Publicly Accessible Galaxy Servers
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 is helping out by installing Galaxy at their institutions and then making those installations either publicly available or open to their organizations or community. This page lists publicly accessible Galaxy servers. To be included here a server must be accessible to any academic researcher anywhere in the world. Some servers may require logins and enforce quotas.
If you maintain a public instance of Galaxy it is recommended to sign up for the public servers mailing list to receive security fixes with priority.
To add your public Galaxy
server to this list describe the server
here
and we'll post it this directory.
There are also a number of Galaxy services that make Galaxy available to research communities, sometimes restricted on a geographical or domain basis. See the Galaxy services list.
In addition to the the main Galaxy and Test ToolSheds, several groups have made their tools available through publicly accessibly ToolSheds.
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.
UseGalaxy Servers
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.
| Name | Links | Summary |
|---|---|---|
| The European UseGalaxy server. | ||
| The Galaxy Project free public server; biomedical research | ||
| The Australian UseGalaxy server. |
General Purpose / Genomics Galaxy Servers
These servers implement a broad range of tools and aren't specific to any part of the tree of life, or to any specific type of analysis. These are servers you can use when want to do general genomic analysis.
| Name | Links | Summary |
|---|---|---|
| General purpose genomics analysis, featuring many standard tools plus many additional tools. Howerver, we are specialized in RNASeq with reference and RNASeq denovo | ||
| 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. | ||
| 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). | ||
| Adds text mining tools, DBCLS DBSearch Tools, semantic web tools | ||
| General purpose genomics analysis, featuring many standard tools plus many additional tools. | ||
| Integrative 'omics data analysis | ||
| Beta version of Galaxy Main | ||
| A general purpose Galaxy server Includes tools developped by Dyliss and GenScale bioinformatics research teams in Rennes, France. | ||
| General purpose genomics analysis 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. | ||
| Standard Galaxy tools set plus SOAPdenovo and SOAPsnp for de novo assembly and SNP calling. | ||
| General purpose Galaxy based on the Genomics Virtual Lab platform. | ||
| Small Galaxy for Training purposes. Loaded with Histories and Tools for Next Gen Sequencing tutorials. | ||
| 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. | ||
| Plataforma de servicios para análisis de datos biomédicos en bioinformática featuring standard Galaxy Tools | ||
| The public, general purpose Galaxy servers of the Pitagora-Galaxy Project. This server is intended for testing and sharing. Heavy analysis should be performed using the project's identical virtual machine (VM) or Amazon Machine Image (AMI). |
Domain Specific Galaxy Servers
Domain servers specialize in either a particular branch of the tree of life or in particular types of analysis. However, within their specializations, domain servers offer a wide variety of tools.
| Name | Links | Summary |
|---|---|---|
| A Galaxy suite for tArgeted MEtagenomics | ||
| Human Communication Science (HCS). | ||
| 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. | ||
| Hosts the BALL (Biochemical Algorithms Library) Project tools, i.e. computer aided drug design and molecular modelling based on protein and ligand structure data. | ||
| Insect genomics (aphids, parasitoïd wasps, lepidopterans) | ||
| Phage biology and automated annotation. | ||
| ChIP-chip/seq and gene expression data | ||
| Tools for solving Galton's problem in Comparative Research and complex network problems in Social Science. | ||
| GWA and NGS tools and modules for functional annotation of genes and gene products | ||
| A free, interactive, web-based platform for large-scale data analysis focused on eukaryotic pathogens. | ||
| Proteomics Informed by Transcriptomics (PIT) methodology, and selection of surrogate peptides for targeted proteomics. | ||
| This is a standard Galaxy instance implemented with specific tools for Biodiversity (Biodiversity Virtual Lab) and NGS (Ion Torrent from the PGTB facility) analysis. | ||
| Galaxy-CEFAP offers a set of tools to perform RNA-Seq and miRNA analysis. | ||
| 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. | ||
| statistical methodology and computing power to handle a variety of biological inquires on genomic datasets | ||
| 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. | ||
| metagenomic and functional genomic analyses, intended for research and academic use | ||
| Image analysis and processing. | ||
| Flow Cytometry Analysis. | ||
| Bioinformatics workbench, with rice-specific data (i.e. genomes) and tools (mostly specialized for the IRRI Genotyping Service Laboratory) installed. | ||
| An open, interoperable web service platform for natural language processing (NLP) research and development. | ||
| Metaproteomics gateway providing access to documentation and other instructional materials, and an opportunity for hands-on training using example datasets and optimized metaproteomics workflows | ||
| Support for analyses of RNA and small RNA sequencing datasets as well as for epigenetics or metagenomics studies. | ||
| allows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data. | ||
| Customized Galaxy, extended with machine learning based tools for sequence and tiling array data analysis. | ||
| A Galaxy based web server for microbiology. Orione includes all post mapping or assembling steps from scaffolding to complete annotation pipelines. | ||
| A software toolset to rationally diagnose druggable molecules. | ||
| Drug discovery | ||
| Large scale computing for medical informatics | ||
| The Populus Genome Integrative Explorer Galaxy instance. | ||
| 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. | ||
| ProteoRE (Proteomics Research Environment) | ||
| Graph-based clustering and characterization of repetitive sequences, and detection of transposable element protein coding domains | ||
| Tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique. | ||
| 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. | ||
| Genomic resource analysis of southern and Mediterranean plants. | ||
| Database of curated cancer stem cell experiments coupled to Galaxy. | ||
| A full Galaxy server that includes reference information and workflows focusing on invertebrate vectors of human pathogens. | ||
| VirAmp is a web-based semi-de novo fast virus genome assembly pipeline designed for extremely high coverage NGS data. | ||
| A collaborative portal dedicated to metabolomics data processing, analysis and annotation. |
Tool Publishing Galaxy Servers
Tool publishing servers expose one or a few tools so that researchers can use the tools without having to install them locally or use command line.
