Galaxy Platform Directory: Servers, Clouds, and Deployable Resources
UseGalaxy Resources
UseGalaxy servers implement a common core set of tools and reference genomes, and are open to anyone to use. They also contain tools and genomes that are local to each server. Each is backed by significant computational resources and they are excellent places to get started with Galaxy, and to share and publish your results.
| Resource | Server | Summary | Keywords |
|---|---|---|---|
| UseGalaxy.eu | Server | The European UseGalaxy server. | UseGalaxy |
| UseGalaxy.org (Main) | Server | The Galaxy Project free public server; biomedical research | UseGalaxy |
| UseGalaxy.org.au | Server | The Australian UseGalaxy server. | UseGalaxy |
All Resources
Complete listing of resources for using Galaxy.
| Resource | Server | Cloud | Deploy- able | Summary | Keywords |
|---|---|---|---|---|---|
| A-Game | Server | A Galaxy suite for tArgeted MEtagenomics | Domain | ||
| AB-OpenLab | Server | FROG stands for FingeRprinting Ontology of Genomic variations. FROG fingerprints have been devised to capture genomic variations at various levels. | Tools | ||
| ABiMS | Server | Analysis and bioinformatics for Marine Science. | Genomics | ||
| ABiMS-Tools | Server | Hosts tools/resources developed at the Station Biologique de Roscoff in collaboration with ABiMS. | Tools | ||
| AGEseq @ AspenDB | Server | This site provides a user-friendly interface for AGEseq (Analysis of Genome Editing by Sequencing) in a Galaxy instance. | Tools | ||
| Alveo: Human Communication Science Virtual Laboratory | Server | Human Communication Science (HCS). | Domain | ||
| Amazon Web Services (AWS) | Commercial | Set up you own general purpose genomics server runing AWS using GVL and CloudMan. | Genomics | ||
| AmrPlusPlus | Container | A Galaxy-based metagenomics pipeline that is intuitive and easy to use. | Tools | ||
| ANASTASIA | Server | Automated Nucleotide Aminoacid Sequences Translational plAtform for Systemic Interpretation and Analysis | Genomics | ||
| Antigen Receptor Galaxy (ARGalaxy) | Server | Automate the analysis and visual reporting of T- and B-cell receptor repertoire sequencing data. | Tools | ||
| APOSTL | Server | Automated Processing of SAINT Templated Layouts (APOSTL) is a freely available software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data. | Tools | ||
| ARGs-OAP | Server | Fast annotation and classification of antibiotic resistance gene-like sequences from metagenomic data. | Tools | ||
| ARIES | Server | Analysis of genomic data in the field of public health and food safety, with the aim of deploying a comprehensive bioinformatics approach to the study of food-borne zoonoses and infectious diseases at the human and animal interface. | Domain | ||
| ballaxy | Container | Hosts the BALL (Biochemical Algorithms Library) Project tools, i.e. computer aided drug design and molecular modelling based on protein and ligand structure data. | Domain | ||
| BF2I-MAP | Server | Locally developed as well as standard tools are available on a 16-core server with 32GB memory, accessible to all users, and located in the BF2I lab. | Tools | ||
| BioBix | Server | A general genomics server. Includes the PROTEOFORMER pipeline tools. | Genomics | ||
| BioCiphers Lab Galaxy | Server | BCL Galaxy gives a user friendly interface for analysis tools developed by the BioCiphers Lab at the University of Pennsylvania. | Tools | ||
| BioMaS | Server | Taxonomic studies of environmental microbial communities | Tools | ||
| Biomina | Server | A general purpose Galaxy instance that includes most standard tools for DNA/RNA sequencing, plus extra tools for panel resequencing, variant annotation and some tools for Illumina SNParray analysis. | Genomics | ||
| BIPAA (BioInformatics Platform for Agroecosystem Arthropods) | Server | Insect genomics (aphids, parasitoïd wasps, lepidopterans) | Domain | ||
| BitLAB | Server | Detailed analysis of metagenomes. | Tools | ||
| CBiB Galaxy | Server | A general purpose Galaxy instance that includes EMBOSS (a software analysis package for molecular biology) and fibronectin (diversity analysis of synthetic libraries of a Fibronectin domain). | Genomics | ||
| Center for Phage Technology (CPT) | Server | Phage biology and automated annotation. | Domain | ||
| ChemFlow | Server | Chemometrics without programming: infrared spectrometry on a Galaxy platform. | Domain | ||
| Chemical Annotation Retrieval Toolkit (CART) | Server | Retrieves annotations on biological effects of chemicals and determines which ones are enriched. | Tools | ||
| ChimeRScope | Server | Fusion gene discovery from transcriptome-sequencing (RNA-seq) datasets. | Tools | ||
| Cistrome Analysis Pipeline | Server | ChIP-chip/seq and gene expression data | Domain | ||
| CLIMB | Academic | The CLIMB project (Cloud Infrastructure for Microbial Bioinformatics) develops and deploys a world leading cyber-infrastructure for microbial bioinformatics; providing free cloud-based compute, storage, and analysis tools for academic microbiologists in the UK. | Genomics | ||
| Codon Harmonizer | Server | Easily generate codon harmonized variants of gene sequences for heterologous expression | Tools | ||
| CoSSci | Server | Tools for solving Galton's problem in Comparative Research and complex network problems in Social Science. | Domain | ||
| CRAVAT-P | Container | A Docker image containing a fully-operational Galaxy instance with pre-installed demonstration material for CRAVAT-P. | Tools | ||
| DBCLS Galaxy | Server | Adds text mining tools, DBCLS DBSearch Tools, semantic web tools | Genomics | ||
| DDBJ Read Annotation Pipeline | VM | Annotates raw sequencing reads from next-generation sequencers(NGS) with high throughput, which are registered in DDBJ Read Archive (DRA). | Tools | ||
| deepTools | Server | Container | deepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from high-throughput DNA sequencing experiments. | Tools | |
