AModels
AlphaFold
DeepMind's protein-structure prediction system, with open AlphaFold 2 code and a public database of predicted structures.
proteinsstructure prediction
View entry RESEARCH CATEGORY
Biology & Biomedical Research
Work with biological data, proteins, and medical imaging. The database currently includes 78 tools, models, databases, or infrastructure entries in this category.
BInfrastructure
Benchling
A cloud platform for biotechnology research that combines electronic lab records, sequence tools, and research data management.
electronic lab notebooksequence design
View entry DInfrastructure
DeepChem
An open-source Python library for applying machine learning to drug discovery, quantum chemistry, biology, and materials problems.
drug discoverymachine learning
View entry NInfrastructure
NVIDIA BioNeMo
A collection of frameworks, models, and deployment tools for generative AI in biomolecular and drug research.
biomolecular AIdrug research
View entry OModels
OpenFold
A trainable open-source implementation of AlphaFold 2 intended for protein-structure research and model development.
proteinsopen model
View entry CAI Tools
ColabFold
An open-source workflow that combines accelerated sequence search with AlphaFold-based structure prediction.
proteinsstructure prediction
View entry NInfrastructure
NCBI BLAST
NCBI sequence-search tools for finding local similarity between nucleotide or protein queries and sequence databases.
sequence searchbioinformatics
View entry GInfrastructure
Galaxy
An open web platform for running, documenting, and sharing reproducible computational biology workflows.
bioinformaticsreproducible workflows
View entry CInfrastructure
CellProfiler
Open-source software for building pipelines that measure cellular and other biological features in microscopy images.
microscopycell analysis
View entry MInfrastructure
MONAI
An open-source framework built on PyTorch for developing and deploying deep-learning workflows in medical imaging.
medical imagingdeep learning
View entry BInfrastructure
Biopython
An open-source Python toolkit for computational biology, including sequence, structure, database, and file-format operations.
bioinformaticsPython
View entry SInfrastructure
Scanpy
An open-source Python toolkit for preprocessing, reducing, clustering, and visualizing single-cell gene-expression data.
single celltranscriptomics
View entry SInfrastructure
scvi-tools
An open-source Python package that provides probabilistic generative models and a shared interface for single-cell omics.
single cellprobabilistic models
View entry NInfrastructure
Nextflow
An open-source workflow system for portable and scalable computational pipelines, widely used in bioinformatics.
workflowsreproducible computing
View entry SInfrastructure
Snakemake
An open-source workflow manager that expresses analysis steps and their dependencies as rules.
workflowsdata pipelines
View entry NInfrastructure
nf-core
A community project that maintains Nextflow pipelines under shared development, testing, and release practices.
bioinformatics pipelinesNextflow
View entry DAI Tools
DeepVariant
An open-source pipeline that uses a deep neural network to call genetic variants from aligned sequencing reads.
variant callingdeep learning
View entry CAI Tools
Cellpose
Open-source deep-learning software for segmenting cells and other objects in microscopy images.
microscopysegmentation
View entry IAI Tools
ilastik
An open-source desktop application for interactive machine-learning workflows such as pixel and object classification.
bioimage analysisinteractive learning
View entry NInfrastructure
napari
An open-source Python viewer for inspecting, annotating, and analyzing multidimensional scientific images.
multidimensional imagingannotation
View entry QInfrastructure
QuPath
Open-source desktop software for digital pathology and whole-slide image analysis.
digital pathologywhole-slide imaging
View entry FInfrastructure
Fiji
A distribution of ImageJ bundled with plugins and update sites for scientific image analysis, especially in life sciences.
scientific imagingImageJ
View entry OInfrastructure
OMERO
An open platform for managing, viewing, sharing, and analyzing microscopy images with their metadata.
image data managementmicroscopy
View entry SInfrastructure
Seurat
An open-source R package for quality control, analysis, integration, and visualization of single-cell transcriptomic data.
single cellR
View entry BInfrastructure
Bioconductor
An open bioinformatics software ecosystem built around R, with analysis, annotation, experiment-data, and workflow packages.
bioinformaticsR
View entry GInfrastructure
GATK
An open-source genomics toolkit from the Broad Institute focused on variant discovery, genotyping, and related sequencing-data processing.
variant callinggenomics
View entry DAI Tools
DeepSomatic
Open-source software that uses a deep neural network to call somatic variants from tumor-normal or tumor-only sequencing data.
somatic variantsdeep learning
View entry SInfrastructure
STAR
An open-source splice-aware aligner designed for RNA sequencing reads.
RNA-seqalignment
View entry SInfrastructure
Salmon
An open-source command-line tool for estimating transcript abundance from RNA-seq data using selective alignment or sketching methods.
