Released Oct 19

Flow-matching model from the Baker lab and NVIDIA that co-designs protein sequence and all-atom structure, covering binders, antibodies, enzymes and small-molecule pockets, with reward-guided search.

Protein structure & designOpen sourcePermissive (commercial OK)#protein-design

All tools

What do these mean?

Illumina's unified cloud environment for genomic and multiomic analysis, bundling DRAGEN, BaseSpace, Emedgene, Connected Multiomics and curated data under one usage-based credit system.

R&D & bioinformatics platformsPaidProprietary (paid or negotiated license)#genomics

Seqera's closed-loop discovery system: AI agents design computational experiments, run thousands of them as Nextflow pipelines, score the results and iterate. Offered as a partnership.

Bio LLM agents & copilotsContactProprietary (paid or negotiated license)#agent

Prompteina

Text-to-structure all-atom protein design: generate monomers and binders from natural-language prompts.

Protein structure & designOpen sourcePermissive (commercial OK)#text-conditioned

Carbon-A

1.2B DNA model that annotates protein-coding genes across eukaryotes; ships a 48K-assembly annotation database.

Genomics & DNA modelsOpen sourceUnknown#genome-annotation

SpliceAI2

Illumina's successor to SpliceAI: predicts splice-site usage and full transcript isoforms from sequence.

Genomics & DNA modelsNo cost (research use)Unknown#splicing

Google DeepMind diffusion pipeline for de novo enzyme design via catalytic motif scaffolding.

Protein structure & designOpen source (non-commercial)Mixed (code vs weights differ)#enzyme-design

Virtual-cell model using curated biological knowledge to predict perturbation responses in unseen contexts.

Single-cell & foundation modelsOpen source (non-commercial)Non-commercial#virtual-cell

TorchX

Changping Lab × Huawei NPU-native all-atom biomolecular model suite: TorchFold (antibody–antigen), TorchScore and TorchCraft (design); MIT weights + training data.

Protein structure & designOpen sourcePermissive (commercial OK)#antibody

CellART

Unified framework for cell segmentation and cell-type annotation in high-resolution spatial transcriptomics such as Xenium and Visium HD.

Spatial omicsOpen sourcePermissive (commercial OK)#segmentation

NV-Reason-CT

NVIDIA's 3D vision-language model for chest and abdominal CT: structured reports, visual QA and step-by-step reasoning.

Clinical & biomedical LLMsOpen sourcePermissive (commercial OK)#ct

InstaNovo-FM

Self-supervised encoder foundation model trained on 1.63B MS/MS spectra; transferable embeddings for de novo and database-independent identification.

Proteomics & metabolomicsOpen source (non-commercial)Mixed (code vs weights differ)#mass-spectrometry

MetaCAT

Metagenome binning plus microbial SNP calling and metagenome-wide association with host traits in one framework.

Microbiome & metagenomicsOpen sourceCopyleft (commercial OK, share-alike)#binning

First predictive model from the UK OpenBind consortium, trained on its experimental protein–ligand dataset.

Drug discovery & moleculesOpen sourceUnknown#binding

Arc Institute's perturbation benchmark: predict CRISPRi knockdown responses in six cell lines never seen perturbed, from their unperturbed state alone.

Datasets & benchmarksNo cost (research use)Unknown#perturb-seq

Nesso-1

Recursion's Apache-2.0 co-folding model for fast protein–ligand binding-affinity prediction.

Drug discovery & moleculesOpen sourcePermissive (commercial OK)#binding-affinity

OpenDDE

Apache-licensed all-atom co-folding foundation model for structure prediction, design and optimization in drug discovery (preview).

Drug discovery & moleculesOpen sourcePermissive (commercial OK)#co-folding

Anthropic's AI workbench for scientists: coordinating agent with 60+ skills and connectors for genomics, single-cell, proteomics and more, plus a reviewer agent (beta).

Bio LLM agents & copilotsPaidProprietary (paid or negotiated license)#workbench

Biohub's protein 'world model': ESMC language model (~2.8B sequences), ESMFold2 complex structure prediction/design, and ESM Atlas (6.8B sequences).

Protein structure & designOpen sourcePermissive (commercial OK)#protein-language-model

Carbon

Hugging Face's family of open generative DNA language models (500M, 3B, 8B) with 6-mer tokens and up to ~786 kbp context; zero-shot variant-effect scoring and sequence generation.

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#dna-model

EPFL's fully open medical LLMs (open weights, training data and recipe) built on Apertus, OLMo-2, EuroLLM and Gemma-3 bases.

Clinical & biomedical LLMsOpen sourceUnknown#llm

AI partner inside the Seqera platform for building, launching and debugging Nextflow bioinformatics pipelines.

Bio LLM agents & copilotsPaidProprietary (paid or negotiated license)#nextflow

AWS antibody-design platform: 40+ hosted biological AI models, agents and no-code pipelines, with wet-lab ordering through partner CROs and results fed back for model refinement.

R&D & bioinformatics platformsPaidProprietary (paid or negotiated license)#antibody

DISCO

Diffusion model that co-designs protein sequence and structure conditioned on ligands, DNA or RNA.

Protein structure & designOpen sourcePermissive (commercial OK)#diffusion-models

EVA

1.4B-parameter long-context generative RNA foundation model trained on 114M full-length RNAs; supports RNA engineering and guide-RNA design.

RNA structure & designOpen sourcePermissive (commercial OK)#rna-language-model

1.1B-parameter open-weight histopathology foundation model trained only on public data.

Imaging & pathologyOpen source (non-commercial)Non-commercial#pathology

~8M-cell in vivo CRISPR perturbation atlas of mouse brain (single-nucleus), downloadable on Hugging Face in Parquet/AnnData/Zarr.

Datasets & benchmarksOpen sourcePermissive (commercial OK)#perturb-seq

Browser-accessible autonomous biology lab on Ginkgo's automation infrastructure, with an AI agent that checks protocol feasibility and pricing.

Cloud labs & wet-lab servicesPaidProprietary (paid or negotiated license)#autonomous-lab

HitSV

Structural variant caller with haplotype-resolved local assembly that works on PacBio HiFi, ONT, hybrid and short-read data.

Sequencing & variant callingOpen sourceCopyleft (commercial OK, share-alike)#structural-variants

OptiPrime

David Liu lab's mechanistic ML model that predicts prime-editing efficiency and outcomes for PE2, PE3 and twinPE, with a web server.