| Dintor | Server | GWA and NGS tools and modules for functional annotation of genes and gene products | Domain | ||
| EGI Marketplace | Academic | Galaxy instances on a European wide federation of research cloud providers. | Genomics | ||
| epiGeEC | Server | Compare user-provided epigenomic datasets with thousands of public datasets. | Tools | ||
| EpiToolKit | Server | Computational immunology for the development of novel epitope-based vaccines. | Tools | ||
| Erasmus MC | Server | General purpose genomics analysis, featuring many standard tools plus many additional tools. | Genomics | ||
| EuPathDB Galaxy | Academic | A free, interactive, web-based platform for large-scale data analysis focused on eukaryotic pathogens. | Domain | ||
| G-OnRamp | Commercial | VM | G-OnRamp provides a user-friendly, web-based platform for collaborative, end-to-end annotation of eukaryotic genomes using UCSC Assembly Hubs and JBrowse/Apollo genome browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNA-Seq data, and repeat finders. | Domain | |
| GalaxEast | Server | Integrative 'omics data analysis | Genomics | ||
| Galaxy basic sequence manipulation | Container | Galaxy Docker repository for basic sequence data analysis. | Domain | ||
| Galaxy BLAST+ | Container | A complete and production ready Galaxy instance with installed BLAST+ tools. | Domain | ||
| Galaxy ChIP-Seq Docker | Container | Galaxy Docker image for ChipSeq analysis | Domain | ||
| Galaxy CSG | Container | Galaxy instance with tools for Constructive Solid Geometry shipped in a Docker container. | Domain | ||
| Galaxy Docker | Container | The Galaxy Docker Image is an easy distributable full-fledged Galaxy installation, that can be used for testing, teaching and presenting new tools and features. | Genomics | ||
| Galaxy Exome-Seq | Container | Galaxy Docker repository for Exome sequencing data analysis | Domain | ||
| Galaxy Genome Annotation | Container | Galaxy Docker repository for genome annotation | Domain | ||
| Galaxy Imaging | Container | Galaxy Docker repository for image analysis | Domain | ||
| Galaxy Integrated Omics (GIO) | Server | Proteomics Informed by Transcriptomics (PIT) methodology, and selection of surrogate peptides for targeted proteomics. | Domain | ||
| Galaxy mothur Toolset Docker | Container | Galaxy Docker image for microbial ecology analysis with mothur | Domain | ||
| Galaxy PGTB (Virtual Biodiversity Lab) | Server | This is a standard Galaxy instance implemented with specific tools for Biodiversity (Biodiversity Virtual Lab) and NGS (Ion Torrent from the PGTB facility) analysis. | Domain | ||
| Galaxy Test | Server | Beta version of Galaxy Main | Genomics | ||
| Galaxy-CEFAP | Server | Galaxy-CEFAP offers a set of tools to perform RNA-Seq and miRNA analysis. | Domain | ||
| Galaxy-P | Server | Galaxy-P is a multiple 'omics' data analysis platform with particular emphasis on mass spectrometry based proteomics. Galaxy-P is developed at the University of Minnesota, deployed at the Minnesota Supercomputing Institute. | Domain | ||
| Galaxy@GenOuest | Server | A general purpose Galaxy server Includes tools developped by Dyliss and GenScale bioinformatics research teams in Rennes, France. | Genomics | ||
| Galaxy@Pasteur | Server | General purpose genomics analysis server. | Genomics | ||
| Galaxy@PRABI | Server | Includes bioinformatics tools developed by the research teams working in the perimeter of the PRABI core facility, including kissplice/kissDE, TETools, SEX-DETector, and priam. | Genomics | ||
| GenAP | Academic | All Canadian researchers are eligible for a GenAP account. International researchers that have a Canadian collaborator can also be sponsored and become eligible to a GenAP account as well. | Genomics | ||
| GeneLab | Server | NASA GeneLab is a comprehensive space-related omics database in which users can upload, download, share, store, and analyze spaceflight and corresponding model organism data. | Genomics | ||
| Genomic Hyperbrowser | Server | Statistical methodology and computing power to handle a variety of biological inquires on genomic datasets | Domain | ||
| GigaGalaxy | Server | GigaGalaxy hosts tools and data analyses from papers published in *GigaScience*. | Genomics | ||
| Globus Genomics | Academic | Globus Genomics provides hardened high-performance Galaxy servers running with Globus on AWS. | Genomics | ||
| GrAPPA | Server | GrAPPA is a web-based interface constructed on the Galaxy framework for graph theoretical tools. It contains novel combinatorial methods integrated into a complete microarray analysis toolchain, from uploading raw high-throughput data to visualization of results. | Domain | ||
| Halogen Bonding | Server | Visualize halogen bond contacts in the protein binding site. Analyze a protein binding site for halogen bonding hotspots. Evaluate halogen contacts with the protein backbone using the scoring function XBScore. | Tools | ||
| Hardwood Genomics | Server | A simplified, workflow-centic interface to Galaxy, focused on genomics data from hardwood trees. | Domain | ||
| HiCExplorer | Server | Tools to process and visualize chromosome conformation. | Domain | ||
| Hunter College Galaxy | Server | A general purpose genomics server | Genomics | ||
| Huttenhower Lab | Server | metagenomic and functional genomic analyses, intended for research and academic use | Domain | ||
| IBERS @ Aberystwyth | Server | Software, tools and pages written by IBERS researchers for release to the wider community. | Tools | ||
| Image Analysis and Processing Toolkit | Server | Image analysis and processing. | Domain | ||
| ImmPort Galaxy | Server | Flow Cytometry Analysis. | Domain | ||
| ImmunoGlobulin Galaxy (IGGalaxy) | VM | Provides a set of tools for easy detection and quantitation of immunoglobulin heavy chain alternative transcripts. | Domain | ||
