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PublicGalaxyServers

80+ Public Galaxy Servers

Contents

  1. General Purpose / Genomics Servers
    1. Andromeda
    2. Biomina
    3. CBiB Galaxy
    4. DBCLS Galaxy
    5. Erasmus MC
    6. GalaxEast
    7. Galaxy@PRABI
    8. Galaxy Main
    9. Galaxy Test
    10. GigaGalaxy
    11. GVL QLD
    12. GVL Tutorial
    13. NELLY
    14. Pitagora-Galaxy
  2. Domain Servers
    1. ballaxy
    2. CAPER
    3. CardioVascular Research Grid (CVRG)
    4. Center for Phage Technology (CPT)
    5. Cistrome Analysis Pipeline
    6. CoSSci
    7. Dintor
    8. Galaxy Integrated Omics (GIO)
    9. Galaxy-P
    10. Galaxy PGTB (Virtual Biodiversity Lab)
    11. Genomic Hyperbrowser
    12. Gene Ontololgy (GO)
    13. Image Analysis and Processing Toolkit
    14. International Rice Research Institute (IRRI) Galaxy
    15. LAPPS Grid
    16. MetaNET
    17. MISSISSIPPI
    18. Nebula
    19. Oqtans
    20. Orione
    21. OSDDlinux LiveGalaxy
    22. OSDD Molecular Property Diagnostic Suite (MPDS)
    23. PopGenIE / PlantGenIE
    24. RepeatExplorer
    25. ReproGenomics Viewer
    26. RiboGalaxy
    27. RNA-Rocket @ Pathogen Portal
    28. RNA-Seq Portal
    29. Stem Cell Discovery Engine
    30. South Green
    31. VectorBase Galaxy
    32. VirAmp
    33. Whale Shark
    34. Workflow4Metabolomics
  3. Tool Publishing Servers
    1. ABiMS Tools
    2. AB-OpenLab
    3. AGEseq @ AspenDB
    4. BioCiphers Lab Galaxy
    5. BioMaS
    6. BISTRO
    7. CNIC.DarwinTree
    8. CTMM-TraIT Demo Galaxy
    9. deepTools2
    10. EpiToolKit
    11. Halogen Bonding
    12. Huttenhower Lab
    13. In Silico Galaxy
    14. Koslicki Lab
    15. kmer-SVM
    16. LiSIs
    17. Majewski Lab
    18. Martin Luther U. Halle-Wittenberg
    19. MBAC Metabiome Portal
    20. MGEScan
    21. MiModD NacreousMap
    22. MPI-HLR Bioinformatics Server
    23. NGS-QC
    24. ODoSE
    25. OPPL Galaxy
    26. Osiris
    27. PIA
    28. PredPharmTox
    29. PreSTIGE
    30. QBRC Galaxy and PIPE-CLIP
    31. RDF2Graph
    32. SIFTED
    33. SymD
    34. Vinther Lab
    35. Wageningen UR
    36. ZBIT Bioinformatics Toolbox
  4. Public ToolSheds
    1. Galaxy Main Tool Shed
    2. Galaxy Test ToolShed
    3. Galaxy@PRABI Tool Shed
    4. DTL ToolShed
    5. GUGGO ToolShed

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 / Genomics 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

Erasmus MC

Erasmus MC Bioinformatics Galaxy Server

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:

    • You must be part of an academic research lab and provide a valid academic email address to get a personal GalaxEast account. Write to galaxy@igbmc.fr to request an account.

    • Academic users are allocated 50GB.
  • Sponsor(s):

Galaxy@PRABI

Galaxy@PRABI
  • Links:

  • Domain/Purpose:

    • A general purpose Galaxy instance that includes bioinformatics tools developed by the research teams working in the perimeter of the PRABI core facility, including kissplice/kissDE, TETools, SexDetector, and priam available through our local toolshed instance.

