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PublicGalaxyServers

60+ Public Galaxy Servers that will not be affected by usegalaxy.org outage

Publicly Accessible Galaxy Servers

The Galaxy Project's public server (UseGalaxy.org, Main) can meet many needs, but it is not suitable for everything (see Choices for why) and cannot possibly scale to meet the entire world's needs.

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 such public or semi-public Galaxy servers.

To add your public Galaxy server to this list, please either just add it (hey, it's a wiki), or describe the server here and we'll post it this directory.

General Purpose Servers

These servers implement a broad range of tools and 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.

Andromeda

Andromeda

Biomina

Biomina Galaxy

CBiB Galaxy

CBiB Galaxy
  • Link:

  • Domain/Purpose:

    • 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).
  • Comments:

    • Dedicated server: 4 CPU Intel Xeon - 8 cores (a total of 32 cores / 64 threads) , 128 GB RAM, 800 GB of disk space.
  • User Support:

    • CBiB Admin <admin DOT cbib AT u-bordeaux2 DOT fr>

  • Quotas:

    • Disk space is limited to 1 GB for unregistered users, registered users are free to use up to 10GB (to have more space, please contact CBiB Admin <admin DOT cbib AT u-bordeaux2 DOT fr>). The maximum file size to upload is 5 GB. FTP is not operational at this time. Data will be kept 60 days after deletion from history or library.

  • Sponsor(s):

DBCLS Galaxy

DBCLS Galaxy

GalaxEast

GalaxEast
  • Links:

  • Domain/Purpose:

    • Integrative 'omics data analysis
  • Comments:

    • From J24: GalaxEast: an open and powerful Galaxy instance for integrative Omics data analysis, poster presented at ECCB'14 by Stephanie Le Gras, Serge Uge, Matthieu Jung, Ludovic Roy, Valerie Cognat, Frederic Plewniak, Irwin Davidson and Julien Seiler:

      • provides access to up-to-date tools and algorithms such as those devoted to Next Generation Sequencing (NGS) data analysis of:
        • Epigenome: MACS, Homer
        • Genomic sequence: GATK, Samtools, BEDtools, Picard
        • Transcriptome: Cufflinks, HTSeq, TopHat

        • Statistical analyses: DeepTools, S-mart, DESeq

      • GalaxEast provides access to workflows developed for:

        • Motif search
        • Repetitive element analyses
        • ChIP-seq data analysis
      • GalaxEast aims at providing a large range of bioinformatics tools for the analysis of various types of Omics data. It supports reproducible computational research by providing an environment for performing and recording bioinformatics analyses.

      • The GalaxEast project has the following main objectives:

        • Provide the academic scientific community with an open and powerful Galaxy instance with a guaranteed availability. The platform offers access to cutting-edge and up-to-date tools for Omics data analysis with help and support.
        • Propose innovative developments and new helpful tools packaged for Galaxy (available in the GalaxEast toolshed)

        • Promote the packaging of new developments for Galaxy (through wrappers and/or toolshed packages).
    • GalaxEast deployment details

  • User Support:

    • Email <galaxy AT igbmc DOT fr>

  • Quotas:

    • Anonymous users are limited to 10MB
    • Academic users can request a login, and are allocated 50GB.
  • Sponsor(s):

Galaxy Main

usegalaxy.org (Main)
  • Link:

  • Domain/Purpose:

  • Comments:

    • Strong on genomics; good central repository for shared Galaxy objects. See Main for more.

  • User Support:

  • Quotas:

    • Storage and computational quotas. See Main for details.

  • Sponsor(s):

Galaxy Test

GeneNetwork

GeneNetwork Galaxy

Genboree

Genboree

GigaGalaxy

GigaGalaxy

GVL QLD

Genomics Virtual Lab

GVL Tutorial

Genomics Virtual Lab

INRA-URGI

INRA URGI
  • Link:

  • Domain/Purpose:

    • Offers S-MART conversion and MAPHiTS tools.
  • Comments:

    • "Mapping Analysis Pipeline for High-Throughput Sequences" (MAPHiTS). "The pipeline allows the detection of single nucleotide polymorphisms (SNPs) and small insertion/deletions (indels) by comparing high-throughput Illumina short-reads (GAIIx or HighSeq) with a reference sequence from the same or a different species. This pipeline is based on public softwares (BWA, Bowtie, SAMtools, VarScan and Tablet) and homemade tools. In particular, we developed tools to filter out short-reads of low quality and to prepare the mapping and SNP calling. We also developed tools to filter out the called SNPs according to genome coverage, allele frequency, pValue, and SNP positions in the read."