| In Silico Galaxy | Server | Construction, analysis, and visualization of gene-gene interaction networks for sequencing data. | Tools | ||
| Insitut Curie | Server | General purpose genomic Galaxy server. Contains tools for Ion Torrent data, many RNA-Seq tools, ncPRO-seq, RSAT, Nebula tools, copy number and LOH tools, and NGS diagnostic tools. | Genomics | ||
| International Rice Research Institute (IRRI) Galaxy | Server | Bioinformatics workbench, with rice-specific data (i.e. genomes) and tools (mostly specialized for the IRRI Genotyping Service Laboratory) installed. | Domain | ||
| IRProfiler | Server | Container | Immune Repertoire Profiler (IRProfiler), a novel software pipeline that delivers a number of core receptor repertoire quantification and comparison functionalities on high-throughput TR and BcR sequencing data. | Tools | |
| Jetstream | Academic | Jetstream is part of XSEDE, a "collection of integrated advanced digital resources and services" and is funded by NSF. | Genomics | ||
| kmer-SVM | Server | Tool suite uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay. | Tools | ||
| Koslicki Lab | Server | Web based access to tools created by the Koslicki Lab at Oregon State University. | Tools | ||
| KREAP | VM | Kinetic Re-Epithelialization Analysis Pipeline | Tools | ||
| Langille Lab | Server | Prediction of the unobserved character states in a community of organisms from phylogenetic information. | Tools | ||
| Laniakea/INDIGO-DataCloud | Academic | Laniakea provides the possibility to automate the creation of Galaxy-based virtualized environments through an easy setup procedure, providing an on-demand workspace ready to be used by life scientists and bioinformaticians, with built-in storage encryption for user data. | Genomics | ||
| LAPPS Grid | Server | An open, interoperable web service platform for natural language processing (NLP) research and development. | Domain | ||
| Lifeportal | Server | a Galaxy instance to satisfy the computational needs of the Norwegian research community in life sciences but also of any other user willing to use the service. | Genomics | ||
| LiSIs | Server | A platform for Virtual Screening. | Tools | ||
| Majewski Lab | Server | Detection of recurrent Allelic Imbalance in tumors using whole Exome sequencing data. | Tools | ||
| Martin Luther U. Halle-Wittenberg | Server | Provides implementations of InMoDe, CRISPRer, TALgetter, TALgetterLong, TALENoffer, and Dimont | Tools | ||
| MBAC Metabiome Portal | Server | Simplifying control, usage, access, and analysis of microbiome, metabolome, and immunome data (the Metabiome). | Tools | ||
| MetaCentrum | Academic | MetaCentrum regional virtual organization of the Czech National Grid Infrastructure (NGI) and is accessible to employees and students of research and academic organizations of the Czech Republic and for scientific purposes only. | Genomics | ||
| Metaproteomics Gateway | Server | Metaproteomics gateway providing access to documentation and other instructional materials, and an opportunity for hands-on training using example datasets and optimized metaproteomics workflows | Domain | ||
| MGEScan | Server | Commercial | Identifying long terminal repeats (LTR) and non-LTR retroelements in eukaryotic genomic sequences. | Tools | |
| miCloud | Container | Leverage cloud technologies to provide an easy-to-use streamlined NGS data analysis using local computational hardware | Genomics | ||
| MiModD NacreousMap | Server | NacreousMap mapping/plotting tool of MiModD for users of MiModD who do not want to install the required dependencies (R and rpy2) for graphical output from this tool on their local system. | Tools | ||
| MISSISSIPPI | Server | Support for analyses of RNA and small RNA sequencing datasets as well as for epigenetics or metagenomics studies. | Domain | ||
| Molecular Property Diagnostic Suite - Diabetes Mellitus Portal (MPDSDM) | Server | A disease-specific open source web portal for Diabetes Mellitus. | Domain | ||
| Molecular Property Diagnostic Suite - Tuberculosis (MPDSTB) | Server | A disease-specific web portal for Tuberculosis for drug discovery and development. | Domain | ||
| MPI-HLR Bioinformatics Server | Server | Hosts the MIRPIPE, ADMIRE, and LimiTT tools | Tools | ||
| Nebula | Server | allows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data. | Domain | ||
| Nectar Cloud | Academic | Set up a Galaxy server on Australia's Nectar research cloud. | Genomics | ||
| NELLY | Server | Plataforma de servicios para análisis de datos biomédicos en bioinformática featuring standard Galaxy Tools | Genomics | ||
| NeLS | Academic | Life Science platform for Norwegian academic researchers. | Genomics | ||
| NGS-QC | Server | Evaluate the quality of your favorite ChIP-seq or enrichment-related NGS dataset using NGS-QC Generator, which also includes a database with preprocessed profiles and a tutorial on how to analyze sequencing profiles yourself. | Tools | ||
| Oqtans | Server | Commercial | Customized Galaxy, extended with machine learning based tools for sequence and tiling array data analysis. | Domain | |
| Orione | Server | A Galaxy based web server for microbiology. Orione includes all post mapping or assembling steps from scaffolding to complete annotation pipelines. | Domain | ||
| OSDDlinux LiveGalaxy | Server | Drug discovery | Domain | ||
| Osiris | Server | Phylogenetics | Tools | ||
| Palfinder | Server | Microsatellite development. | Tools | ||
| PhenoMeNal | Server | Large scale computing for medical informatics | Domain | ||
| PIA | Server | Phylogenetics and gene interaction | Tools | ||
| PIPE-CLIP | Server | Reliable analysis of data generated by three types of CLIP-seq protocol: HITS-CLIP, PAR-CLIP and iCLIP. | Tools | ||
| Pitagora-Galaxy | Server | Commercial | VM | The Pitagora-Galaxy Project server intended for testing and sharing. Heavy analysis should be performed using the project's identical virtual machine (VM) or Amazon Machine Image (AMI). | Genomics |