CRISPR & gene editingNo cost (research use)Unknown#prime-editing

IsoDDE

Isomorphic Labs Drug Design Engine: proprietary system predicting protein–ligand and antibody–antigen structures, binding affinity and cryptic pockets beyond AlphaFold 3.

Drug discovery & moleculesContactProprietary (paid or negotiated license)#co-folding

Biomni Lab

Phylo's 'integrated biology environment': a workspace where biologists orchestrate AI agents across 300+ databases, tools and software (preview).

Bio LLM agents & copilotsContactProprietary (paid or negotiated license)#agent-workspace

Protein2PAM

Profluent's protein language model that predicts a Cas enzyme's PAM specificity from its sequence and guides PAM-engineering of Cas9 variants.

CRISPR & gene editingOpen source (non-commercial)Non-commercial#pam

BIOS

AI scientist from BIO with planning, literature, data-analysis and novelty-detection subagents; hosted at chat.bio.xyz (the earlier open BioAgents framework is archived).

Bio LLM agents & copilotsNo-cost tier + paid plansProprietary (paid or negotiated license)#ai-scientist

RNAPro

NVIDIA RNA 3D folding model built with hosts and winners of the Stanford RNA 3D Folding Kaggle competition.

RNA structure & designOpen sourcePermissive (commercial OK)#rna-structure

Stack

Arc Institute model trained on 149M human cells using tabular attention for in-context learning; used to generate the Perturb Sapiens atlas (28 tissues, 201 perturbations).

Single-cell & foundation modelsOpen source (non-commercial)Non-commercial#foundation-model

Atlas 2

Pathology foundation model family built for clinical deployment (Aignostics and collaborators).

Imaging & pathologyContactUnknown#pathology

Multi-species DNA foundation model with 1 Mb single-base context; predicts ~16k functional tracks, annotates genomes, and designs enhancers.

Genomics & DNA modelsOpen source (non-commercial)Non-commercial#dna-language-model

GigaTIME

Microsoft and Providence model that turns routine H&E slides into virtual multiplex immunofluorescence maps of 21 proteins.

Imaging & pathologyOpen sourceUnknown#pathology

ODesign

All-atom generative world model for designing proteins, ligands, nucleic acids and cyclic peptides that bind a given target.

Protein structure & designResearch releaseUnknown#protein

BoltzGen

Open generative model for designing protein and peptide binders against diverse targets.

Protein structure & designOpen sourcePermissive (commercial OK)#binder-design

Kosmos

Edison Scientific's AI scientist: long autonomous runs that read ~1,500 papers and write tens of thousands of lines of analysis code per run.

Bio LLM agents & copilotsPaidProprietary (paid or negotiated license)#ai-scientist

OpenFold3

Open-source AlphaFold3-style model predicting structures of proteins, nucleic acids and small-molecule complexes (preview release).

Protein structure & designOpen sourcePermissive (commercial OK)#structure-prediction

Tahoe-x1

Perturbation-trained single-cell foundation models up to 3B parameters, pretrained on Tahoe-100M and fine-tuned for cancer tasks.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#foundation-model

Open library of 177 Agent Skills and 100+ scientific database connectors that give coding agents validated procedures for biology, chemistry, medicine and drug discovery.

Bio LLM agents & copilotsOpen sourcePermissive (commercial OK)#agent

GPN-Star

Phylogeny-aware genomic language model over whole-genome alignments and species trees for genome-wide variant effect and constraint prediction.

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#variant-effect

RFdiffusion3

All-atom diffusion model from the Baker lab for designing protein binders to DNA, proteins and small molecules, plus enzymes; ~10x faster than RFdiffusion2.

Protein structure & designOpen sourcePermissive (commercial OK)#protein-design

CytoVI

Deep generative model in scvi-tools that integrates flow cytometry, mass cytometry and CITE-seq data across panels, with protein imputation, differential expression and annotation.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#cytometry

Baichuan-M2

Baichuan's open 32B medical reasoning model trained with a patient simulator and clinical-rubric RL; reported as the top open model on HealthBench at release.

Clinical & biomedical LLMsOpen sourcePermissive (commercial OK)#llm

SVPG

Pangenome-guided structural variant caller for long reads that can also add new samples to an existing pangenome graph.

Sequencing & variant callingOpen sourcePermissive (commercial OK)#structural-variants

La-Proteina

NVIDIA latent flow model for joint atomistic protein sequence-structure generation.

Protein structure & designOpen sourcePermissive (commercial OK)#design

AlphaGenome

DeepMind model predicting regulatory effects of DNA variants at base resolution.

Genomics & DNA modelsNo cost (research use)Mixed (code vs weights differ)#regulatory

Lingshu

Alibaba DAMO's multimodal medical LLMs (7B/32B) for medical image understanding, reasoning, VQA and report generation.

Clinical & biomedical LLMsOpen sourcePermissive (commercial OK)#multimodal

AI-ready DDA mass-spectrometry corpus (1.54B MS/MS spectra, 548M PSMs, 35 species) in a Parquet tensor format (MSDT), plus XuanjiNovo, a non-autoregressive transformer for de novo peptide sequencing trained on 100M PSMs.

Proteomics & metabolomicsOpen sourcePermissive (commercial OK)#mass-spec

Biomni

General-purpose biomedical AI agent with 150+ tools and databases.

Bio LLM agents & copilotsOpen sourcePermissive (commercial OK)#agent

State

Arc Institute virtual-cell model predicting transcriptomic responses to perturbations across cell contexts.

Single-cell & foundation modelsOpen source (non-commercial)Non-commercial#virtual-cell

MedGemma

Google's open Gemma 3 variants for medical text and image comprehension.

Clinical & biomedical LLMsOpen sourceUnknown#llm

Robin

FutureHouse multi-agent system automating hypothesis generation and data analysis for drug discovery.

Bio LLM agents & copilotsOpen sourcePermissive (commercial OK)#multi-agent

OMol25

Meta FAIR's open dataset of DFT calculations on diverse molecules, with evaluations and baseline models.

Datasets & benchmarksOpen sourceUnknown#dft

CZI cross-species generative single-cell foundation model trained on 112M cells from 12 species.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#foundation-model

Visual–omics foundation model aligning H&E histology with spatial transcriptomics for tissue alignment, cell-type decomposition and expression prediction.

Spatial omicsOpen source (non-commercial)Non-commercial#foundation-model

RFdiffusion2

Atom-level enzyme active-site scaffolding with diffusion, no sequence-position constraints.

Protein structure & designOpen sourcePermissive (commercial OK)#enzyme-design

MedSAM2

Promptable segmentation for 3D medical images and videos, built on SAM 2.

