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PublicGalaxyServers

50+ 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 contact Galaxy Outreach <outreach AT galaxyproject DOT org>.

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

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

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
  • Link:

  • Domain/Purpose:

  • Comments:

    • ballaxy is a workflow framework for structure based computational biology based on the Galaxy workflow engine and the BALL (Biochemical Algorithms Library) application framework. It is tailored to handle structural molecular data (pdb, mol, mol2, hin, xyz, smiles) and to offer tools for modelling tasks like chemical shift prediction "NightShift" or optimal bond order assignment of ligands "BOA Constructor".

  • User Support:

  • Quotas:

    • A login is required and everybody can create a login, but there is no guarantee how long any data will be preserved.

  • Sponsor(s):

CAPER

CAPER

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

Globus Genomics Proteomics

Globus Genomics Proteomics Galaxy Server

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):

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

PopGenIE

PopGenIE

RepeatExplorer

RepeatExplorer

RNA-Rocket @ Pathogen Portal

RNA-Rocket @ Pathogen Portal

Stem Cell Discovery Engine

Stem Cell Discovery Engine (SCDE)

South Green

South Green

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

GWIPS-viz

GWIPS-viz
  • Link:

  • Domain/Purpose:

    • Tools for the analysis of protein synthesis.
  • Comments:

    • The Galaxy server is at the stage of early development. At present it includes tools for motif searches and visualization:

      • MEME - Multiple Em for Motif Elicitation
      • FIMO - Find Individual Motif Occurrences
      • Sequence Logo generator for fasta (e.g. Clustal alignments)
      • Codon Logo generator for fasta (e.g. Clustal alignments)'

  • User Support:

  • Quotas:

  • Sponsor(s):

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):

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):

Netherlands Metabolomics

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

PredPharmTox

PredPharmTox

PreSTIGE

PreSTIGE

QBRC Galaxy and PIPE-CLIP

QBRC Galaxy

Regulatory Genomics

Regulatory Genomics

SunLab

SunLab Galaxy Server
  • Links:

  • Domain/Purpose:

  • Comments:

  • User Support:

    • Email <lxia AT usc DOT edu>

  • Quotas:

    • "Due to the limited computational resources, we refer users not using the tools developed by SunLab to the main public Galaxy site. We also encourage user applying SunLab tools to large data sets to install their standalone version of the specific tools, or install this version of Galaxy server with SunLab tools integrated.

  • Sponsor(s):

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):

USP-FCFRP

Laboratory of Biological Physics at USP-FCFRP
  • Link:

  • Domain/Purpose:

    • Summary of the currently available tools:
      • ProtPred-GROMACS: Ab initio protein structure prediction framework which uses evolutionary algorithms to optimize objective functions such as potential energy, number of hydrogen bonds and solvent accessible surface area.

        • 2PG: Faster and simpler algorithm in which one objective function is optimized

        • 3PG: A more robust approach in which multiple objective functions are optimized at the same time
      • Protein Validation: Check the integrity of a PDB file

      • Protein Desolvation: Remove a solvation layer around your protein.

  • Comments:

  • User Support:

  • Quotas:

    • "You can use tools developed at our laboratory and by our colaborators for free. You just need to sign up to the server using your academic e-mail."
  • Sponsor(s):

ValidatorMAX

ValidatorMAX at The University of Chicago

Wageningen University

Wageningen University

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.