| PL-Grid | Academic | The PL-Grid project is free of charge for any Polish scientist. It is also free for any foreign collaborator of Polish scientists. | Genomics | ||
| PlantGenIE | Server | Plant Genome Integrative Explorer Galaxy instance | Domain | ||
| PreSTIGE | Server | Predicting Specific Tissue Interactions of Genes and Enhancers | Tools | ||
| Proteogenomics Gateway | Server | Provides access to documentation and other instructional materials, and an opportunity for hands-on training using example datasets and optimized proteogenomics workflows. The main goal of this server is to provide documentation to facilitate training and mastery of these software and workflows. | Domain | ||
| ProteoRE | Server | ProteoRE (Proteomics Research Environment) | Domain | ||
| QBRC Galaxy | Server | Hosts custom tools developed by members of the Quantitative Biomedical Research Center @ University of Texas Southwestern for statistical analysis of various High Throughput Sequencing experiments. | Tools | ||
| QuanTP | Container | A Docker image containing a fully-operational Galaxy instance with pre-installed QuanTP tools. | Tools | ||
| RDF2Graph | Server | RDF2Graph recovers the structure of an RDF resource. | Tools | ||
| RepeatExplorer | Server | Graph-based clustering and characterization of repetitive sequences, and detection of transposable element protein coding domains. | Domain | ||
| RiboGalaxy | Server | Container | Tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique. | Domain | |
| RNA Workbench | Server | Container | more than 50 bioinformatics tools dedicated to different research areas of RNA biology, including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-Seq analysis, and RNA target prediction. | Domain | |
| RNA-Rocket @ Pathogen Portal | Server | Supports comparative analysis of host response to pathogens. It provides an RNA-Seq pipeline to characterize the transcriptome of all NIAID Bioinformatic Resource Center (BRC) pathogens and their key hosts. | Domain | ||
| RNAcommender | Container | RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. It is a recommender system capable of suggesting RNA targets to unexplored RNA binding proteins, by propagating the available interaction information, taking into account the protein domain composition and the RNA predicted secondary structure. | Tools | ||
| SIFTED | Server | Specificity Inference For TAL-Effector Design (SIFTED) | Tools | ||
| SMAGEXP | Container | SMAGEXP (Statistical Meta-Analysis for Gene EXPression) provides a unified way to carry out meta-analysis of gene expression data, while taking care of their specificities. | Tools | ||
| SNIC Science Cloud (SSC) | Academic | A national-scale cloud infrastructure for Swedish Academia | Genomics | ||
| South Green | Server | Genomic resource analysis of southern and Mediterranean plants. | Domain | ||
| Splicescope | Server | Prediction of neuronal maturation using splicing profiles | Tools | ||
| Stem Cell Discovery Engine | Server | Database of curated cancer stem cell experiments coupled to Galaxy. | Domain | ||
| SymD | Server | a platform for detecting internally symmetric protein structures | Domain | ||
| TreeGenes | Server | TreeGenes integrates genotype, phenotype, and environmental data that can be processed for association mapping and landscape genomics, with a focus on forest trees. This functionality is provided by Tripal Galaxy, a module for Tripal that provides seamless support for running Galaxy workflows directly in the site. Users can analyze data provided by TreeGenes or their own. | Domain | ||
| UseGalaxy.eu | Server | The European UseGalaxy server. | UseGalaxy | ||
| UseGalaxy.org (Main) | Server | The Galaxy Project free public server; biomedical research | UseGalaxy | ||
| UseGalaxy.org.au | Server | The Australian UseGalaxy server. | UseGalaxy | ||
| USMI Galaxy Demonstrator | Server | This Galaxy implementation is meant to demonstrate integration of microbial domain Biological Resource Center (mBRC) catalogues into the bioinformatics data integration environment. | Tools | ||
| VarCap | Server | Reliable prediction of different types of variants even at low frequencies. | Tools | ||
| VectorBase Galaxy | Academic | A full Galaxy server that includes reference information and workflows focusing on invertebrate vectors of human pathogens. | Domain | ||
| Vinther Lab | Server | RNA structure-probing data analysis to improve the prediction of RNA secondary and tertiary structure and allow structural changes to be identified and investigated. | Tools | ||
| VirAmp | Server | VirAmp is a web-based semi-de novo fast virus genome assembly pipeline designed for extremely high coverage NGS data. | Domain | ||
| Wageningen UR | Server | Includes microarray tools, the MUMmer suite, and many conversion tools. Strong focus on multi-omics: next to genomics tools it also contains proteomics and metabolomics tools | Tools | ||
| Workflow4Metabolomics | Server | Container | A collaborative portal dedicated to metabolomics data processing, analysis and annotation. | Domain | |
| ZBIT Bioinformatics Toolbox | Server | This customized version of the Galaxy webservice framework was set up to allow the public access of our bioinformatics tools. These tools were developed and implemented by members of the Department of Cognitive Systems at the University of Tübingen. | Tools |
Public Servers
Public Servers are acccessible to (at least) any academic researcher in the world. Some require you to create/request an account, aand they may have restrictive quotas, but often, to use these, just go the website and start running analyses. These are free to use.
The folks are Freiburg have put together a public Galaxy server dashboard to track the status and some of the supported features of the servers listed here. See the blog post for more info.