Clinical & biomedical LLMsOpen sourcePermissive (commercial OK)#segmentation

ClairS-TO

Deep-learning tumor-only somatic small-variant caller for long reads, from the Clair3 team.

Sequencing & variant callingOpen sourcePermissive (commercial OK)#variant-calling

Proteina

NVIDIA flow-matching model for large-scale protein backbone generation.

Protein structure & designOpen source (non-commercial)Non-commercial#design

Tahoe-100M

100M-cell single-cell drug perturbation atlas.

Datasets & benchmarksOpen sourcePermissive (commercial OK)#perturbation

Evo 2

Genome language model across all domains of life with 1M-token context.

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#dna-lm

scGPT continually pretrained on spatial transcriptomics for spatial-aware embeddings, deconvolution and imputation.

Spatial omicsOpen sourcePermissive (commercial OK)#foundation-model

RNAbpFlow

SE(3) flow-matching model that generates RNA 3D structures and conformer ensembles conditioned on base pairing.

RNA structure & designOpen sourceCopyleft (commercial OK, share-alike)#3d-structure

VirTues

Bunne lab's spatial proteomics foundation model for multiplexed tissue imaging, from molecules to cells to tissue, for diagnostics and case retrieval.

Spatial omicsOpen sourceMixed (code vs weights differ)#spatial-proteomics

METAGENE-1

7B-parameter metagenomic foundation model pretrained on 1.5T+ base pairs of human-wastewater DNA/RNA for pathogen detection and biosurveillance.

Microbiome & metagenomicsOpen sourcePermissive (commercial OK)#foundation-model

HuatuoGPT-o1

Open medical reasoning LLMs trained with verifiable medical problems and RL for complex clinical reasoning.

Clinical & biomedical LLMsOpen sourcePermissive (commercial OK)#llm

Protenix

Trainable PyTorch reproduction of AlphaFold 3 by ByteDance.

Protein structure & designOpen sourcePermissive (commercial OK)#structure

BioEmu

Generative model emulating protein equilibrium structural ensembles.

Protein structure & designOpen sourcePermissive (commercial OK)#dynamics

TITAN

Multimodal whole-slide pathology foundation model pretrained on 335,645 WSIs with vision–language alignment.

Imaging & pathologyOpen source (non-commercial)Non-commercial#pathology

RhoFold+

RNA language-model-based method for 3D RNA structure prediction.

RNA structure & designOpen sourcePermissive (commercial OK)#rna-structure

BiomedParse

Foundation model for joint segmentation, detection and recognition across nine biomedical imaging modalities.

Imaging & pathologyOpen sourcePermissive (commercial OK)#segmentation

Boltz

Open biomolecular interaction models (Boltz-1, Boltz-2) for complex structure and binding-affinity prediction.

Protein structure & designOpen sourcePermissive (commercial OK)#structure

Orthrus

Bo Wang lab's mature-RNA foundation model trained with contrastive learning on splice isoforms and orthologs, for RNA half-life and other property prediction.

RNA structure & designOpen sourcePermissive (commercial OK)#foundation-model

BindCraft

One-shot de novo binder design pipeline with AF2 hallucination.

Protein structure & designOpen sourcePermissive (commercial OK)#binder

DeepPolisher

Transformer-based polisher that reduces base errors in PacBio HiFi genome assemblies.

Sequencing & variant callingOpen sourcePermissive (commercial OK)#assembly

PaperQA2

High-accuracy RAG agent over scientific papers.

Bio LLM agents & copilotsOpen sourcePermissive (commercial OK)#rag

Chai-1

Multimodal foundation model for molecular structure prediction.

Protein structure & designOpen sourcePermissive (commercial OK)#structure

Novae

Graph-based foundation model for spatial transcriptomics: zero-shot spatial domains and cross-slide/cross-technology integration.

Spatial omicsOpen sourcePermissive (commercial OK)#foundation-model

Aviary

Gymnasium for training language agents on scientific tasks (molecular cloning, literature QA).

Bio LLM agents & copilotsOpen sourcePermissive (commercial OK)#training

Seal

Troyanskaya lab's sequence-to-expression transfer-learning model: predicts gene expression and variant effects across 802 developing-brain contexts (26 regions, 30 cell types, 7 stages).

Genomics & DNA modelsOpen source (non-commercial)Non-commercial#variant-effect

DeepSomatic

Google's deep-learning somatic small-variant caller for tumor/normal data across Illumina, PacBio and Oxford Nanopore.

Sequencing & variant callingOpen sourcePermissive (commercial OK)#variant-calling

gLM2 / OMG

Tatta Bio's mixed-modality (protein + DNA) genomic language model trained on the OMG open metagenomic corpus.

Microbiome & metagenomicsOpen sourcePermissive (commercial OK)#language-model

Raygun

Template-based protein design: edits an existing protein by insertions, deletions and substitutions while keeping its fold and function.

Protein structure & designResearch releaseUnknown#protein

Helical

Python framework that runs bio foundation models such as Geneformer, scGPT, UCE and Evo 2 through one interface for embedding and fine-tuning, with an MCP integration for OpenAI Codex.

R&D & bioinformatics platformsOpen sourceCopyleft (commercial OK, share-alike)#foundation-model

Multimodal generative protein language model over sequence, structure and function (ESM3; also ESM C embeddings).

Protein structure & designNo-cost tier + paid plansPermissive (commercial OK)#plm

Merlin

Stanford's 3D vision-language model for abdominal CT, pretrained on scans, EHR codes and radiology reports for classification, retrieval and report generation.

Clinical & biomedical LLMsOpen sourcePermissive (commercial OK)#ct

scFoundation

100M-parameter foundation model trained on 50M human single-cell transcriptomes.

Single-cell & foundation modelsOpen sourceUnknown#foundation-model

Cellist

Scalable cell segmentation for subcellular-resolution spatial transcriptomics that combines staining images with transcript signals across platforms.

Spatial omicsOpen sourceCopyleft (commercial OK, share-alike)#segmentation

LLM agent that designs genetic perturbation experiments (e.g. CRISPR screens).

Bio LLM agents & copilotsOpen sourcePermissive (commercial OK)#experiment-design

Whole-slide digital pathology foundation model.

Imaging & pathologyOpen sourceUnknown#pathology

HERRO

Deep-learning error correction of nanopore simplex reads that enables telomere-to-telomere phased assemblies.

Sequencing & variant callingOpen sourceUnknown#error-correction

CHIEF

Pathology foundation model for cancer detection, tumor-origin and molecular-profile prediction and prognosis from whole slides.