The distinction between domain servers and tool publishing servers is fuzzy. In general, tool publishing servers expose tools from a particular organization, while domain servers include tools / datasets from other organizations and have a larger goal in mind.
| Name | Links | Summary |
|---|---|---|
| FROG stands for FingeRprinting Ontology of Genomic variations. FROG fingerprints have been devised to capture genomic variations at various levels. | ||
| Hosts tools/resources developed at the Station Biologique de Roscoff in collaboration with ABiMS. | ||
| This site provides a user-friendly interface for AGEseq (Analysis of Genome Editing by Sequencing) in a Galaxy instance. | ||
| Automate the analysis and visual reporting of T- and B-cell receptor repertoire sequencing data. | ||
| Automated Processing of SAINT Templated Layouts (APOSTL) is a freely available software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data. | ||
| Fast annotation and classification of antibiotic resistance gene-like sequences from metagenomic data. | ||
| 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. | ||
| BCL Galaxy gives a user friendly interface for analysis tools developed by the BioCiphers Lab at the University of Pennsylvania. | ||
| Taxonomic studies of environmental microbial communities | ||
| Detailed analysis of metagenomes. | ||
| Retrieves annotations on biological effects of chemicals and determines which ones are enriched. | ||
| Fusion gene discovery from transcriptome-sequencing (RNA-seq) datasets. | ||
| Easily generate codon harmonized variants of gene sequences for heterologous expression | ||
| deepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from high-throughput DNA sequencing experiments. | ||
| Computational immunology for the development of novel epitope-based vaccines. | ||
| 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. | ||
| Software, tools and pages written by IBERS researchers for release to the wider community. | ||
| Construction, analysis, and visualization of gene-gene interaction networks for sequencing data. | ||
| 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. | ||
| 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. | ||
| Web based access to tools created by the Koslicki Lab at Oregon State University. | ||
| Prediction of the unobserved character states in a community of organisms from phylogenetic information. | ||
| A platform for Virtual Screening. | ||
| Detection of recurrent Allelic Imbalance in tumors using whole Exome sequencing data. | ||
| Provides implementations of InMoDe, CRISPRer, TALgetter, TALgetterLong, TALENoffer, and Dimont | ||
| Simplifying control, usage, access, and analysis of microbiome, metabolome, and immunome data (the Metabiome). | ||
| Identifying long terminal repeats (LTR) and non-LTR retroelements in eukaryotic genomic sequences. | ||
| 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. | ||
| Hosts the MIRPIPE, ADMIRE, and LimiTT tools | ||
| 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. | ||
| Phylogenetics | ||
| Microsatellite development. | ||
| Phylogenetics and gene interaction | ||
| Reliable analysis of data generated by three types of CLIP-seq protocol: HITS-CLIP, PAR-CLIP and iCLIP. | ||
| Large Scale Predictive Pharmacology and Toxicology | ||
| Predicting Specific Tissue Interactions of Genes and Enhancers | ||
| 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. | ||
| RDF2Graph recovers the structure of an RDF resource. | ||
| Specificity Inference For TAL-Effector Design (SIFTED) is a computational model for predicting the DNA-binding specificity of any Transcription activator-like effector (TALE) proteins. | ||
| Prediction of neuronal maturation using splicing profiles | ||
| This Galaxy implementation is meant to demonstrate integration of microbial domain Biological Resource Center (mBRC) catalogues into the bioinformatics data integration environment. | ||
| Reliable prediction of different types of variants even at low frequencies. | ||
| RNA structure-probing data analysis to improve the prediction of RNA secondary and tertiary structure and allow structural changes to be identified and investigated. | ||
| 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 | ||
| 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. |