| Resource | Link | Summary | Keywords |
|---|---|---|---|
| A-Game | Server | A Galaxy suite for tArgeted MEtagenomics | Domain |
| AB-OpenLab | Server | FROG stands for FingeRprinting Ontology of Genomic variations. FROG fingerprints have been devised to capture genomic variations at various levels. | Tools |
| ABiMS | Server | Analysis and bioinformatics for Marine Science. | Genomics |
| ABiMS-Tools | Server | Hosts tools/resources developed at the Station Biologique de Roscoff in collaboration with ABiMS. | Tools |
| AGEseq @ AspenDB | Server | This site provides a user-friendly interface for AGEseq (Analysis of Genome Editing by Sequencing) in a Galaxy instance. | Tools |
| Alveo: Human Communication Science Virtual Laboratory | Server | Human Communication Science (HCS). | Domain |
| ANASTASIA | Server | Automated Nucleotide Aminoacid Sequences Translational plAtform for Systemic Interpretation and Analysis | Genomics |
| Antigen Receptor Galaxy (ARGalaxy) | Server | Automate the analysis and visual reporting of T- and B-cell receptor repertoire sequencing data. | Tools |
| APOSTL | Server | Automated Processing of SAINT Templated Layouts (APOSTL) is a freely available software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data. | Tools |
| ARGs-OAP | Server | Fast annotation and classification of antibiotic resistance gene-like sequences from metagenomic data. | Tools |
| ARIES | Server | Analysis of genomic data in the field of public health and food safety, with the aim of deploying a comprehensive bioinformatics approach to the study of food-borne zoonoses and infectious diseases at the human and animal interface. | Domain |
| BF2I-MAP | Server | Locally developed as well as standard tools are available on a 16-core server with 32GB memory, accessible to all users, and located in the BF2I lab. | Tools |
| BioBix | Server | A general genomics server. Includes the PROTEOFORMER pipeline tools. | Genomics |
| BioCiphers Lab Galaxy | Server | BCL Galaxy gives a user friendly interface for analysis tools developed by the BioCiphers Lab at the University of Pennsylvania. | Tools |
| BioMaS | Server | Taxonomic studies of environmental microbial communities | Tools |
| Biomina | Server | A general purpose Galaxy instance that includes most standard tools for DNA/RNA sequencing, plus extra tools for panel resequencing, variant annotation and some tools for Illumina SNParray analysis. | Genomics |
| BIPAA (BioInformatics Platform for Agroecosystem Arthropods) | Server | Insect genomics (aphids, parasitoïd wasps, lepidopterans) | Domain |
| BitLAB | Server | Detailed analysis of metagenomes. | Tools |
| CBiB Galaxy | Server | A general purpose Galaxy instance that includes EMBOSS (a software analysis package for molecular biology) and fibronectin (diversity analysis of synthetic libraries of a Fibronectin domain). | Genomics |
| Center for Phage Technology (CPT) | Server | Phage biology and automated annotation. | Domain |
| ChemFlow | Server | Chemometrics without programming: infrared spectrometry on a Galaxy platform. | Domain |
| Chemical Annotation Retrieval Toolkit (CART) | Server | Retrieves annotations on biological effects of chemicals and determines which ones are enriched. | Tools |
| ChimeRScope | Server | Fusion gene discovery from transcriptome-sequencing (RNA-seq) datasets. | Tools |
| Cistrome Analysis Pipeline | Server | ChIP-chip/seq and gene expression data | Domain |
| Codon Harmonizer | Server | Easily generate codon harmonized variants of gene sequences for heterologous expression | Tools |
| CoSSci | Server | Tools for solving Galton's problem in Comparative Research and complex network problems in Social Science. | Domain |
| DBCLS Galaxy | Server | Adds text mining tools, DBCLS DBSearch Tools, semantic web tools | Genomics |
| deepTools | Server | deepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from high-throughput DNA sequencing experiments. | Tools |
| Dintor | Server | GWA and NGS tools and modules for functional annotation of genes and gene products | Domain |
| epiGeEC | Server | Compare user-provided epigenomic datasets with thousands of public datasets. | Tools |
| EpiToolKit | Server | Computational immunology for the development of novel epitope-based vaccines. | Tools |
| Erasmus MC | Server | General purpose genomics analysis, featuring many standard tools plus many additional tools. | Genomics |
| GalaxEast | Server | Integrative 'omics data analysis | Genomics |
| Galaxy Integrated Omics (GIO) | Server | Proteomics Informed by Transcriptomics (PIT) methodology, and selection of surrogate peptides for targeted proteomics. | Domain |
| Galaxy PGTB (Virtual Biodiversity Lab) | Server | This is a standard Galaxy instance implemented with specific tools for Biodiversity (Biodiversity Virtual Lab) and NGS (Ion Torrent from the PGTB facility) analysis. | Domain |
| Galaxy Test | Server | Beta version of Galaxy Main | Genomics |
| Galaxy-CEFAP | Server | Galaxy-CEFAP offers a set of tools to perform RNA-Seq and miRNA analysis. | Domain |
| Galaxy-P | Server | Galaxy-P is a multiple 'omics' data analysis platform with particular emphasis on mass spectrometry based proteomics. Galaxy-P is developed at the University of Minnesota, deployed at the Minnesota Supercomputing Institute. | Domain |
| Galaxy@GenOuest | Server | A general purpose Galaxy server Includes tools developped by Dyliss and GenScale bioinformatics research teams in Rennes, France. | Genomics |
| Galaxy@Pasteur | Server | General purpose genomics analysis server. | Genomics |
| Galaxy@PRABI | Server | Includes bioinformatics tools developed by the research teams working in the perimeter of the PRABI core facility, including kissplice/kissDE, TETools, SEX-DETector, and priam. | Genomics |
| GeneLab | Server | NASA GeneLab is a comprehensive space-related omics database in which users can upload, download, share, store, and analyze spaceflight and corresponding model organism data. | Genomics |
| Genomic Hyperbrowser | Server | Statistical methodology and computing power to handle a variety of biological inquires on genomic datasets | Domain |
| GigaGalaxy | Server | GigaGalaxy hosts tools and data analyses from papers published in *GigaScience*. | Genomics |
| GrAPPA | Server | GrAPPA is a web-based interface constructed on the Galaxy framework for graph theoretical tools. It contains novel combinatorial methods integrated into a complete microarray analysis toolchain, from uploading raw high-throughput data to visualization of results. | Domain |
| Halogen Bonding | Server | Visualize halogen bond contacts in the protein binding site. Analyze a protein binding site for halogen bonding hotspots. Evaluate halogen contacts with the protein backbone using the scoring function XBScore. | Tools |
| Hardwood Genomics | Server | A simplified, workflow-centic interface to Galaxy, focused on genomics data from hardwood trees. | Domain |