  • Comments:

    • Dedicated server: PowerEdge R920 Rack Server - 64 CPU, 512 GB RAM, 15To GB of disk space.

  • User Support:

    • galaxy@prabi user list (in French)

    • Email support: <galaxy DASH support AT listes DOT univ-lyon1 DOT fr>

    • We also provide galaxy training courses for RNA-seq and ChIP-seq data analysis.

  • Quotas:

    • Disk space is limited to 100 MB for unregistered users, registered users are free to use up to 50 GB.
    • Users from the FRBioenvis and LECA teams are free to use up to 250 GB disk space.
    • Can be increased up to 1-2 TB in collaborative projects (please contact galaxy@PRABI Admins <galaxy DASH support AT listes DOT univ-lyon1 DOT fr>.)

  • 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

GigaGalaxy

GigaGalaxy

GVL QLD

Genomics Virtual Lab

GVL Tutorial

Genomics Virtual Lab

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

CoSSci

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

Dintor

Dintor: Data Integrator Tool Suite
  • Link:

  • Domain/Purpose:

    • A "suite of tools that facilitate working with GWA and NGS data" and "offers modules for high level functional annotation of genes and gene products such as gene set prioritization, functional similarity of proteins, or clinical significance of variation data. Each of these tools has been designed to perform a basic task independently."
  • Comments:

    • Includes "more than thirty modules ready for use by bioinformaticians and biologists working in genomics research."
    • "The Galaxy server has been set up to facilitate access to our Dintor tools by biologists with little background in bioinformatics. A second, expert mode of invocation is given by command line access to the tool suite, which can be downloaded"

    • Admin and deployment documentation is available.

    • Dintor: functional annotation of genomic and proteomic data, Christian X. Weichenberger, Hagen Blankenburg, Antonia Palermo, Yuri D’Elia, Eva König, Erik Bernstein and Francisco S. Domingues, BMC Genomics 201516:1081 DOI: 10.1186/s12864-015-2279-5

  • User Support:

  • Quotas:

    • Anyone can create a login. Anonymous use is also supported.
  • Sponsor(s):

Galaxy Integrated Omics (GIO)

Galaxy Integrated Omics (GIO)

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

LAPPS Grid

LAPPS Grid Galaxy Workflow Engine
  • Links:

  • Domain/Purpose:

    • "An open, interoperable web service platform for natural language processing (NLP) research and development. The LAPPS Grid provides facilities to select from hundreds of NLP tools to create workflows, composite services, and applications, and to evaluate, reproduce, and share them with others."
  • Comments:

    • "This is a Work In Progress. Many of the services here are undergoing active development and their behaviour is likely to change without notice."

    • See The Language Application Grid by Nancy Ide, James Pustejovsky, Christopher Cieri, Eric Nyberg, Denise DiPersio, Chunqi Shi, Keith Suderman, Marc Verhagen, Di Wang, Jonathan Wright. Worldwide Language Service Infrastructure, Volume 9442 of the series Lecture Notes in Computer Science pp 51-70

  • User Support:

  • Quotas:

    • Anyone can create a login, or it can be used anonymously
  • Sponsor(s):

MetaNET

MetaNET

MISSISSIPPI

MISSIPPI

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

ReproGenomics Viewer

The ReproGenomics Viewer
  • Link:

  • Domain/Purpose:

    • "The ReproGenomics Viewer (RGV) is a cross-species genomic toolbox for the reproductive community. The system is based on the implementation of a JBrowse genome browser and a Galaxy bioinformatics workflow environment. It was developed to provide a one-stop genomic working environment and aims to assist scientists in the analysis and the mining of a wide range of high-throughput repro-genomics data, including sequencing data.

      RGV allows hosting, visualization, and direct comparison of users’ data to published genomics studies as well as to relevant genetic variations linked to reproduction. One way it does this is by enabling various genomic file format conversions.