Imaging & pathologyOpen source (non-commercial)Non-commercial#pathology

Structure prediction of proteins, nucleic acids, ligands and their complexes; hosted web server plus open code, weights on request for non-commercial use.

Protein structure & designNo cost (research use)Mixed (code vs weights differ)#structure

CRISPR-GPT

LLM agent that plans and automates gene-editing experiments: system selection, guide design, protocols and analysis.

CRISPR & gene editingResearch releaseUnknown#agent

OpenCRISPR-1

AI-designed Cas9-like gene editor from Profluent's language models, released openly.

CRISPR & gene editingOpen sourcePermissive (commercial OK)#generative

Nicheformer

Foundation model pretrained on dissociated and spatial single-cell data.

Spatial omicsOpen sourcePermissive (commercial OK)#foundation-model

CONCH

Vision-language foundation model for histopathology.

Imaging & pathologyOpen source (non-commercial)Non-commercial#pathology

UNI

General-purpose self-supervised foundation model for computational pathology.

Imaging & pathologyOpen source (non-commercial)Non-commercial#pathology

RFantibody

Structure-based de novo antibody and nanobody design with fine-tuned RFdiffusion, ProteinMPNN and RF2.

Protein structure & designOpen sourcePermissive (commercial OK)#antibody

STARLING

Latent diffusion model that predicts coarse-grained conformational ensembles of intrinsically disordered regions from sequence.

Protein structure & designResearch releaseUnknown#protein

Caduceus

Bidirectional, reverse-complement-equivariant DNA language model.

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#dna-lm

CytoTRACE 2

Interpretable deep learning model that predicts cellular potency and absolute developmental potential from scRNA-seq.

Single-cell & foundation modelsResearch releaseUnknown#single-cell

HEST

HEST-1k dataset of 1,276 paired spatial transcriptomics and H&E whole-slide samples, plus a library and benchmark for histology foundation models.

Spatial omicsResearch releaseUnknown#spatial-transcriptomics

RiNALMo

General-purpose RNA language model that generalizes to unseen RNA families on secondary-structure prediction.

RNA structure & designOpen sourcePermissive (commercial OK)#language-model

Evo

7B genomic foundation model (StripedHyena) for prokaryotic DNA, RNA and protein design at single-nucleotide resolution.

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#dna-lm

RibonanzaNet

RNA foundation model trained on Ribonanza chemical-mapping data for structure and reactivity.

RNA structure & designOpen sourcePermissive (commercial OK)#rna-structure

BioMistral

Open 7B medical LLM based on Mistral, further pretrained on PubMed Central.

Clinical & biomedical LLMsOpen sourcePermissive (commercial OK)#llm

AbLang-2

Paired-chain antibody language model trained to reduce germline bias.

Protein structure & designOpen sourcePermissive (commercial OK)#antibody

tangermeme

Toolkit for using trained genomic deep learning models: batched predictions, DeepLIFT/SHAP attributions, variant effects, ablations, seqlet calling, motif annotation and DNA design.

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#interpretability

COMEBin

Contrastive multi-view representation learning for binning metagenomic contigs into genomes.

Microbiome & metagenomicsOpen sourceCopyleft (commercial OK, share-alike)#binning

LigandMPNN

Protein sequence design that explicitly models small molecules, nucleotides and metals, and also outputs side-chain conformations.

Protein structure & designOpen sourcePermissive (commercial OK)#inverse-folding

Coscientist

GPT-4-driven agent that plans and executes chemistry experiments on lab hardware.

Bio LLM agents & copilotsOpen source (non-commercial)Non-commercial#lab-automation

ProteinGym

Benchmarks for protein fitness and mutation effect prediction.

Datasets & benchmarksOpen sourcePermissive (commercial OK)#benchmark

DreaMS

Self-supervised transformer foundation model for tandem mass spectra of small molecules.

Proteomics & metabolomicsOpen sourcePermissive (commercial OK)#metabolomics

Cross-species zero-shot universal cell embedding foundation model.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#foundation-model

Meditron

Open medical LLMs (7B/70B) adapted from Llama 2 on curated medical corpora.

Clinical & biomedical LLMsOpen sourceUnknown#llm

Giotto Suite

Comprehensive R toolbox for spatial data analysis and visualization.

Spatial omicsOpen sourceUnknown#r

sylph

Ultrafast species-level metagenome profiler using abundance-corrected k-mer sketching (ANI-based containment).

Microbiome & metagenomicsOpen sourcePermissive (commercial OK)#profiling

CellSAM

Foundation model for cell segmentation across imaging modalities, pairing a cell-detection prompter with SAM.

Imaging & pathologyOpen sourcePermissive (commercial OK)#segmentation

PocketGen

Generates full-atom ligand-binding protein pockets, co-designing residue sequence and structure.

Drug discovery & moleculesOpen sourcePermissive (commercial OK)#generative

REINVENT 4

AstraZeneca's generative molecular design framework.

Drug discovery & moleculesOpen sourcePermissive (commercial OK)#generative

GPN-MSA

Genomic language model over multi-species alignments for genome-wide variant effect prediction.

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#variant-effect

Generalized biomolecular modeling for proteins, nucleic acids, small molecules.

Protein structure & designOpen sourcePermissive (commercial OK)#structure

SaProt

Protein language model with a structure-aware vocabulary combining amino acids with Foldseek 3Di tokens.

Protein structure & designOpen sourcePermissive (commercial OK)#alphafold2

AlphaMissenseArchived repo

Proteome-wide pathogenicity predictions for 71M missense variants (repo archived; precomputed scores available).

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#variant-effect

Turns expression profiles into ranked gene "cell sentences" so LLMs (up to 27B) can model and generate single-cell data.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#single-cell

Borzoi

Predicts RNA-seq coverage from DNA sequence.

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#expression

InstaNovo

Transformer and diffusion models for de novo peptide sequencing from tandem mass spectra.

Proteomics & metabolomicsOpen source (non-commercial)Mixed (code vs weights differ)#de-novo

GEARS

Graph-based prediction of transcriptional outcomes of genetic perturbations.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#perturbation

PoseBusters

Plausibility checks and benchmark for docking/structure poses.

Datasets & benchmarksOpen sourcePermissive (commercial OK)#benchmark

ThermoMPNN

Graph neural network built on ProteinMPNN that predicts stability changes (ddG) for protein point mutations.