  • User Support:

  • Quotas:

  • Sponsor(s):

NELLY

University of Costa Rica

Pitagora-Galaxy

Pitagora-Galaxy
  • Links:

  • Domain/Purpose:

    • 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).

  • Comments:

    • We are running a website for sharing users' know-how, and distributing a virtual environment where we configured Galaxy with selected workflows and tools. Now, you can perform our analysis workflows on the following three environments.
      • Access to the public web site for testing.
      • Download the virtual machine to your own PC or server.
      • Launch AMI (Amazon machine image) on AWS cloud.
      Since Pitagora-Galaxy enables us to run the same workflows on any infrastructure and rebuild the environments in any time, we can quickly use Galaxy, and at the same time, ensure the reproducibility of the analyses. In addition, we plan to add a connector for Garuda Desktop, a desktop application platform, for data analyses that cannot be covered only with Galaxy tools.
  • User Support:

    • Email: Ryota Yamanaka <yamanaka AT genome DOT rcast.u-tokyo.ac.jp>

  • Quotas:

    • Public Server:
    • VM and AMI:
      • None.
  • Sponsor(s):

Domain 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.

ballaxy

ballaxy

CAPER

CAPER

CardioVascular Research Grid (CVRG)

CardioVascular Research Grid (CVRG)

Center for Phage Technology (CPT)

Center for Phage Technology (CPT)

Cistrome Analysis Pipeline

Cistrome Analysis Pipeline

CNIC.DarwinTree

CNIC.DarwinTree

CoSSci

CoSSci; Women's work map: cycles of lines contain local autocorrelation regions

Galaxy-P

Galaxy-P
  • Links:

  • Domain/Purpose:

  • Comments:

    • As of 2013/08:
      • Pending imminent hardware upgrades, usegalaxyp.org is running with fairly limited computational resources and on disk that is not backed up. Galaxy-P is under active development - things will break and things will change, so your patience is requested.
  • User Support:

    • MSI Email Support <help@msi.umn.edu>

  • Quotas:

  • Sponsor(s):

Galaxy PGTB (Virtual Biodiversity Lab)

PGTB Galaxy

Genomic Hyperbrowser

Genomic Hyperbrowser

Gene Ontololgy (GO)

GO Galaxy

Image Analysis and Processing Toolkit

Image Analysis and Processing ToolKit
  • Links:

  • Domain/Purpose:

    • Image analysis and processing.
  • Comments:

    • This service provides a novel way of carrying out image analysis, reconstruction and processing tasks using cloud based service provided on the Australian National eResearch Collaboration Tools and Resources (NeCTAR) infrastructure. The toolbox allows access to a wide range of useful blocks of functionalities (imaging functions) that can be connected together in workflows allowing creation of even more complex algorithms that can be re-run on different data sets, shared with others or additionally adjusted. The functions given are in the area of cellular imaging, advanced X-ray image analysis, computed tomography and 3D medical imaging and visualisation. The service is currently available on the website.

  • User Support:

  • Quotas:

    • A login is required to access the site. Logins are free and can be requested via email <admin@cloudimaging.net.au>

  • Sponsor(s):

International Rice Research Institute (IRRI) Galaxy

IRRI Galaxy

MetaNET

MetaNET

Nebula

Nebula
  • Link:

  • Domain/Purpose:

    • "allows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data."
  • Comments:

    • "Nebula is a web service provided by Institut Curie."
  • User Support:

  • Quotas:

    • Only 10 jobs can be run simultaneously. Other jobs will be put into queue.
    • Jobs running over than 24hrs (after the job actually runs on the server) will automatically been terminated.
    • Each registered user have a 50GB quota and unregistered user have a 15GB quota (which is enough to run the tutorial with examples).
    • Datasets will be automatically deleted after 4 weeks.
    • Unused accounts will be automatically deleted after 8 weeks.
  • Sponsor(s):

Oqtans

Oqtans

Orione

Orione
  • Links:

  • Domain/Purpose:

    • A Galaxy based web server for microbiology. Orione includes all post mapping or assembling steps from scaffolding to complete annotation pipelines.

