Public Links

Protein Sequence and Function

UniProt

Comprehensive resource for protein sequence, function, annotation, and proteome information.

InterPro

Protein family, domain, and functional site annotation resource with InterProScan support.

NCBI Gene

Gene-centered portal linking sequence records, annotation, variation, and related resources.

UniProt BLAST

Sequence similarity search against UniProt protein datasets.

Protein Structure Resources

RCSB PDB

Primary portal for experimentally determined macromolecular 3D structures.

AlphaFold Protein Structure Database

Large-scale resource of predicted protein structures from AlphaFold.

RCSB Mol* 3D Viewer

Interactive web viewer for exploring and comparing 3D molecular structures.

Genome and Annotation Databases

NCBI Genomes

Genome portal for assemblies, annotation, and large-scale genomics resources.

NCBI Datasets

Download portal for genomes and related sequence data across the tree of life.

Ensembl

Genome browser and annotation resource for vertebrates and other eukaryotes.

Ensembl Plants

Plant-focused genome browser and comparative genomics resource.

GenBank

NIH nucleotide sequence archive and part of the INSDC data exchange network.

NCBI Genome Data Viewer

Interactive genome browser for browsing assemblies and annotations.

Pathways, Systems Biology, and Functional Context

KEGG

Integrated resource for pathways, genes, compounds, drugs, and biological systems.

KEGG PATHWAY

Manually curated pathway maps for metabolism, signaling, and cellular processes.

KEGG GENES

Gene and protein collection linked to KEGG orthology and pathway systems.

KEGG DRUG

Drug knowledgebase linked to therapeutic targets and molecular interaction context.

Small Molecules and Drug Discovery

PubChem

Large open NIH resource for chemical structures, properties, and associated bioactivity information.

PubChem Structure Search

Chemical structure and substructure search entry point for PubChem.

ChEMBL

Curated chemogenomics database linking compounds, bioactivity, and targets.

ChEMBL Compounds

Browse compound records and chemistry-focused entries in ChEMBL.

ChEMBL Drugs

Browse drug entries and related annotations in ChEMBL.

DrugBank

Drug and target knowledgebase spanning drugs, targets, interactions, and clinical context.

Programming, Open Source, and Community Resources

Bioconductor

Major open-source ecosystem for reproducible analysis of biological data in R.

Bioconductor Books

Online books and workflows for modern genomic and transcriptomic data analysis.

GitHub

Software hosting and collaboration platform widely used for open-source scientific software.

GitHub Community

Community discussions, learning resources, and support for GitHub users.

GitHub Open Source

Open-source maintainer and contributor resources hosted by GitHub.

Useful Search and Download Entry Points

NCBI Search

Unified search across NCBI biomedical and genomic databases.

UniProt Downloads

Download help and dataset access for UniProt resources.

RCSB PDB Downloads

Bulk download access for structures and related archive files.

InterPro Downloads

Download portal for InterPro, InterProScan, and related signature databases.

Ensembl Downloads

Download access for Ensembl data, software, and FTP resources.

Plant and Crop Genomics

TAIR

Primary community resource for Arabidopsis thaliana genetics, genomics, and molecular biology.

TAIR Search

Entry point for gene, genome position, polymorphism, and functional searches in TAIR.

Ensembl Plants

Genome browser and annotation resource for plant species of scientific and agricultural interest.

Ensembl Plants Tools

Access BLAST, BioMart, VEP, and related analysis tools for plant genomes.

Gramene

Comparative plant genomics resource covering crops and model plant species.

Plant Reactome

Curated pathway knowledgebase for crops and model plants within the Gramene ecosystem.

Aging and Longevity Resources

Aging Atlas

Multi-omics resource for aging-related transcriptomic, epigenomic, proteomic, and pharmacogenomic datasets.

Aging Atlas Gene Sets

Curated aging-related gene sets collected from the literature and organized by category.

Aging Atlas Help

Documentation and usage guidance for the Aging Atlas resource.

PubMed

Primary literature search resource for aging biology, geroscience, and translational biomedicine.

AI for Computational Biology

AlphaFold Protein Structure Database

Open access database of large-scale predicted protein structures for biological discovery.

AlphaFold DB Downloads

Bulk download access for AlphaFold DB predictions and associated resources.

OpenFold

Trainable and memory-efficient open-source PyTorch reproduction of AlphaFold-style structure prediction.

Hugging Face

Major platform for sharing and discovering AI models, datasets, and applications.

Hugging Face Models

Searchable index of public models, including biological and biomedical foundation models.

Hugging Face Datasets

Repository of datasets useful for ML, LLM, multimodal, and bioinformatics workflows.

scGPT

Foundation-model framework for single-cell and multi-omics analysis using generative AI.

scGPT-spatial

Spatial transcriptomics extension of scGPT for large-scale spatial omics modeling.

scGenePT

Single-cell perturbation modeling framework integrating foundation-model ideas with gene-level embeddings.