| HiCExplorer | Server | Tools to process and visualize chromosome conformation. | Domain |
| Hunter College Galaxy | Server | A general purpose genomics server | Genomics |
| Huttenhower Lab | Server | metagenomic and functional genomic analyses, intended for research and academic use | Domain |
| IBERS @ Aberystwyth | Server | Software, tools and pages written by IBERS researchers for release to the wider community. | Tools |
| Image Analysis and Processing Toolkit | Server | Image analysis and processing. | Domain |
| ImmPort Galaxy | Server | Flow Cytometry Analysis. | Domain |
| In Silico Galaxy | Server | Construction, analysis, and visualization of gene-gene interaction networks for sequencing data. | Tools |
| Insitut Curie | Server | General purpose genomic Galaxy server. Contains tools for Ion Torrent data, many RNA-Seq tools, ncPRO-seq, RSAT, Nebula tools, copy number and LOH tools, and NGS diagnostic tools. | Genomics |
| International Rice Research Institute (IRRI) Galaxy | Server | Bioinformatics workbench, with rice-specific data (i.e. genomes) and tools (mostly specialized for the IRRI Genotyping Service Laboratory) installed. | Domain |
| IRProfiler | Server | Immune Repertoire Profiler (IRProfiler), a novel software pipeline that delivers a number of core receptor repertoire quantification and comparison functionalities on high-throughput TR and BcR sequencing data. | Tools |
| kmer-SVM | Server | Tool suite uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay. | Tools |
| Koslicki Lab | Server | Web based access to tools created by the Koslicki Lab at Oregon State University. | Tools |
| Langille Lab | Server | Prediction of the unobserved character states in a community of organisms from phylogenetic information. | Tools |
| LAPPS Grid | Server | An open, interoperable web service platform for natural language processing (NLP) research and development. | Domain |
| Lifeportal | Server | a Galaxy instance to satisfy the computational needs of the Norwegian research community in life sciences but also of any other user willing to use the service. | Genomics |
| LiSIs | Server | A platform for Virtual Screening. | Tools |
| Majewski Lab | Server | Detection of recurrent Allelic Imbalance in tumors using whole Exome sequencing data. | Tools |
| Martin Luther U. Halle-Wittenberg | Server | Provides implementations of InMoDe, CRISPRer, TALgetter, TALgetterLong, TALENoffer, and Dimont | Tools |
| MBAC Metabiome Portal | Server | Simplifying control, usage, access, and analysis of microbiome, metabolome, and immunome data (the Metabiome). | Tools |
| Metaproteomics Gateway | Server | Metaproteomics gateway providing access to documentation and other instructional materials, and an opportunity for hands-on training using example datasets and optimized metaproteomics workflows | Domain |
| MGEScan | Server | Identifying long terminal repeats (LTR) and non-LTR retroelements in eukaryotic genomic sequences. | Tools |
| MiModD NacreousMap | Server | NacreousMap mapping/plotting tool of MiModD for users of MiModD who do not want to install the required dependencies (R and rpy2) for graphical output from this tool on their local system. | Tools |
| MISSISSIPPI | Server | Support for analyses of RNA and small RNA sequencing datasets as well as for epigenetics or metagenomics studies. | Domain |
| Molecular Property Diagnostic Suite - Diabetes Mellitus Portal (MPDSDM) | Server | A disease-specific open source web portal for Diabetes Mellitus. | Domain |
| Molecular Property Diagnostic Suite - Tuberculosis (MPDSTB) | Server | A disease-specific web portal for Tuberculosis for drug discovery and development. | Domain |
| MPI-HLR Bioinformatics Server | Server | Hosts the MIRPIPE, ADMIRE, and LimiTT tools | Tools |
| Nebula | Server | allows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data. | Domain |
| NELLY | Server | Plataforma de servicios para análisis de datos biomédicos en bioinformática featuring standard Galaxy Tools | Genomics |
| NGS-QC | Server | Evaluate the quality of your favorite ChIP-seq or enrichment-related NGS dataset using NGS-QC Generator, which also includes a database with preprocessed profiles and a tutorial on how to analyze sequencing profiles yourself. | Tools |
| Oqtans | Server | Customized Galaxy, extended with machine learning based tools for sequence and tiling array data analysis. | Domain |
| Orione | Server | A Galaxy based web server for microbiology. Orione includes all post mapping or assembling steps from scaffolding to complete annotation pipelines. | Domain |
| OSDDlinux LiveGalaxy | Server | Drug discovery | Domain |
| Osiris | Server | Phylogenetics | Tools |
| Palfinder | Server | Microsatellite development. | Tools |
| PhenoMeNal | Server | Large scale computing for medical informatics | Domain |
| PIA | Server | Phylogenetics and gene interaction | Tools |
| PIPE-CLIP | Server | Reliable analysis of data generated by three types of CLIP-seq protocol: HITS-CLIP, PAR-CLIP and iCLIP. | Tools |
| Pitagora-Galaxy | Server | The Pitagora-Galaxy Project server intended for testing and sharing. Heavy analysis should be performed using the project's identical virtual machine (VM) or Amazon Machine Image (AMI). | Genomics |
| PlantGenIE | Server | Plant Genome Integrative Explorer Galaxy instance | Domain |
| PreSTIGE | Server | Predicting Specific Tissue Interactions of Genes and Enhancers | Tools |
| Proteogenomics Gateway | Server | Provides access to documentation and other instructional materials, and an opportunity for hands-on training using example datasets and optimized proteogenomics workflows. The main goal of this server is to provide documentation to facilitate training and mastery of these software and workflows. | Domain |
| ProteoRE | Server | ProteoRE (Proteomics Research Environment) | Domain |
| QBRC Galaxy | Server | Hosts custom tools developed by members of the Quantitative Biomedical Research Center @ University of Texas Southwestern for statistical analysis of various High Throughput Sequencing experiments. | Tools |
| RDF2Graph | Server | RDF2Graph recovers the structure of an RDF resource. | Tools |
| RepeatExplorer | Server | Graph-based clustering and characterization of repetitive sequences, and detection of transposable element protein coding domains. | Domain |
| RiboGalaxy | Server | Tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique. | Domain |
| RNA Workbench | Server | more than 50 bioinformatics tools dedicated to different research areas of RNA biology, including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-Seq analysis, and RNA target prediction. | Domain |
| RNA-Rocket @ Pathogen Portal | Server | Supports comparative analysis of host response to pathogens. It provides an RNA-Seq pipeline to characterize the transcriptome of all NIAID Bioinformatic Resource Center (BRC) pathogens and their key hosts. | Domain |