  • Comments:

    • From the GCC2013 poster "Engaging Galaxy in Microbiology"

      • We started on selecting the relevant software in the microbiology area, developing then all the necessary tools to integrate them into the Galaxy ecosystem. In addition to that, we made available several specialized workflows covering major applications such as bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-seq, gene annotation and metagenomics. Orione provides additional capabilities to perform integrative, reproducible and transparent bioinformatic data analysis in microbiology thus expanding the constellation of specialized Galaxy based web servers as Nebula, Cistrome and several others.

  • User Support:

    • email <galaxyadmin AT crs4 DOT it>

  • Quotas:

    • This installation of Galaxy has been configured such that anonymous users can operate in a limited way. If you need to store data on this website and/or use advanced Galaxy features such as sharing and workflows, please send us an email <galaxyadmin AT crs4 DOT it> with a short request.

  • Sponsor(s):

OSDDlinux LiveGalaxy

OSDDlinux LiveGalaxy

OSDD Molecular Property Diagnostic Suite (MPDS)

Molecular Property Diagnostic Suite (MPDS)
  • Links:

  • Domain/Purpose:

    • "The mission of the OSDD-Chemoinformatics is to promote and co-ordinate world-class research (and training) in Chemoinformatics within India and to provide state-of-the-art Chemoinformatics support to Indian researchers working on myriad aspects of Chemoinformatics. Present portal introduces readers to MPDS (Molecular Property Diagnostic Suite), a software toolset that rationally diagnoses (druggable) molecules."
  • Comments:

    • "MPDS 1.0 consists of six modules. It covers informatics (DataBases, File format conversion), structure and analogue based drug design approaches (Property calculation, QSAR, Docking)."

  • User Support:

  • Quotas:

  • Sponsor(s):

PopGenIE / PlantGenIE

PopGenIE

RepeatExplorer

RepeatExplorer

RiboGalaxy

RiboGalaxy
  • Link:

  • Domain/Purpose:

    • RiboGalaxy provides on-line tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique.

  • Comments:

    • RiboGalaxy is a freely available web server for processing and analysing ribosome profiling (ribo-seq) data with the visualization functionality provided by GWIPS-viz. RiboGalaxy provides a compact suite of tools specifically tailored for the alignment and visualization of ribo-seq and corresponding mRNA-seq data. Users can take advantage of the published workflows on RiboGalaxy which reduce the multi-step alignment process to a minimum of inputs.

  • User Support:

  • Quotas:

    • Anonymous users can use RiboGalaxy. However, the upload and processing of datasets larger than 2GB and the use of advanced features such as published workflows, will require the user to be registered on RiboGalaxy.

  • Sponsor(s):

RNA-Rocket @ Pathogen Portal

RNA-Rocket @ Pathogen Portal

Stem Cell Discovery Engine

Stem Cell Discovery Engine (SCDE)

South Green

South Green

VectorBase Galaxy

VectorBase Galaxy

Whale Shark

Whale Shark Galaxy @ The Georgia Aquarium

Tool Publishing 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.

BioCiphers Lab Galaxy

BioCiphers Galaxy

CTMM-TraIT Demo Galaxy

CTMM-TraIT Demo Galaxy


deepTools

deepTools Galaxy Server


Dostie Lab Galaxy

Dostie Lab Galaxy @ McGill University
  • Link:

  • Domain/Purpose:

    • Chromosome Conformation Capture (3C) and 3C Carbon Copy (5C) analysis tools.
  • Comments:

    • "Recent studies indicate that genomes are organized into dynamic three-dimensional physical networks, which are required for correct gene expression. The functional (physical) connectivity between genes and regulatory DNA elements must be mapped to understand how correct gene expression is obtained and ultimately how the genome functions." These tools quantitatively measure the intensity of individual DNA contacts within the genome.
  • User Support:

  • Quotas:

    • Must create a login to run tools. Anyone can create a login.
  • Sponsor(s):

Fast UniFrac

Fast UniFrac

GWIS

GWIS

Huttenhower Lab

Huttenhower Lab
  • Link:

  • Domain/Purpose:

    • "metagenomic and functional genomic analyses, intended for research and academic use"
  • Comments:

    • Implements
      • LEfSe - LDA Effect Size
      • MetaPhlAn - Metagenomic Phylogenetic Analysis

      • GraPhlAn - Graphical phylogenetic analysis

      • microPITA - microbiome: Picking Interesting Taxonomic.

      • MaAsLin - Multivariate Analysis by Linear Models

      • PICRUSt - Phylogenetic Investigation of Communities by Reconstruction of Unobserved States

  • User Support:

    • If you have any comments, questions, or suggestions, please contact Dr. Huttenhower.