RNA-seqquantification
View entry KInfrastructure
kallisto
An open-source tool that uses pseudoalignment to estimate transcript abundance from bulk or single-cell RNA-seq data.
RNA-seqpseudoalignment
View entry HInfrastructure
Hail
An open-source Python framework for scalable genomic data analysis across local, cloud, and Spark environments.
population genomicsdistributed computing
View entry PInfrastructure
PLINK 2
An open-source command-line toolset for genome-wide association studies, genotype quality control, and population-genetic analysis.
GWASgenotypes
View entry SInfrastructure
SAMtools
An open-source command-line suite for reading, converting, sorting, indexing, and summarizing SAM, BAM, and CRAM alignment files.
alignment filessequencing
View entry MInfrastructure
MultiQC
An open-source tool that aggregates outputs from many bioinformatics programs and samples into a unified quality-control report.
quality controlbioinformatics reports
View entry CInfrastructure
Cell Ranger
A set of 10x Genomics pipelines for processing Chromium single-cell data, including barcode handling, UMI counting, and selected immune-receptor analyses.
single-cell sequencing10x Genomics
View entry BInfrastructure
BCFtools
An open-source command-line suite for manipulating, querying, filtering, summarizing, and calling variants in VCF, BCF, and gVCF data.
variant filesgenomics
View entry EInfrastructure
Ensembl VEP
An open-source Ensembl tool that annotates the potential consequences of genomic variants on transcripts, proteins, and regulatory regions.
variant annotationfunctional consequences
View entry EDatabases
Ensembl
An open research resource providing vertebrate genomes, gene annotation, comparative genomics, and variation data through browsers and programmatic interfaces.
genome databasegene annotation
View entry UDatabases
UniProt
A public knowledgebase that integrates protein sequences, functional information, and cross-references, with both reviewed and computationally annotated records.
protein databasefunctional annotation
View entry IDatabases
InterPro
A public resource that integrates protein signatures from member databases to classify families and identify domains and functional sites.
protein familiesdomains
View entry IInfrastructure
IGV
An open-source genome viewer for interactively examining sequencing, variation, annotation, and other data positioned on reference genomes.
genome browservisualization
View entry SAI Tools
StarDist
Open-source deep-learning software for instance segmentation of approximately star-convex objects in two- and three-dimensional microscopy images.
microscopyinstance segmentation
View entry IInfrastructure
ImageJ
Extensible open-source desktop software for displaying, processing, measuring, and analyzing scientific images.
scientific imagesimage analysis
View entry MInfrastructure
Micro-Manager
Open-source software for controlling automated microscope hardware and running time-lapse, multichannel, and z-stack acquisitions.
microscope controlimage acquisition
View entry SInfrastructure
Squidpy
An open-source Python tool for spatial molecular data analysis, including neighborhood graphs, spatial statistics, and tissue-image integration.
spatial omicssingle cell
View entry SInfrastructure
SpatialData
An open-source data framework, schema, and serialization format for representing, transforming, and querying uni- and multimodal spatial omics data.
spatial omicsdata framework
View entry GAI Tools
GNINA
An open-source command-line program that integrates convolutional-neural-network scoring and ligand optimization into molecular docking.
molecular dockingdeep learning
View entry TInfrastructure
TorchDrug
An open-source PyTorch toolbox for graph representation learning in drug discovery, with components for molecules, proteins, reactions, and knowledge graphs.
drug discoverygraph neural networks
View entry TDatabases
Therapeutics Data Commons
An open research resource and Python package providing therapeutic machine-learning tasks, datasets, evaluation functions, benchmarks, and leaderboards.
therapeutic dataML benchmarks
View entry DInfrastructure
DeepPurpose
An open-source deep-learning toolkit for drug-target interaction, molecular-property, and related biomedical prediction tasks.
drug-target interactiondeep learning
View entry GInfrastructure
GROMACS
Open-source high-performance software for molecular-dynamics simulation, energy minimization, and trajectory analysis.
molecular dynamicssimulation
View entry SInfrastructure
SwissDock
A free research service for submitting protein-small-molecule docking jobs through a web interface and examining candidate poses.
molecular dockingweb service
View entry SInfrastructure
SwissADME
A free web tool that calculates molecular descriptors and predicts selected ADME, pharmacokinetic, and drug-likeness properties.