Expression, Perturbation, and Single-Cell Resources

NCBI GEO

Major public repository for functional genomics data, including array- and sequence-based studies with search and download tools.

GEO DataSets

Curated GEO study records for browsing experiments, metadata, and downloadable expression datasets.

GEO Profiles

Gene-centered view of curated expression profiles derived from GEO datasets.

GEO2R

Browser-based differential expression tool for rapid comparisons within GEO studies.

ArrayExpress

EMBL-EBI functional genomics collection for expression and other high-throughput studies, with links to associated sequence archives.

ArrayExpress in BioStudies

Overview of ArrayExpress content integration with BioStudies at EMBL-EBI.

ArrayExpress Studies

Browse released ArrayExpress studies through the BioStudies interface.

NIH LINCS Program

NIH resource for large-scale perturbational datasets spanning small molecules, ligands, genetic perturbations, and multiple assay types.

LINCS L1000 Access Guide

Practical entry point for finding and downloading LINCS L1000 perturbation data.

iLINCS Workflows

Analysis entry point for LINCS transcriptomic and proteomic signatures through iLINCS workflows.

CZ CELLxGENE Discover

Curated platform for finding, downloading, and visually exploring standardized single-cell biology datasets.

CELLxGENE Collections

Browse dataset collections organized for discovery and reuse across tissues, diseases, and organisms.

CELLxGENE Datasets

Searchable dataset index for published single-cell studies in CELLxGENE Discover.

CELLxGENE Gene Expression

Gene-centric exploration view across curated single-cell datasets.

Literature and Preprints

PubMed

Primary literature search resource for biomedical, genomics, and life science research.

PubMed Advanced Search

Fielded query builder for more precise literature searches in PubMed.

PubMed Central (PMC)

Free full-text archive of biomedical and life sciences journal literature.

Europe PMC

Broad life sciences literature platform with abstracts, full text, citations, and linked research outputs.

Europe PMC Advanced Search

Advanced query interface for literature, grants, preprints, and full-text content in Europe PMC.

Europe PMC Downloads

Download access for open-access full text and metadata from Europe PMC.

bioRxiv

Major preprint server for life sciences research prior to peer review.

bioRxiv Latest Articles

Browse recently posted life science preprints on bioRxiv.

bioRxiv Subject Collections

Browse preprints by topic area across the life sciences.

medRxiv

Major preprint server for health sciences and translational biomedical research prior to peer review.

medRxiv Latest Articles

Browse recently posted health science preprints on medRxiv.

medRxiv Subject Areas

Browse medRxiv preprints by clinical and biomedical topic area.

Analysis Tools and Portals

UCSC Genome Browser

Major genome browser for viewing assemblies, annotations, tracks, and comparative genomics data.

UCSC Genome Browser Gateway

Direct entry point for selecting assemblies and navigating genomic regions of interest.

UCSC Genome Browser Training

Tutorials, workshops, and teaching materials for effective use of the UCSC Genome Browser.

UCSC Genome Browser User’s Guide

Documentation for browser navigation, track configuration, and genomic data visualization.

IGV

High-performance interactive viewer for genomic alignments, variants, annotations, and other omics tracks.

IGV Web App

Browser-based version of IGV for quick interactive data exploration and sharable sessions.

IGV Desktop Documentation

Documentation and usage guidance for the desktop Integrative Genomics Viewer.

STRING

Protein association network resource for functional interactions, evidence channels, and enrichment analysis.

STRING API

Programmatic access to STRING interaction networks and supporting evidence.

Reactome

Open, curated, and peer-reviewed pathway database for pathway browsing, analysis, and systems biology context.

Reactome Pathway Browser

Interactive pathway exploration interface for navigating curated biological pathways.

Reactome Analysis Tools

Pathway analysis entry point for gene lists, expression results, and other molecular datasets.

Reactome Downloads

Download access for pathway data and standard export formats.

cBioPortal

Cancer genomics portal for exploring mutations, copy number changes, expression, and clinical associations across studies.

cBioPortal Studies

Browsable collection of cancer genomics studies and cohorts available in cBioPortal.

Sequence Search and Alignment

NCBI BLAST

Standard sequence similarity search tool for comparing nucleotide or protein sequences against major public databases.

NCBI Nucleotide BLAST

BLAST entry point for nucleotide-versus-nucleotide sequence searches.

NCBI Protein BLAST

BLAST entry point for protein-versus-protein sequence similarity searches.

EMBL-EBI NCBI BLAST

Alternative BLAST interface through the EMBL-EBI job dispatcher framework.

HMMER

Sensitive homology search tools for sequence and profile-based searches against protein databases.