  • Quotas:

    • The tools are available without account creation. However, you are strongly invited to create an account for having access to the history, saved analyses, datasets and workflows.
  • Sponsor(s):

IM-PET

IM-PET

In Silico Galaxy

In Silico Galaxy
  • Link:

  • Domain/Purpose:

    • Construction, analysis, and visualization of gene-gene interaction networks for sequencing data. Implements Encore, "an open source network analysis pipeline for genome-wide association studies and rare variant data. Encore constructs Genetic Association Interaction Networks or epistasis networks using two optional approaches: our previous information-theory method or a generalized linear model approach. Additionally, Encore includes multiple data filtering options, including Random Forest/Random Jungle for main effect enrichment and Evaporative Cooling and Relief-F filters for enrichment of interaction effects. Encore implements SNPrank network centrality for identifying susceptibility hubs (nodes containing a large amount of disease susceptibility information through the combination of multivariate main effects and multiple gene-gene interactions in the network)"

  • Comments:

  • User Support:

  • Quotas:

    • Must create a login/

    • Disk is "limited to reflect server resources but still allow users to demo tools prior to local installation. We are working on enabling instantiation of In Silico Galaxy on the cloud."
  • Sponsor(s):

kmer-SVM

kmer-SVM

LiSIs

LiSIs
  • Link:

  • Domain/Purpose:

    • A platform for Virtual Screening.
  • Comments:

    • The LiSIs platform has been developed in the context of the cross-disciplinary GRANATUM project aiming to bridge the gap between biomedical researchers by ensuring their seamless access to the globally available information needed to perform complex experiments and to conduct studies on large-scale datasets.

  • User Support:

  • Quotas:

    • Must create a login, but anyone can create a login either on LiSIs or GRANATUM.

    • There are storage quotas.

    • There will be computational quotas in the near future.
  • Sponsor(s):

Majewski Lab

Majewski Lab: ExomeAI

Martin Luther U. Halle-Wittenberg

Martin Luther University Halle-Wittenberg
  • Link:

  • Domain/Purpose:

    • Provides implementations of these tools:
      • CRISPRer is a tool for genome-wide selection and assessment of CRISPR/Cas protospacers.
      • TALgetter allows you to scan input sequences for putative target sites of a given TAL (transcription activator-like) effector as typically expressed by many Xanthomonas bacteria.
      • TALgetterLong allows you to scan input sequences for putative target sites of a given TAL (transcription activator-like) effector as typically expressed by many Xanthomonas bacteria in large input data, but lacks some of the features of TALgetter (e.g., computation of empirical p-values).
      • TALENoffer is a tool for predicting off-targets of TAL effector nucleases (TALENs).
      • Dimont (beta) is a universal tool for de-novo motif discovery. Dimont has successfully been applied to ChIP-seq, ChIP-exo and protein-binding microarray (PBM) data.
  • Comments:

  • User Support:

    • Email <grau AT informatik DOT uni DASH halle DOT de>

  • Quotas:

  • Sponsor(s):

MBAC Metabiome Portal

MBAC Metabiome Portal
  • Link(s):

  • Domain/Purpose:

    • We have developed the MBAC Metabiome Portal, a flexible and customizable webserver, with the aim of simplifying control, usage, access, and analysis of microbiome, metabolome, and immunome data (the Metabiome).

  • Comments:

    • The Portal uses a relational database management system and distributed analytical resources and includes several tools such as sequence clustering, filtering sequencing artifacts, taxonomic analysis, and functional annotation. Users access the MBAC Metabiome Portal through a Galaxy based web browser to perform individual and group analysis and share their results. Programming support is also available to configure and run customized pipelines.
  • User Support:

    • Email <pgilleve AT gmu DOT edu>

  • Quotas:

    • We have opened up the MBAC Metabiome Portal to unregistered users to share data and analysis tools. Computationally intensive tools are restricted to in house use. Anonymous users are restricted to a 50 mb disk quota.

    • Anonymous users can view a demo of the Metabiome Database here.

  • Sponsor(s):

MGTAXA

MGTAXA
  • Link:

  • Domain/Purpose:

    • Prediction of metagenomic taxonomy
  • Comments:

    • Provides a flexible interface to the tools the MGTAXA team have developed for the prediction of metagenomic taxonomy. Server also exposes some of the standard Galaxy tools that can be useful in the context of the MGTAXA project.