Protein structure & designOpen sourcePermissive (commercial OK)#protein

PyLabRobot

Hardware-agnostic Python interface for liquid-handling robots and lab automation.

Bio LLM agents & copilotsOpen sourcePermissive (commercial OK)#lab-automation

HyenaDNA

Long-range genomic foundation model at single-nucleotide resolution.

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#dna-lm

DNABERT-2

Efficient multi-species genome foundation model.

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#dna-lm

BioChatter

Framework for LLM-based conversational biomedical research.

Bio LLM agents & copilotsOpen sourcePermissive (commercial OK)#llm

ChemCrow

LLM chemistry agent augmented with 18 expert tools for synthesis and molecule tasks.

Bio LLM agents & copilotsOpen sourcePermissive (commercial OK)#chemistry

Polaris

Benchmarking platform for ML in drug discovery.

Datasets & benchmarksOpen sourcePermissive (commercial OK)#benchmark

LLaVA-Med

Biomedical vision-language assistant trained on PubMed Central figure-caption data.

Clinical & biomedical LLMsOpen source (non-commercial)Non-commercial#vlm

Geneformer

Transformer pretrained on ~30M single-cell transcriptomes for network biology predictions.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#foundation-model

Deep learning structure prediction for antibodies, nanobodies and TCRs (ABodyBuilder2 etc.).

Protein structure & designOpen sourcePermissive (commercial OK)#antibody

gRNAde

Geometric deep learning for 3D RNA inverse design (sequence design from backbone).

RNA structure & designOpen sourcePermissive (commercial OK)#rna-design

BiomedGPT

Generalist vision-language foundation model for biomedical images and text, covering VQA, captioning, report generation and classification.

Clinical & biomedical LLMsOpen source (non-commercial)Non-commercial#clinical

moscot

Multi-omics single-cell optimal transport for space and time mapping.

Spatial omicsOpen sourcePermissive (commercial OK)#optimal-transport

micro-sam

Segment Anything fine-tuned for light and electron microscopy, with interactive napari annotation tools.

Imaging & pathologyOpen sourcePermissive (commercial OK)#segmentation

PrimateAI-3D

Missense variant pathogenicity model trained on primate population variation and 3D protein structure.

Genomics & DNA modelsOpen source (non-commercial)Non-commercial#variant-effect

scGPT

Generative pretrained transformer foundation model for single-cell multi-omics.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#foundation-model

DeepPrime

Deep-learning prediction of prime-editing efficiency across PE systems and cell types (Hyongbum Kim lab).

CRISPR & gene editingOpen sourceUnknown#prime-editing

MedSAM

Segment Anything adapted to medical images: promptable segmentation across CT, MRI, ultrasound, endoscopy and more.

Clinical & biomedical LLMsOpen sourcePermissive (commercial OK)#segmentation

gLM

Genomic language model trained on metagenomic contigs that learns gene context to predict protein co-regulation and function.

Microbiome & metagenomicsOpen source (non-commercial)Non-commercial#language-model

SpatialData

Unified data framework for spatial omics technologies.

Spatial omicsOpen sourcePermissive (commercial OK)#data-format

IgFold

Fast antibody structure prediction using AntiBERTy embeddings and graph networks.

Protein structure & designOpen source (non-commercial)Non-commercial#antibody

BiomedCLIP

Microsoft's biomedical vision-language model pretrained on 15M PubMed Central figure–caption pairs.

Clinical & biomedical LLMsOpen sourcePermissive (commercial OK)#vision-language

AlphaDIA

DIA proteomics search engine without feature detection, with transfer learning from AlphaPeptDeep.

Proteomics & metabolomicsOpen sourcePermissive (commercial OK)#dia

MetaPhlAn 4

Marker-gene-based taxonomic profiling of metagenomes, including uncharacterized species.

Microbiome & metagenomicsOpen sourcePermissive (commercial OK)#metagenomics

SE(3) diffusion model for protein backbone generation over residue frames.

Protein structure & designOpen sourcePermissive (commercial OK)#protein

Living benchmarks for single-cell analysis tasks.

Datasets & benchmarksOpen sourcePermissive (commercial OK)#benchmark

ChromBPNet

Bias-corrected base-resolution deep learning models of ATAC/DNase-seq chromatin accessibility and TF motifs.

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#epigenomics

PRIDICT

Attention-based model predicting prime editing efficiency to design pegRNAs.

CRISPR & gene editingOpen sourcePermissive (commercial OK)#prime-editing

DNA foundation models pretrained on 3,200+ human and 850 species genomes.

Genomics & DNA modelsOpen source (non-commercial)Non-commercial#dna-lm

CellCharter

Scalable identification and comparison of spatial cell niches across samples and technologies (scverse ecosystem).

Spatial omicsOpen sourcePermissive (commercial OK)#niches

SemiBin2

Self-supervised deep learning metagenomic binning for short and long reads.

Microbiome & metagenomicsOpen sourcePermissive (commercial OK)#binning

CZ CELLxGENE

Curated single-cell data portal and Census API with 100M+ cells.

Datasets & benchmarksOpen sourcePermissive (commercial OK)#atlas

RFdiffusion

Diffusion model for de novo protein backbone design and binder design.

Protein structure & designOpen sourcePermissive (commercial OK)#design

Dorado

Oxford Nanopore's production basecaller: transformer/LSTM models turning raw nanopore signal into reads, with modified-base calling and duplex.

Sequencing & variant callingOpen sourceUnknown#basecalling

DiffDock

Diffusion generative model for molecular docking.

Drug discovery & moleculesOpen sourcePermissive (commercial OK)#docking

DiffSBDD

Equivariant diffusion model that designs small molecules directly inside a protein pocket.

Drug discovery & moleculesOpen sourcePermissive (commercial OK)#ddpm

Casanovo

Transformer for de novo peptide sequencing directly from MS/MS spectra.

Proteomics & metabolomicsOpen sourcePermissive (commercial OK)#de-novo

geNomad

Neural-network and marker-based identification of viruses and plasmids in sequencing data.

Microbiome & metagenomicsOpen source (non-commercial)Non-commercial#virus

GraphST

Graph self-supervised contrastive learning for spatial transcriptomics.

Spatial omicsOpen sourceCopyleft (commercial OK, share-alike)#contrastive

ESM-2 / ESMFoldArchived repo

Protein language models and single-sequence structure prediction (Meta repo archived; models still widely used via Hugging Face).

Protein structure & designOpen sourcePermissive (commercial OK)#plm

NicheCompass

Graph deep learning model that learns cell embeddings from communication programs to identify niches across spatial samples.