EMBL-EBI Job Dispatcher

Portal for sequence search and alignment tools provided by EMBL-EBI through web and programmatic interfaces.

Clustal Omega

Widely used multiple sequence alignment tool for protein and nucleotide sequences.

UniProt Align Tool

Convenient sequence alignment entry point integrated with UniProt and powered by Clustal Omega.

MAFFT

High-quality multiple sequence alignment software with options ranging from fast large-scale alignment to more accurate modes.

MAFFT Documentation

Manual and usage guide for running MAFFT with different alignment strategies and parameters.

Variants and Clinical Interpretation

ClinVar

Public archive of human variants with disease and drug-response interpretations and supporting evidence.

ClinVar Introduction

Overview of ClinVar content, submission model, and interpretation framework.

ClinVar Search Help

Guide for searching ClinVar by gene, HGVS notation, genomic region, and related fields.

ClinVar Advanced Search

Fielded search builder for more precise variant and phenotype queries.

gnomAD

Large population reference database for human genetic variation and allele frequencies.

gnomAD News and Releases

Release notes and updates for new datasets, browser features, and frequency resources.

dbSNP

NCBI archive for single nucleotide polymorphisms and related small genetic variants.

dbSNP Release Updates

Recent NCBI update page for dbSNP build releases and expanded variant content.

Ensembl VEP

Variant Effect Predictor for annotating SNPs, indels, CNVs, and structural variants against genes, transcripts, proteins, and regulatory regions.

Ensembl VEP Web Interface

Browser-based VEP workflow for interactive variant annotation and filtering.

Ensembl VEP Command Line

Command-line documentation for scalable variant annotation and plugin-based workflows.

Expression and Pathway Enrichment Tools

GSEA / MSigDB

Gene set enrichment analysis platform and home of the Molecular Signatures Database for enrichment-based interpretation of expression results.

MSigDB

Curated collection of human and mouse gene sets for pathway, perturbation, ontology, and cell-state enrichment analyses.

MSigDB Human Collections

Browse hallmark, pathway, perturbation, ontology, and regulatory gene-set collections for human analyses.

GSEA Downloads

Download the GSEA desktop software and related resources for enrichment analysis workflows.

GSEA Documentation

User guide and documentation for running and interpreting GSEA analyses.

DAVID

Widely used functional annotation and enrichment resource for interpreting gene lists with biological context.

DAVID Functional Annotation

Entry point for annotation, clustering, and enrichment-oriented analysis tools in DAVID.

Enrichr

Interactive web tool for gene-list enrichment analysis across many pathway, ontology, and perturbation libraries.

Enrichr Libraries

Overview of available enrichment libraries, including pathways, ontologies, transcription factors, and perturbation signatures.

clusterProfiler

Bioconductor package for statistical enrichment analysis and visualization of functional profiles for genes and gene clusters.

clusterProfiler Documentation

Package landing page with vignettes, reference manual, and installation details.

DOSE

Bioconductor package for disease ontology semantic analysis and enrichment workflows that often complement clusterProfiler.

Single-Cell and Spatial Analysis Tools

Scanpy

Scalable Python toolkit for preprocessing, visualization, clustering, and downstream analysis of single-cell gene expression data.

Scanpy Tutorials

Curated tutorials covering core workflows, visualization, trajectory analysis, and spatial data analysis with Scanpy.

Seurat

Widely used R toolkit for QC, analysis, integration, and exploration of single-cell transcriptomic data.

Seurat Getting Started

Introductory tutorials and walkthroughs for building standard Seurat-based single-cell workflows.

Seurat Guided Clustering Tutorial

Classic end-to-end tutorial for preprocessing, clustering, and visualizing single-cell RNA-seq data in Seurat.

OSCA: Orchestrating Single-Cell Analysis with Bioconductor

Comprehensive Bioconductor book for processing, analyzing, visualizing, and exploring single-cell RNA-seq data.

SingleCellExperiment

Core Bioconductor data structure for storing expression matrices, cell metadata, and feature annotation in synchronized form.

Bioconductor Single-Cell Installation Guide

Practical setup guide for getting started with single-cell analysis in R and Bioconductor.

Squidpy

Python toolkit for the analysis and visualization of spatial molecular data built on top of Scanpy and AnnData.

Squidpy Tutorials

Tutorial collection demonstrating core Squidpy workflows on diverse spatial datasets.

Squidpy API

Reference documentation for graph, image, and spatial analysis functions in Squidpy.

Visium Analysis with Squidpy

Worked example for analyzing 10x Visium spatial transcriptomics data with tissue-image context.

Cloud and Workflow Platforms

Galaxy Project

Open, web-based platform for accessible, reproducible, and transparent computational biomedical research.