| SIFTED | Server | Specificity Inference For TAL-Effector Design (SIFTED) | Tools |
| South Green | Server | Genomic resource analysis of southern and Mediterranean plants. | Domain |
| Splicescope | Server | Prediction of neuronal maturation using splicing profiles | Tools |
| Stem Cell Discovery Engine | Server | Database of curated cancer stem cell experiments coupled to Galaxy. | Domain |
| SymD | Server | a platform for detecting internally symmetric protein structures | Domain |
| TreeGenes | Server | TreeGenes integrates genotype, phenotype, and environmental data that can be processed for association mapping and landscape genomics, with a focus on forest trees. This functionality is provided by Tripal Galaxy, a module for Tripal that provides seamless support for running Galaxy workflows directly in the site. Users can analyze data provided by TreeGenes or their own. | Domain |
| UseGalaxy.eu | Server | The European UseGalaxy server. | UseGalaxy |
| UseGalaxy.org (Main) | Server | The Galaxy Project free public server; biomedical research | UseGalaxy |
| UseGalaxy.org.au | Server | The Australian UseGalaxy server. | UseGalaxy |
| USMI Galaxy Demonstrator | Server | This Galaxy implementation is meant to demonstrate integration of microbial domain Biological Resource Center (mBRC) catalogues into the bioinformatics data integration environment. | Tools |
| VarCap | Server | Reliable prediction of different types of variants even at low frequencies. | Tools |
| Vinther Lab | Server | RNA structure-probing data analysis to improve the prediction of RNA secondary and tertiary structure and allow structural changes to be identified and investigated. | Tools |
| VirAmp | Server | VirAmp is a web-based semi-de novo fast virus genome assembly pipeline designed for extremely high coverage NGS data. | Domain |
| Wageningen UR | Server | Includes microarray tools, the MUMmer suite, and many conversion tools. Strong focus on multi-omics: next to genomics tools it also contains proteomics and metabolomics tools | Tools |
| Workflow4Metabolomics | Server | A collaborative portal dedicated to metabolomics data processing, analysis and annotation. | Domain |
| ZBIT Bioinformatics Toolbox | Server | This customized version of the Galaxy webservice framework was set up to allow the public access of our bioinformatics tools. These tools were developed and implemented by members of the Department of Cognitive Systems at the University of Tübingen. | Tools |
Academic Cloud Services
These are academic cloud providers where ready to run Galaxy instances are available. Many of these are restricted to users within a particular geographic domain, for example, a country, province, or consortium of countries. These are often free to eligible researchers.
| Resource | Link | Summary | Purview | Keywords |
|---|---|---|---|---|
| CLIMB | Academic | The CLIMB project (Cloud Infrastructure for Microbial Bioinformatics) develops and deploys a world leading cyber-infrastructure for microbial bioinformatics; providing free cloud-based compute, storage, and analysis tools for academic microbiologists in the UK. | United Kingdom | Genomics |
| EGI Marketplace | Academic | Galaxy instances on a European wide federation of research cloud providers. | Global | Genomics |
| EuPathDB Galaxy | Academic | A free, interactive, web-based platform for large-scale data analysis focused on eukaryotic pathogens. | Global | Domain |
| GenAP | Academic | All Canadian researchers are eligible for a GenAP account. International researchers that have a Canadian collaborator can also be sponsored and become eligible to a GenAP account as well. | Canada | Genomics |
| Globus Genomics | Academic | Globus Genomics provides hardened high-performance Galaxy servers running with Globus on AWS. | Global | Genomics |
| Jetstream | Academic | Jetstream is part of XSEDE, a "collection of integrated advanced digital resources and services" and is funded by NSF. | United States | Genomics |
| Laniakea/INDIGO-DataCloud | Academic | Laniakea provides the possibility to automate the creation of Galaxy-based virtualized environments through an easy setup procedure, providing an on-demand workspace ready to be used by life scientists and bioinformaticians, with built-in storage encryption for user data. | Italy | Genomics |
| MetaCentrum | Academic | MetaCentrum regional virtual organization of the Czech National Grid Infrastructure (NGI) and is accessible to employees and students of research and academic organizations of the Czech Republic and for scientific purposes only. | Czechia | Genomics |
| Nectar Cloud | Academic | Set up a Galaxy server on Australia's Nectar research cloud. | Australia | Genomics |
| NeLS | Academic | Life Science platform for Norwegian academic researchers. | Norway | Genomics |
| PL-Grid | Academic | The PL-Grid project is free of charge for any Polish scientist. It is also free for any foreign collaborator of Polish scientists. | Poland | Genomics |
| SNIC Science Cloud (SSC) | Academic | A national-scale cloud infrastructure for Swedish Academia | Sweden | Genomics |
| VectorBase Galaxy | Academic | A full Galaxy server that includes reference information and workflows focusing on invertebrate vectors of human pathogens. | Global | Domain |
Commercial Cloud Services
These are commercial cloud providers where ready to run Galaxy instances are available. You need to pay for these, but you only need to pay for as long as you need the instance to be up.
| Resource | Link | Summary | Keywords |
|---|---|---|---|
| Amazon Web Services (AWS) | Commercial | Set up you own general purpose genomics server runing AWS using GVL and CloudMan. | Genomics |
| G-OnRamp | Commercial | G-OnRamp provides a user-friendly, web-based platform for collaborative, end-to-end annotation of eukaryotic genomes using UCSC Assembly Hubs and JBrowse/Apollo genome browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNA-Seq data, and repeat finders. | Domain |
| MGEScan | Commercial | Identifying long terminal repeats (LTR) and non-LTR retroelements in eukaryotic genomic sequences. | Tools |
| Oqtans | Commercial | Customized Galaxy, extended with machine learning based tools for sequence and tiling array data analysis. | Domain |
| Pitagora-Galaxy | Commercial | The Pitagora-Galaxy Project server intended for testing and sharing. Heavy analysis should be performed using the project's identical virtual machine (VM) or Amazon Machine Image (AMI). | Genomics |
Containers
These Galaxy instances are prepackaged using container technology, usually Docker. You run these locally by first installing the container technology (Docker is easy), and then launching the containerized Galaxy within that technology. These use local resources.