Spatial omicsOpen sourcePermissive (commercial OK)#deep-learning

CheckM2

Machine-learning estimation of completeness and contamination of metagenome-assembled genomes.

Microbiome & metagenomicsOpen sourceCopyleft (commercial OK, share-alike)#mags

FoldingDiff

Diffusion model that generates protein backbones by denoising internal backbone angles.

Protein structure & designOpen sourcePermissive (commercial OK)#diffusion

Deep learning framework predicting peptide MS2 spectra, retention time and CCS for proteomics.

Proteomics & metabolomicsOpen sourcePermissive (commercial OK)#mass-spec

ProGen2

Protein language models (up to 6.4B) for sequence generation and fitness prediction.

Protein structure & designOpen sourcePermissive (commercial OK)#language-model

Broad GPP model for SpCas9 sgRNA on-target activity, used in CRISPick.

CRISPR & gene editingOpen sourcePermissive (commercial OK)#guide-design

ProteinMPNN

Deep-learning inverse folding: designs sequences for given backbones.

Protein structure & designOpen sourcePermissive (commercial OK)#inverse-folding

Pocket2Mol

E(3)-equivariant graph neural network that samples drug-like molecules atom by atom inside 3D protein pockets.

Drug discovery & moleculesOpen sourcePermissive (commercial OK)#drug-discovery

BANKSY

Neighborhood-augmented clustering that unifies cell typing and tissue-domain segmentation in spatial omics.

Spatial omicsOpen source (non-commercial)Non-commercial#clustering

Uses general protein language models to recommend affinity-improving mutations, applied to human antibodies.

Protein structure & designOpen sourcePermissive (commercial OK)#protein

Sniffles2

Fast structural-variant caller for long reads with population-scale and mosaic SV detection.

Sequencing & variant callingOpen sourcePermissive (commercial OK)#structural-variants

RNA-FM

RNA foundation model pretrained on 23M non-coding RNAs for structure and function tasks.

RNA structure & designOpen sourcePermissive (commercial OK)#foundation-model

Latch Bio

Cloud platform for bioinformatics workflows and data.

R&D & bioinformatics platformsNo-cost tier + paid plansPermissive (commercial OK)#workflows

GeoDiff

Geometric diffusion model that generates 3D molecular conformations from molecular graphs (ICLR 2022).

Drug discovery & moleculesOpen sourcePermissive (commercial OK)#molecule

Foldseek

Fast and accurate protein structure search.

Protein structure & designOpen sourceCopyleft (commercial OK, share-alike)#search

Squidpy

Spatial single-cell analysis toolkit in the scverse ecosystem.

Spatial omicsOpen sourcePermissive (commercial OK)#python

AbLang

Antibody language model for heavy/light chains, used for residue restoration and embeddings.

Protein structure & designOpen sourcePermissive (commercial OK)#antibody

Transformer that corrects PacBio HiFi consensus reads, increasing yield and accuracy.

Sequencing & variant callingOpen sourcePermissive (commercial OK)#pacbio

AntiBERTy

BERT-style antibody language model trained on 558M OAS sequences.

Protein structure & designOpen sourcePermissive (commercial OK)#antibody

Remora

Models for detecting modified bases (e.g. 5mC, 6mA) from nanopore signal.

Sequencing & variant callingOpen sourceUnknown#methylation

OpenFold

Trainable open-source reproduction of AlphaFold2 in PyTorch.

Protein structure & designOpen sourcePermissive (commercial OK)#structure

TorchDrug

PyTorch platform for drug discovery machine learning: property prediction, generation and retrosynthesis.

Drug discovery & moleculesOpen sourcePermissive (commercial OK)#pytorch

scBasset

Sequence-based deep learning model for single-cell ATAC-seq representation and TF activity.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#scatac

STAGATE

Graph attention autoencoder for spatial domain identification.

Spatial omicsOpen sourcePermissive (commercial OK)#domains

GLUE

Graph-linked variational autoencoders that integrate unpaired single-cell multi-omics data and infer regulatory interactions.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#bioinformatics

BioPhi

Antibody humanization (Sapiens) and humanness evaluation (OASis) platform.

Protein structure & designOpen sourcePermissive (commercial OK)#antibody

Sei

Predicts 21,907 chromatin profiles from sequence and maps variants to regulatory sequence classes.

Genomics & DNA modelsOpen source (non-commercial)Non-commercial#epigenomics

ColabFold

Fast, accessible protein folding with MMseqs2 + AlphaFold in Colab.

Protein structure & designOpen sourcePermissive (commercial OK)#structure

AlphaFold 2

DeepMind's open-source protein structure prediction model (monomer and multimer).

Protein structure & designOpen sourcePermissive (commercial OK)#structure

RoseTTAFold

Baker lab's three-track neural network for protein structure and protein-protein complex prediction.

Protein structure & designOpen source (non-commercial)Mixed (code vs weights differ)#protein

Multimodal omics framework for single-cell multi-omics in Python.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#multimodal

Clair3

Deep-learning germline small-variant caller for long reads (ONT, PacBio) and short reads.

Sequencing & variant callingOpen sourcePermissive (commercial OK)#variant-calling

CellTypist

Automated cell type annotation with logistic regression models trained on curated atlases.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#annotation

Enformer

Predicts gene expression from sequence with long-range interactions.

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#expression

PASTE

Optimal-transport alignment and integration of spatial transcriptomics slices.

Spatial omicsOpen sourcePermissive (commercial OK)#optimal-transport

Fast, widely used open-source molecular docking engine.

Drug discovery & moleculesOpen sourcePermissive (commercial OK)#docking

ML-ready datasets and benchmarks for therapeutics.

Datasets & benchmarksOpen sourcePermissive (commercial OK)#benchmark

MS2DeepScore

Siamese neural network predicting structural similarity between MS/MS spectra for metabolomics.

Proteomics & metabolomicsOpen sourcePermissive (commercial OK)#metabolomics

EVE

Unsupervised evolutionary VAE for predicting pathogenicity of missense variants.

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#variant-effect

CellOracle

In silico gene perturbation via GRN inference from single-cell multi-omics.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#grn

HUMAnN 3

Functional profiling of metagenomes and metatranscriptomes (gene families and pathways).

Microbiome & metagenomicsOpen sourcePermissive (commercial OK)#metagenomics

PaddleHelix

Baidu's bio-computing platform built on PaddlePaddle, including HelixFold structure prediction and molecular representation models.