ADMEpharmacokinetics
View entry BModels
Boltz
An open-source family of models and inference software for biomolecular complex structure and selected binding-affinity predictions.
biomolecular structurebinding affinity
View entry RModels
RFdiffusion
Open-source research code and model weights for diffusion-based generation of protein backbones, motif scaffolds, and symmetric structures.
protein designdiffusion model
View entry IInfrastructure
Imaris
Proprietary modular software for visualizing, segmenting, tracking, and quantitatively measuring two- to four-dimensional microscopy images.
microscopy imaging3D analysis
View entry HAI Tools
HALO
A proprietary digital-pathology platform for quantitative analysis of whole-slide images through configurable tissue, cell, and biomarker modules.
digital pathologywhole-slide imaging
View entry AAI Tools
Aivia
A proprietary platform for visualizing, segmenting, tracking, and phenotyping two- to five-dimensional microscopy images.
microscopy imagingimage analysis
View entry ZAI Tools
ZEISS arivis Pro
Proprietary software for visualizing, segmenting, and building repeatable analysis pipelines for large two-, three-, and four-dimensional microscopy datasets.
microscopy imagingimage segmentation
View entry FInfrastructure
FastQC
Open-source software for checking raw high-throughput sequencing data and producing modular plots, tables, and HTML reports.
sequencing QCFASTQ
View entry FInfrastructure
fastp
An open-source command-line tool for quality control and preprocessing of short-read FASTQ data, including filtering, trimming, and HTML or JSON reporting.
FASTQ preprocessingshort-read sequencing
View entry CInfrastructure
Cutadapt
An open-source tool that finds and removes specified adapters, primers, poly-A tails, and other unwanted sequences from high-throughput sequencing reads.
adapter trimmingFASTQ
View entry SInfrastructure
SeqKit
A cross-platform open-source command-line toolkit for querying, transforming, summarizing, sampling, and indexing FASTA and FASTQ files.
sequence filesFASTA/FASTQ
View entry MInfrastructure
minimap2
An open-source aligner for mapping DNA or mRNA sequences to a reference, with modes for long reads, short reads, spliced transcripts, and assembly comparison.
sequence alignmentlong reads
View entry BInfrastructure
Bowtie 2
An open-source FM-index aligner for mapping sequencing reads to long reference sequences in local, end-to-end, gapped, and paired-end modes.
short-read alignmentreference genome
View entry BInfrastructure
BEDTools
An open-source command-line suite for intersecting, merging, comparing, covering, and otherwise analyzing genomic intervals.
genomic intervalsset operations
View entry BInfrastructure
BWA-MEM2
An optimized implementation of the BWA-MEM algorithm for aligning short-read DNA sequencing data to a reference genome and producing SAM output.
short-read alignmentgenomics
View entry HInfrastructure
HISAT2
An open-source sequence aligner built on hierarchical graph FM indexes, with splice-aware alignment for RNA sequencing reads against genomes or transcript sets.
RNA-seqsplice-aware alignment
View entry VInfrastructure
VCFtools
An open-source command-line suite for filtering, summarizing, and converting genetic-variant data in VCF format.
VCFvariant processing
View entry SInfrastructure
SnpEff
An open-source variant annotation program that predicts gene-, transcript-, and protein-level consequences using a selected genome annotation database.
variant annotationfunctional consequences
View entry CInfrastructure
CNVkit
An open-source Python toolkit for inferring and visualizing copy-number variation from targeted, exome, or whole-genome sequencing data.
copy-number variationsequencing analysis
View entry SInfrastructure
scVelo
An open-source Python toolkit for estimating RNA velocity, latent time, and transcriptional dynamics from spliced and unspliced counts in single-cell transcriptomic data.
RNA velocitysingle-cell dynamics
View entry MInfrastructure
Monocle 3
An open-source R toolkit for clustering, trajectory reconstruction, pseudotime ordering, and differential analysis of single-cell RNA sequencing data.
single-cell trajectoriespseudotime
View entry CAI Tools
CellTypist
An open-source Python tool that uses logistic-regression classifiers and built-in or custom reference models to predict cell types in single-cell RNA sequencing data.
cell-type annotationmachine learning
View entry NAI Tools
nnU-Net
An open-source biomedical image-segmentation framework that adapts preprocessing, U-Net configuration, training, and inference to a dataset.
medical image segmentationdeep learning
View entry DAI Tools
DeepLabCut
An open-source deep-learning toolbox for markerless estimation of user-defined animal or object keypoints from video.
pose estimationbehavior analysis
View entry IInfrastructure
ITK-SNAP
An open-source desktop application for navigating, annotating, and segmenting three-dimensional medical images through manual and semi-automatic methods.
medical imagingimage segmentation
View entry UInfrastructure
UGENE
An open-source cross-platform bioinformatics suite that combines sequence viewing, alignment, annotation, phylogenetics, and visual workflows.
sequence analysisbioinformatics workbench
View entry