UseGalaxy Servers

Public Galaxy servers with synchronized tools and reference resources for broad community use.

Galaxy Training Network

Extensive tutorials and training materials for learning Galaxy-based workflows and analyses.

Terra

Cloud-native platform for biomedical data access, analysis, and collaboration at scale.

Terra Overview

Getting-started overview of Terra’s data, analysis, and collaborative workflow model.

Terra Interactive Analysis

Entry point for notebooks, cloud environments, and interactive analysis workflows on Terra.

Dockstore

Free and open-source platform for sharing reusable and scalable analytical tools and workflows.

Dockstore Quick Start

Practical introduction to finding, launching, and developing tools and workflows on Dockstore.

Dockstore API / Swagger

Programmatic access to Dockstore resources for integration and workflow automation.

nf-core

Community framework for high-quality open-source Nextflow components and pipelines.

nf-core Pipelines

Browse currently available nf-core pipelines across many common genomics and bioinformatics applications.

nf-core Configs

Collection of institutional and platform-specific configuration profiles for running nf-core workflows.

Snakemake

Widely used workflow system for reproducible and scalable data analysis.

Snakemake Documentation

Documentation for building, scaling, and deploying Snakemake workflows.

ML and AI Toolkits

PyTorch

Widely used open-source deep learning framework for tensor computation, neural networks, and research-oriented model development.

PyTorch Tutorials

Official tutorials for tensors, neural networks, training workflows, and model deployment in PyTorch.

PyTorch Ecosystem

Overview of libraries, tools, and projects built around the PyTorch framework.

TensorFlow

End-to-end machine learning platform for model development, training, and deployment across research and production settings.

TensorFlow Tutorials

Official tutorials covering neural networks, structured data, time series, images, and text.

Keras

High-level deep learning API for building and training neural networks with a streamlined interface.

Keras Examples

Collection of practical examples for deep learning workflows across images, text, timeseries, graphs, and generative models.

XGBoost

High-performance gradient boosting framework widely used for classification, regression, ranking, and feature-rich tabular data.

XGBoost Python Package

Documentation for building, training, and tuning XGBoost models in Python.

XGBoost R Package

R interface for gradient boosting workflows with XGBoost.

LightGBM

Gradient boosting framework optimized for speed and efficiency on large-scale tabular datasets.

CatBoost

Gradient boosting toolkit designed for strong performance on tabular data, including categorical features.

scikit-learn

Core Python machine learning library for classification, regression, clustering, preprocessing, and model selection.

scikit-learn User Guide

Comprehensive guide to estimators, preprocessing pipelines, evaluation, and common ML workflows.

Hugging Face

Major platform for sharing AI models, datasets, inference tools, and application workflows.

Hugging Face Models

Searchable model hub including language, vision, multimodal, and biology-relevant foundation models.

Hugging Face Datasets

Repository of datasets for machine learning, LLM, multimodal, and computational biology workflows.

Weights & Biases

Experiment tracking, model evaluation, and collaboration platform for machine learning workflows.

MLflow

Open-source platform for experiment tracking, model packaging, and ML workflow management.

ONNX

Open format and ecosystem for interoperable machine learning models across frameworks and runtimes.

tidymodels

R ecosystem for modeling, preprocessing, tuning, workflows, and reproducible machine learning pipelines.

caret

Classic R toolkit for streamlined model training and evaluation across many machine learning methods.

torch for R

Native R interface for tensors, autodiff, neural networks, and deep learning workflows inspired by PyTorch.

torch for R - Get Started

Introductory documentation and installation guide for deep learning in R with torch.

keras3 for R

R interface for Keras workflows, including deep learning model construction and training.

tensorflow for R

R interface and guides for TensorFlow-based machine learning workflows.

LLMs and Agent Frameworks

LangChain

Framework for building LLM-powered applications and agents with model integrations, memory, tools, and orchestration components.

LangChain Quickstart

Fast entry point for building a first LangChain-based application or agent.

LangChain Learn

Tutorials, conceptual guides, and learning resources for LangChain and LangGraph workflows.

LlamaIndex

Framework for building LLM-powered agents and retrieval workflows over external documents, databases, and private data.

LlamaIndex Quickstart

Getting-started entry point for building LlamaIndex applications in Python or TypeScript.

LlamaIndex Workflows

Guide to building multi-step agent workflows and retrieval pipelines with LlamaIndex.

Ollama

Platform for running and managing open models locally for chat, embeddings, coding, and multimodal workflows.

Ollama Download

Installation entry point for macOS, Linux, and Windows.

Ollama Model Library

Browsable catalog of open models available through Ollama.

vLLM

High-performance inference and serving engine for large language models.

vLLM Quickstart

Quickstart guide for installing and running vLLM for inference and serving.

vLLM Supported Models

Reference list of model architectures supported by vLLM.