Biopython

Development

The foundational open-source library for biological computation and bioinformatics in Python.

Seurat

Healthcare

Seurat is an R package designed for single-cell RNA-seq data analysis, exploration, and integration of diverse single-cell data types.

Arcadia Science

Development

Accelerating biological discovery through open-source software and AI-driven research workflows.

GenePattern

Bioinformatics

The premier open-source genomic workflow system for reproducible scientific research and advanced omics analysis.

Polly

Data Science

The AI-Ready Data Platform for Biomedical Data

GeneMANIA

Bioinformatics

Advanced gene function prediction and association network integration for precision genomics.

Genoox (Franklin)

Healthcare & Biotech

AI-driven genomic data analysis and variant interpretation platform.

STRING

Bioinformatics

STRING is a database of known and predicted protein-protein interactions.

MetaCyc

Bioinformatics

The gold-standard database of experimentally validated metabolic pathways and biochemical reactions.

Galaxy

Developer

Galaxy is a web-based platform for data intensive biomedical research.

Minimap2

Bioinformatics

A versatile pairwise aligner for genomic and spliced nucleotide sequences.

BioGRID

Development

The foundational open-access repository for curated protein and genetic interaction datasets.

National Center for Biotechnology Information (NCBI)

Bioinformatics & Genomics

The global backbone for biomedical data, genomic intelligence, and clinical research informatics.

Foldit

Bioinformatics

Gamified Protein Folding: Harnessing human intuition to solve complex biochemical puzzles for drug discovery.

STAR

Bioinformatics

A fast spliced aligner for RNA-seq data.

Galaxy Project

Bioinformatics Platform

The open-source ecosystem for data-intensive science, workflow automation, and reproducible research.

Burrow-Wheeler Aligner (BWA)

Bioinformatics

A software package for mapping DNA sequences against a large reference genome.

Monocle

Healthcare

Monocle is a toolkit for analyzing single-cell RNA-seq data, enabling researchers to build trajectories, classify cells, and find differentially expressed genes.

NAMD

Bioinformatics

Petascale parallel molecular dynamics for high-fidelity biomolecular simulations.

MODELLER

Bioinformatics

The Industry Standard for Protein Comparative Modeling and Structural Bio-Refinement.

ModelSEED

Developer

ModelSEED is a computational platform for genome-scale metabolic model reconstruction and analysis.

KEGG

Bioinformatics

The gold standard for biological pathway mapping and genomic functional annotation.

GATK (Genome Analysis Toolkit)

Bioinformatics

The industry-standard engine for high-throughput genomic variant discovery and clinical-grade sequencing analysis.

Scanpy

Bioinformatics

Scalable toolkit for analyzing single-cell gene expression data in Python.

kallisto | bustools

Bioinformatics

A workflow for pre-processing single-cell RNA-seq data, enabling cell x gene matrix generation and analysis.

Personal Genome Diagnostics (PGDx)

Bioinformatics

Empowering local laboratories with automated, IVD-cleared genomic profiling for precision oncology.

Human Protein Atlas

Healthcare

The Human Protein Atlas is an open-access resource that maps all human proteins in cells, tissues, and organs.

Open Targets

Bioinformatics

Systematic drug target identification and prioritization through large-scale genomic and clinical data integration.

OmicsBox

Bioinformatics

The all-in-one bioinformatics platform for high-performance NGS data analysis and functional interpretation.

WikiPathways

Healthcare

WikiPathways is an open science platform for biological pathways contributed, updated, and used by the research community.

OmicsDI

Bioinformatics Platform

The premier multi-omics discovery index for cross-repository data orchestration and meta-analysis.

Bioconductor

Development

The gold standard for high-throughput genomic data analysis and reproducible bioinformatics.

EBI (European Bioinformatics Institute)

Education

EMBL-EBI provides freely available data resources and bioinformatics services to the scientific community, supporting research and innovation in molecular biology and related fields.

Integrative Genomics Viewer (IGV)

Bioinformatics

The industry-standard interactive visualization tool for integrated exploration of large-scale genomic datasets.

BioJulia

Development

High-performance computational biology and bioinformatics infrastructure for the Julia language.

STAR

Bioinformatics

Spliced Transcripts Alignment to a Reference (STAR) is an ultrafast RNA-seq aligner.

Reactome

Healthcare

Reactome is a free, open-source, curated and peer-reviewed pathway database for visualizing, interpreting and analyzing pathway knowledge.

Robetta

Bioinformatics

A protein structure prediction service using deep learning and comparative modeling.

AlphaFold Protein Structure Database

Bioinformatics

Open access database of protein structure predictions to accelerate scientific research.