| Resource | Link | Summary | Keywords |
|---|---|---|---|
| AmrPlusPlus | Container | A Galaxy-based metagenomics pipeline that is intuitive and easy to use. | Tools |
| ballaxy | Container | Hosts the BALL (Biochemical Algorithms Library) Project tools, i.e. computer aided drug design and molecular modelling based on protein and ligand structure data. | Domain |
| CRAVAT-P | Container | A Docker image containing a fully-operational Galaxy instance with pre-installed demonstration material for CRAVAT-P. | Tools |
| deepTools | Container | deepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from high-throughput DNA sequencing experiments. | Tools |
| Galaxy basic sequence manipulation | Container | Galaxy Docker repository for basic sequence data analysis. | Domain |
| Galaxy BLAST+ | Container | A complete and production ready Galaxy instance with installed BLAST+ tools. | Domain |
| Galaxy ChIP-Seq Docker | Container | Galaxy Docker image for ChipSeq analysis | Domain |
| Galaxy CSG | Container | Galaxy instance with tools for Constructive Solid Geometry shipped in a Docker container. | Domain |
| Galaxy Docker | Container | The Galaxy Docker Image is an easy distributable full-fledged Galaxy installation, that can be used for testing, teaching and presenting new tools and features. | Genomics |
| Galaxy Exome-Seq | Container | Galaxy Docker repository for Exome sequencing data analysis | Domain |
| Galaxy Genome Annotation | Container | Galaxy Docker repository for genome annotation | Domain |
| Galaxy Imaging | Container | Galaxy Docker repository for image analysis | Domain |
| Galaxy mothur Toolset Docker | Container | Galaxy Docker image for microbial ecology analysis with mothur | Domain |
| IRProfiler | Container | Immune Repertoire Profiler (IRProfiler), a novel software pipeline that delivers a number of core receptor repertoire quantification and comparison functionalities on high-throughput TR and BcR sequencing data. | Tools |
| miCloud | Container | Leverage cloud technologies to provide an easy-to-use streamlined NGS data analysis using local computational hardware | Genomics |
| QuanTP | Container | A Docker image containing a fully-operational Galaxy instance with pre-installed QuanTP tools. | Tools |
| RiboGalaxy | Container | Tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique. | Domain |
| RNA Workbench | Container | more than 50 bioinformatics tools dedicated to different research areas of RNA biology, including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-Seq analysis, and RNA target prediction. | Domain |
| RNAcommender | Container | RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. It is a recommender system capable of suggesting RNA targets to unexplored RNA binding proteins, by propagating the available interaction information, taking into account the protein domain composition and the RNA predicted secondary structure. | Tools |
| SMAGEXP | Container | SMAGEXP (Statistical Meta-Analysis for Gene EXPression) provides a unified way to carry out meta-analysis of gene expression data, while taking care of their specificities. | Tools |
| Workflow4Metabolomics | Container | A collaborative portal dedicated to metabolomics data processing, analysis and annotation. | Domain |
Virtual Machines (VMs)
VMs are similar to containers but use a different technology. Containers take significant advantage of your computer's underlying operating system. Virtual Machines include an entire supporting operating system, and are significantly larger than containers. You run these locally by first installing a VM player like VirtualBox, and then downloading and launching the VM within that player. These use local resources.
| Resource | Link | Summary | Keywords |
|---|---|---|---|
| DDBJ Read Annotation Pipeline | VM | Annotates raw sequencing reads from next-generation sequencers(NGS) with high throughput, which are registered in DDBJ Read Archive (DRA). | Tools |
| G-OnRamp | VM | G-OnRamp provides a user-friendly, web-based platform for collaborative, end-to-end annotation of eukaryotic genomes using UCSC Assembly Hubs and JBrowse/Apollo genome browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNA-Seq data, and repeat finders. | Domain |
| ImmunoGlobulin Galaxy (IGGalaxy) | VM | Provides a set of tools for easy detection and quantitation of immunoglobulin heavy chain alternative transcripts. | Domain |
| KREAP | VM | Kinetic Re-Epithelialization Analysis Pipeline | Tools |
| Pitagora-Galaxy | VM | The Pitagora-Galaxy Project server intended for testing and sharing. Heavy analysis should be performed using the project's identical virtual machine (VM) or Amazon Machine Image (AMI). | Genomics |
About This Directory
The Galaxy Project's public server usegalaxy.org can meet many needs, but it is not suitable for everything (see Choices for why). Fortunately the Galaxy Community has created Galaxy instances in many different forms and for many different applications.
This directory lists publicly accessible
- Galaxy servers,
- cloud services that support Galaxy instances, and
- virtual machines and containers that can be easily deployed for your own server.
If you want to use Galaxy with little or no effort creating an instance, this is where you should start.
Resource Keywords
Each resource has a set of keywords associated with them.
Real keywords
(What about listing these by the resource's domain, for example, the research methodology (e.g., RNA-Seq), the clade (e.g., crops), or field e.g., metagenomics) that a resource is targeted at? We are working on it.)Scope
Initially, there is only one keyword per resource and that defines the scope of the resource:
UseGalaxy
UseGalaxy servers implement a common core set of tools and reference genomes, and are open to anyone to use. See the [UseGalaxy directory below](#usegalaxy-dir).
Genomics
These servers implement a broad range of tools and aren't specific to any part of the tree of life, or to any type of analysis.
Domain
Domain resources specialize in either a particular branch of the tree of life or in particular types of analysis. Within their specializations, domain resources offer a wide variety of tools.
Tool Publishing
Tool publishing resources make tools easily available so that researchers can use them without having to install and use command line versions. The distinction between domain resources and tool publishing resources is fuzzy. In general, tool publishing resources expose tools from a particular organization, while domain resources include tools / datasets from other organizations and have a larger goal in mind.
Add a resource to this directory
If you maintain a Galaxy resource that can be listed on this directory, then please describe your Galaxy resource here. We'll contact you with any question and then post it this directory.