Protein structure & designResearch releaseUnknown#biocomputing

CellRank

Cell fate mapping using Markov chains on single-cell data.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#trajectory

SpaGCN

Graph convolutional network that combines gene expression, spatial location and histology to find spatial domains and spatially variable genes.

Spatial omicsOpen sourcePermissive (commercial OK)#spatial-transcriptomics

Bayesian mapping of fine-grained cell types in spatial transcriptomics.

Spatial omicsOpen sourcePermissive (commercial OK)#deconvolution

Haplotype-aware variant calling pipeline for nanopore reads combining PEPPER, Margin and DeepVariant.

Sequencing & variant callingOpen sourcePermissive (commercial OK)#variant-calling

scvi-tools

Probabilistic deep generative models for single-cell omics (scVI, totalVI, scANVI...).

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#vae

BayesSpace

Bayesian clustering and resolution enhancement of spatial transcriptomics.

Spatial omicsOpen sourcePermissive (commercial OK)#clustering

Tangram

Maps single-cell profiles onto spatial data with deep learning.

Spatial omicsOpen sourcePermissive (commercial OK)#mapping

UFold

Fast image-like U-Net for RNA secondary structure prediction.

RNA structure & designOpen sourcePermissive (commercial OK)#secondary-structure

EternaFold

RNA secondary structure model trained via multitask learning on Eterna player data.

RNA structure & designOpen sourcePermissive (commercial OK)#secondary-structure

matchms

Python library for importing, cleaning and comparing mass spectra for metabolomics.

Proteomics & metabolomicsOpen sourcePermissive (commercial OK)#metabolomics

ProtTrans

Transformer protein language models (ProtT5, ProtBERT and others) pretrained on UniRef and BFD, used for embeddings and fine-tuning.

Protein structure & designOpen sourcePermissive (commercial OK)#protein

Robust cell type decomposition for spatial transcriptomics.

Spatial omicsOpen sourceCopyleft (commercial OK, share-alike)#deconvolution

ArchR

Scalable single-cell chromatin accessibility (scATAC-seq) analysis in R.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#atac

scDeepSort

Pretrained weighted graph neural network for cell-type annotation of scRNA-seq data.

Single-cell & foundation modelsOpen sourceCopyleft (commercial OK, share-alike)#single-cell

SidechainNet

All-atom protein structure dataset extending ProteinNet with sidechain angles and coordinates, with PyTorch loaders for ML.

Datasets & benchmarksOpen sourcePermissive (commercial OK)#machine-learning

Bonito

Oxford Nanopore's research basecaller for training and testing new basecalling models.

Sequencing & variant callingOpen sourceUnknown#basecalling

TorchMD

PyTorch molecular dynamics engine that mixes classical force fields with neural network potentials.

Drug discovery & moleculesOpen sourcePermissive (commercial OK)#molecular-dynamics

Cellpose

Generalist deep learning model for cellular segmentation.

Imaging & pathologyOpen sourceUnknown#segmentation

DeepLC

Deep learning retention-time predictor that generalizes to unseen peptide modifications.

Proteomics & metabolomicsOpen sourcePermissive (commercial OK)#retention-time

napari

Fast, interactive multi-dimensional image viewer for Python.

Imaging & pathologyOpen sourcePermissive (commercial OK)#viewer

SPOT-RNA

Deep learning RNA secondary structure prediction including non-canonical pairs and pseudoknots.

RNA structure & designOpen sourceWeak copyleft (commercial OK, share-alike)#secondary-structure

scVelo

RNA velocity estimation with dynamical modeling.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#velocity

AtacWorks

NVIDIA's deep learning toolkit that denoises ATAC-seq coverage tracks and calls peaks from low-coverage or low-quality data.

Genomics & DNA modelsResearch releaseUnknown#genomics

BPNet

Base-resolution neural network for TF binding profiles (ChIP-nexus/ChIP-seq) and motif syntax discovery.

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#epigenomics

QIIME 2

Extensible platform for microbiome (amplicon and shotgun) data science.

Microbiome & metagenomicsOpen sourcePermissive (commercial OK)#amplicon

TAPE

Benchmark of five protein tasks with pretraining corpus and pretrained language model weights for evaluating protein embeddings.

Protein structure & designOpen sourcePermissive (commercial OK)#deep-learning

CHOPCHOP

Web tool for designing CRISPR-Cas9, Cas12 and TALEN targets with efficiency predictions.

CRISPR & gene editingNo cost (research use)Non-commercial#guide-design

scDblFinder

Doublet detection for single-cell data using gradient-boosted trees trained on artificial doublets.

Single-cell & foundation modelsOpen sourceCopyleft (commercial OK, share-alike)#single-cell

SIRIUS

Metabolomics software for molecular formula and structure annotation from MS/MS with CSI:FingerID and CANOPUS.

Proteomics & metabolomicsNo cost (research use)Mixed (code vs weights differ)#metabolomics

MaSIF

Geometric deep learning on protein molecular surfaces to predict interaction sites, ligand pockets and binding partners.

Protein structure & designOpen sourcePermissive (commercial OK)#protein-surface

CellBender

Deep generative model that removes ambient RNA and other technical background from droplet scRNA-seq count matrices.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#single-cell

Chemprop

Message passing neural networks for molecular property prediction.

Drug discovery & moleculesOpen sourcePermissive (commercial OK)#property-prediction

MS2PIP

Predicts peptide fragmentation spectra (and with DeepLC/IM2Deep) for spectral libraries and rescoring.

Proteomics & metabolomicsOpen sourcePermissive (commercial OK)#mass-spec

SpliceAIArchived repo

Deep learning prediction of splicing effects from pre-mRNA sequence (repo archived).

Genomics & DNA modelsOpen source (non-commercial)Non-commercial#splicing

VAMB

Variational autoencoder for metagenomic binning.

Microbiome & metagenomicsOpen sourcePermissive (commercial OK)#binning

Harmony

Fast, sensitive batch integration of single-cell data.

Single-cell & foundation modelsOpen sourceCopyleft (commercial OK, share-alike)#integration

CRISPResso2

Analysis of genome-editing outcomes from amplicon sequencing, including base and prime editing.

CRISPR & gene editingOpen source (non-commercial)Non-commercial#editing-outcomes

ivis

Siamese neural network for structure-preserving dimensionality reduction of very large single-cell datasets.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#machine-learning

Selene

PyTorch library for training and applying sequence-level deep learning models (DeepSEA-style).

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#library

Kraken 2

Fast k-mer based taxonomic classification of metagenomic reads.