      The ReproGenomics Viewer currently hosts datasets that are oriented mainly towards testis biology and spermatogenesis. In the near future, these will extend to other areas of reproduction, including gonad development, urogenital cancers, and reproductive toxicology."

  • Comments:

  • User Support:

    • Email <support@genouest.org>

  • Quotas:

  • Sponsor(s):

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.

    • Audrey M. Michel, James P.A. Mullan, Vimalkumar Velayudhan, Patrick B.F. O'Connor, Claire A. Donohue & Pavel V. Baranov (2016): RiboGalaxy: a browser based platform for the alignment, analysis and visualization of ribosome profiling data, RNA Biology, DOI: 10.1080/15476286.2016.1141862

  • 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

RNA-Seq Portal

RNA-Seq Portal - Analyzing RNA-seq Data for Agricultural Animal Species
  • Links:

  • Domain/Purpose:

    • Analyzing RNA-seq Data for Agricultural Animal Species.
  • Comments:

    • From the portal landing page:

      • The goal of this project is to develop a web portal with integrated tools for RNA-seq based gene expression analysis for agricultural animals.
        • improve genome annotation of agricultural animal species, including (but not limiting to) cattle, pig, chicken, turkey, horse, sheep, and goat as well as catfish;
        • develop and integrate needed bioinformatics tools and pipelines, visualization interfaces, and statistical methods;
        • build a web portal that enable RNA-seq based transcriptomics analysis in aforementioned animal species.
  • User Support:

  • Quotas:

  • Sponsor(s):

Stem Cell Discovery Engine

Stem Cell Discovery Engine (SCDE)

South Green

South Green

VectorBase Galaxy

VectorBase Galaxy

VirAmp

VirAmp
  • Link:

  • Domain/Purpose:

    • VirAmp is a web-based semi-de novo fast virus genome assembly pipeline designed for extremely high coverage NGS data.

  • Comments:

    • from VirAmp: a galaxy-based viral genome assembly pipeline, Yinan Wan, Daniel W Renner, Istvan Albert and Moriah L Szpara, GigaScience 2015, 4:19 doi:10.1186/s13742-015-0060-y

      • VirAmp "combines existing tools and techniques and presents them to end users via a web-enabled Galaxy interface. Our pipeline allows users to assemble, analyze, and interpret high coverage viral sequencing data with an ease and efficiency that was not possible previously. Our software makes a large number of genome assembly and related tools available to life scientists and automates the currently recommended best practices into a single, easy to use interface. We tested our pipeline with three different datasets from human herpes simplex virus (HSV)."

  • User Support:

  • Quotas:

  • Sponsor(s):

Whale Shark

Whale Shark Galaxy @ The Georgia Aquarium

Workflow4Metabolomics

Workflow4metabolomics Galaxy server

Workflow4Metabolomics Sponsors
Sponsors

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.

ABiMS Tools

ABiMS Tools Galaxy Server
  • Link:

  • Domain/purpose:

  • Comments:

    • Available tools:
      • MicRhoDE workflow: places query sequences into MicRhoDE tree (type-1 rhodopsin phylogeny).

      • Renkan Blast: blast query sequences on 18S and 28S radiolaria databases (blastn).

      • WiseScaffolder: genome scaffolding of pre-assembled contigs using mate-pair data.

      • HECTAR: HEterokont subCellular TARgeting is a statistical prediction method designed to assign proteins to five different categories of subcellular targeting: Signal peptides, type II signal anchors, chloroplast transit peptides, mitochondrion transit peptides and proteins which do not possess any N-terminal target peptide.

  • User support:

    • For any question or request for tools or account, send an email at ABiMS Support <support.abims@sb-roscoff.fr>

  • Sponsor(s):

AB-OpenLab

FingeRprinting Ontology of Genomic variations (FROG)
  • Link:

  • Domain/purpose:

    • "FROG stands for FingeRprinting Ontology of Genomic variations. FROG fingerprints have been devised to capture genomic variations at various levels."