  • User Support:

  • Quotas:

  • Sponsor(s):

MIRPIPE

MIRPIPE - the miRNA identification pipeline
  • Link:

  • Domain/Purpose:

    • Quantification of microRNA based on smallRNA sequencing reads
  • Comments:

    • From the home page:
      • In opposition to present algorithms that generally rely on genomic data to identify miRNAs, MIRPIPE focuses on niche model organisms that lack such information. Among the MIRPIPE features are automatic trimming and adapter removal of raw RNA-Seq reads originating from various sequencing instruments, clustering of isomiRs, and quantification of detected miRNAs by homology search versus public or user uploaded reference databases.
  • User Support:

  • Quotas:

    • Can access with or without a login. Anyone can create a login.
  • Sponsor(s):

NGS-QC

Gronemeyer Lab Galaxy and NGS-QC Generator

ODoSE

ODoSE: Ortholog Direction of Selection Engine
  • Link:

  • Domain/Purpose:

    • ODoSE is a webserver for genome-wide calculation of adaptive divergence in prokaryotes.

  • Comments:

    • "The web-based graphical user-interface ODoSE (Ortholog Direction of Selection Engine) identifies all orthologs between a set of strains and allows the calculation of a novel extension of the [McDonald Kreitman] MK test, the Direction of Selection (DoS) statistic as well as the calculation of the Neutrality Index (NI) statistic for all genes shared by two taxonomic groups combined. The engine also generates the site frequency spectrum for each gene allowing one to apply more advanced methods for estimating the distribution of fitness effects and rates of adaptive evolution."

    • See ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes by Michiel Vos, Tim A. H. te Beek, Marc A. van Driel, Martijn A. Huynen, Adam Eyre-Walker, Mark W. J. van Passel; PLoS ONE, Vol. 8, No. 5. (6 May 2013), e62447, doi:10.1371/journal.pone.0062447

  • User Support:

  • Quotas:

  • Sponsor(s):

    • "MV is supported by investment from the European Regional Development Fund to the European Centre for Environment and Human Health, University of Exeter. MWJvP is funded by the Netherlands Organization for Scientific Research (NWO) via a VENI grant. TAHtB and MAvD are funded by the BioAssist/BRS programme of the Netherlands Bioinformatics Centre (NBIC), which is supported by the Netherlands Genomics Initiative (NGI). We thank the developers of programs used in ODoSE for making their software publicly available."

OPPL Galaxy

OPPL Galaxy

Osiris

Osiris

P-Galaxy

P-Galaxy

PIA

PIA

PredPharmTox

PredPharmTox

PreSTIGE

PreSTIGE

QBRC Galaxy and PIPE-CLIP

QBRC Galaxy

Regulatory Genomics

Regulatory Genomics

SymD

SymD
  • Links:

  • Domain/Purpose:

    • "SymD is a tool for detecting internally symmetric protein structures."
  • Comments:

    • SymD "works through an “alignment scan” procedure in which a protein structure is aligned to itself after circularly permuting the second copy by all possible number of residues.

    • Input to SymD is a PDB format coordinate file. SymD reports T‐score, Zscore, transformed structure at the position of the best Z‐score, as well as the symmetry axis, the rotation angle and any translation along the symmetry axis (for helical symmetry).
  • User Support:

  • Quotas:

  • Sponsor(s):

Wageningen UR

Wageningen UR Galaxy

ZBIT Bioinformatics Toolbox

ZBIT Bioinformatics Toolbox

Public ToolSheds

Galaxy Main Tool Shed

Sits at http://toolshed.g2.bx.psu.edu/, is supported by the Galaxy Team, and is the main Tool Shed of choice.

Galaxy Test ToolShed

Test Tool Shed is made for breaking. If you have some tools you want to try out first before making them public in the Main Tool Shed this is the place to go. Test Tool Shed is at http://testtoolshed.g2.bx.psu.edu/.

DTL ToolShed

DTL ToolShed

The Dutch Techcentre for Life Sciences (DTL) has made its Galaxy ToolShed publicly available. The DTL ToolShed has almost 70 tools in it, from ANNOVAR to VCF-2-VariantList. This ToolShed was originally started at NBIC.

GenOuest ToolShed

The GenOuest public ToolShed contains over 60 valid tools in 36 repositories in 9 categories.

If you have or know of a public server that is not listed here please add it, or send its information to Galaxy Outreach.