Microbiome & metagenomicsOpen sourcePermissive (commercial OK)#metagenomics

StarDist

Star-convex object detection for nuclei segmentation.

Imaging & pathologyOpen sourcePermissive (commercial OK)#segmentation

DeepCell

Van Valen lab deep learning library for cell segmentation (Mesmer) and tracking in 2D/3D biological images.

Imaging & pathologyOpen sourcePermissive (commercial OK)#deep-learning

TorchANI

PyTorch library for training and running ANI neural-network interatomic potentials, maintained by the Roitberg group.

Drug discovery & moleculesOpen sourcePermissive (commercial OK)#deep-learning

deeptime

Python library for learning dynamical models from time series, from Markov state models to VAMPnets and deep MSMs.

Drug discovery & moleculesOpen sourceWeak copyleft (commercial OK, share-alike)#time-series-analysis

DIA-NN

Neural-network-powered data-independent acquisition (DIA) proteomics processing software.

Proteomics & metabolomicsNo cost (research use)Non-commercial#dia

GTDB-Tk

Assigns GTDB taxonomy to bacterial and archaeal genomes and MAGs.

Microbiome & metagenomicsOpen sourceCopyleft (commercial OK, share-alike)#taxonomy

Medaka

Neural-network consensus polishing and variant calling for nanopore assemblies.

Sequencing & variant callingOpen sourceUnknown#polishing

Scanpy

Scalable Python toolkit for single-cell gene expression analysis.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#python

Basenji

Sequence-to-function CNNs predicting chromatin accessibility, histone marks and expression tracks from DNA.

Genomics & DNA modelsOpen sourcePermissive (commercial OK)#epigenomics

Random-forest classifier on gene pairs that assigns cell types to scRNA-seq data across species and platforms.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#single-cell

DeepVariant

Google deep learning variant caller for Illumina, PacBio HiFi and ONT data.

Sequencing & variant callingOpen sourcePermissive (commercial OK)#variant-calling

QuPath

Open-source software for digital pathology and whole slide image analysis.

Imaging & pathologyOpen sourceCopyleft (commercial OK, share-alike)#pathology

CRISPOR

Web tool for CRISPR guide selection with on-target efficiency and off-target scoring for 500+ genomes.

CRISPR & gene editingOpen source (non-commercial)Non-commercial#guide-design

DeepChem

Deep learning toolkit for drug discovery, materials and biology.

Drug discovery & moleculesOpen sourcePermissive (commercial OK)#ml

Seurat

R toolkit for single-cell genomics, integration and multimodal analysis.

Single-cell & foundation modelsOpen sourcePermissive (commercial OK)#r

OpenMM

High-performance molecular dynamics toolkit with GPU support.

Drug discovery & moleculesOpen sourceWeak copyleft (commercial OK, share-alike)#molecular-dynamics

ViennaRNA

Standard RNA secondary structure prediction and design package (RNAfold, RNAinverse).

RNA structure & designOpen sourcePermissive (commercial OK)#secondary-structure

CellProfiler

Image analysis software for high-throughput cell phenotyping.

Imaging & pathologyOpen sourcePermissive (commercial OK)#high-content

MZmine

Open-source platform for LC-MS and imaging-MS data processing in metabolomics.

Proteomics & metabolomicsOpen sourcePermissive (commercial OK)#metabolomics

Public single-cell and spatial (Visium, Xenium) example datasets.

Datasets & benchmarksOpen sourceUnknown#spatial

Cloud lab for protein expression and binding characterization, binder design competitions.

Cloud labs & wet-lab servicesContactProprietary (paid or negotiated license)#protein

200M+ predicted protein structures from DeepMind and EMBL-EBI.

Protein structure & designOpen sourcePermissive (commercial OK)#database

R&D cloud with ELN, molecular biology and AI tooling.

R&D & bioinformatics platformsContactProprietary (paid or negotiated license)#eln

Critical Assessment of protein Structure Prediction community experiment.

Datasets & benchmarksOpen sourceUnknown#benchmark

AI search engine over peer-reviewed research.

Bio LLM agents & copilotsNo-cost tier + paid plansProprietary (paid or negotiated license)#literature

FutureHouse's hosted AI scientist agents (Crow, Falcon, Owl, Phoenix) for literature search, precedent search and chemistry.

Bio LLM agents & copilotsNo-cost tier + paid plansProprietary (paid or negotiated license)#agent

AI research assistant for literature search and data extraction.

Bio LLM agents & copilotsNo-cost tier + paid plansProprietary (paid or negotiated license)#literature

Remote-controlled cloud laboratory running 200+ instrument types.

Cloud labs & wet-lab servicesContactProprietary (paid or negotiated license)#automation

Cell programming platform and automated lab services.

Cloud labs & wet-lab servicesContactProprietary (paid or negotiated license)#synthetic-biology

Hugging Face Hub listing of biology-tagged models, from protein and DNA language models to single-cell models.

Datasets & benchmarksNo cost (research use)Unknown#hub

Data portal of the Human Cell Atlas consortium.

Datasets & benchmarksOpen sourceUnknown#atlas

NVIDIA platform and NIMs for training and deploying biology foundation models.

Drug discovery & moleculesNo-cost tier + paid plansPermissive (commercial OK)#platform

Open-source liquid-handling robots with a Python Protocol API and AI protocol generation.

Cloud labs & wet-lab servicesPaidPermissive (commercial OK)#lab-automation

Archive of experimentally determined 3D biomolecular structures.

Datasets & benchmarksOpen sourceUnknown#structure

Open-source cheminformatics and machine learning toolkit.

Drug discovery & moleculesOpen sourcePermissive (commercial OK)#cheminformatics

Cloud computational chemistry platform with ML-accelerated simulations.

R&D & bioinformatics platformsNo-cost tier + paid plansProprietary (paid or negotiated license)#quantum-chemistry

Marketplace for outsourced R&D and CRO services.

Cloud labs & wet-lab servicesContactProprietary (paid or negotiated license)#cro

Robotic cloud lab automation for life sciences.

Cloud labs & wet-lab servicesContactProprietary (paid or negotiated license)#automation

No-code web platform running 100+ protein and molecular ML models.

R&D & bioinformatics platformsNo-cost tier + paid plansProprietary (paid or negotiated license)#no-code

Synthetic DNA, gene fragments and antibody discovery services.

Cloud labs & wet-lab servicesContactProprietary (paid or negotiated license)#dna-synthesis

Comprehensive resource of protein sequence and function.

Datasets & benchmarksOpen sourcePermissive (commercial OK)#protein
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