  • Comments:

    • The assigned fingerprints enables FROG to make the large number of genomic variations computationally efficient in terms of memory requirements and faster retrieval. This interface has been designed to explore the structure of FROG fingerprints and search mitochondrial variations using fingerprints with a combination of various FROG properties.
    • See FROG - Fingerprinting Genomic Variation Ontology, by E. Abinaya, Pankaj Narang, Anshu Bhardwaj, PLoS ONE 10(8): e0134693. doi:10.1371/journal.pone.0134693

  • User support:

  • Quotas:

    • Anyone can create an account. FROG can also be accessed anonymously.
  • Sponsor(s):

AGEseq @ AspenDB

AGEseq Galaxy @ AspenDB
  • Link:

  • Domain/Purpose:

    • This site provides a user-friendly interface for AGEseq (Analysis of Genome Editing by Sequencing) in a Galaxy instance.
  • Comments:

    • AGEseq compares amplicon sequences with expected target sequences and finds insertion/deletion sites in the amplicon sequences.
    • AGEseq can be used for SNP calling.
    • AGEseq supports NGS short reads as well as Sanger sequences in multiple file formats
    • AGEseq is also available from the Galaxy Tool Shed for installation into your local Galaxy instance.

    • Xue LJ and Tsai CJ (2015) AGEseq: Analysis of Genome Editing by Sequencing. Molecular Plant. doi:10.1016/j.molp.2015.06.001

  • User Support:

    • Please email questions and suggestions to Liangjiao Xue <lxue AT uga DOT edu>.

  • Quotas:

  • Sponsor(s):

BioCiphers Lab Galaxy

BioCiphers Galaxy

BioMaS

BioMaS Galaxy
  • Link:

  • Domain/Purpose:

    • Taxonomic studies of environmental microbial communities
  • Comments:

    • BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) supports taxonomic studies of environmental microbial communities, "comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment."
    • See BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS by Bruno Fosso, Monica Santamaria, Marinella Marzano, Daniel Alonso-Alemany, Gabriel Valiente, Giacinto Donvito, Alfonso Monaco, Pasquale Notarangelo and Graziano Pesole, BMC Bioinformatics 2015, 16:203 doi:10.1186/s12859-015-0595-z

  • User Support:

    • Please email questions and suggestions to Bruno Fosso <bruno DOT fosso AT gmail.com> and/or to Giacinto Donvito <giacinto DOT donvito AT ba.infn.it>.

  • Quotas:

    • Requires an account. Interested users may ask for the creation of a BioMaS account sending a request to recas@lists.ba.infn.it.

  • Sponsor(s):

BISTRO

BISTRO Galaxy
  • Link:

  • Domain/Purpose:

    • Taxonomic studies of environmental microbial communities
  • Comments:

    • Publishes the PipeAlign workflow and supporting tools. These tools include ballast, RASCAL, LEON, and MACSIMS.

  • User Support:

    • Email support <akress@unistra.fr>

  • Quotas:

    • Supports anonymous access and creation of user logins.
  • Sponsor(s):

CNIC.DarwinTree

CNIC.DarwinTree

CTMM-TraIT Demo Galaxy

CTMM-TraIT Demo Galaxy


deepTools2

deepTools Galaxy Server


EpiToolKit

EpiToolKit Galaxy Server
  • Link:

  • Domain/Purpose:

    • Computational immunology for the development of novel epitope-based vaccines.
  • Comments:

    • EpiToolKit "provides a collection of methods from computational immunology for the development of novel epitope-based vaccines including HLA ligand or potential T-Cell epitope prediction, an epitope selection framework for vaccine design, and a method to design optimal string-of-beads vaccines. Additionally, EpiToolKit provides several other tools ranging from HLA typing based on NGS data, to prediction of polymorphic peptides."

    • See EpiToolKit—a web-based workbench for vaccine design by Benjamin Schubert, Hans-Philipp Brachvogel, Christopher Jürges and Oliver Kohlbacher, Bioinformatics (2015) 31 (13): 2211-2213. doi: 10.1093/bioinformatics/btv116

  • User Support:

  • Quotas:

    • Anyone can create an account. Alternatively, a guest account is provided with login test_user@informatik.uni-tuebingen.de and password workflowTest. Please note that the guest account shares uploaded data with all other guest users.

    • Data of unregistered users and delete data will be permanently deleted after 7 days.
  • Sponsor(s):

Halogen Bonding

Halogen Bonding Webserver

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):

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):

Koslicki Lab

Koslicki Lab Server

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.

    • See LiSIs: An Online Scientific Workflow System for Virtual Screening, by Christos C. Kannas, Ioanna Kalvari, George Lambrinidis, Christiana M. Neophytou, Christiana G. Savva, Ioannis Kirmitzoglou, Zinonas Antoniou, Kleo G. Achilleos, David Scherf, Chara A. Pitta, Christos A. Nicolaou, Emanuel Mikros, Vasilis J. Promponas, Clarissa Gerhauser, Rajendra G. Mehta, Andreas I. Constantinou, Constantinos S. Pattichis, Combinatorial chemistry & high throughput screening, Vol. 18, No. 3. (2015), pp. 281-295

  • 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):

MGEScan

MGEScan on Galaxy Workflow System

MiModD NacreousMap

Baumeister Lab Galaxy featuring MiModD
  • Link:

  • Domain/Purpose:

    • This server exposes the 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. MiModD is a comprehensive software package for the identification and annotation of mutations in the genomes of model organisms from whole-genome sequencing (WGS) data.

  • Comments:

    • CloudMap users can replot data produced with the Hawaiian Variant Mapping tool using the NacreousMap engine to obtain optimized (much smaller files that display faster) plots.

    • To install the complete MiModD package for use as a command line tool or for integration into any local Galaxy follow the installation instructions in the MiModD User Guide.

  • User Support:

  • Quotas:

    • The quota for anonymous usage is 50MB, registered users have 250MB available.
    • You can analyze/plot data in VCF format or the "Per variant report" format generated by local runs of the MiModD NacreousMap tool. The latter has the advantage of being up to 20 times smaller than the corresponding VCF file.

  • Sponsor(s):

MPI-HLR Bioinformatics Server

MPI-HLR Bioinformatics Server

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

PIA

PIA

PredPharmTox

PredPharmTox
  • Link:

  • Domain/Purpose:

    • "PredPharmTox is an e-infrastructure for Large Scale Predictive Pharmacology and Toxicology, providing easy access to chemical and omics data in toxicology and pharmacology, together with methods and predictions available via user-friendly tools."

  • Comments:

    • "The infrastructure will support open standards and be developed in close collaboration with European initiatives, and implemented as a Platform as a Service (PaaS) linking to the cloud resource of the Swedish National Infrastructure for Computing (SNIC). The infrastructure will enable Swedish researchers to perform world class science such as integrated pharmacology/toxicology approaches, chemical safety assessment, toxicogenomics and pharmacogenomics with mechanistic interpretations and discovery of chemically-initiated pathways, as well as including omics data in predictive toxicology and pharmacology modeling."
    • Implements
      • QuantMap tools for grouping chemicals by biological activity,

      • ToxMap for visual representations of the toxicogenomic space occupied by a query signature

    • See "Automated QuantMap for rapid quantitative molecular network topology analysis" by Schaal1, et al., Bioinformatics (2013)

  • User Support:

  • Quotas:

  • Sponsor(s):

    • "This work was supported by the Swedish Research Council [VR-2011-6129]; and the Swedish Strategic Research Program eSSENCE."

PreSTIGE

PreSTIGE

QBRC Galaxy and PIPE-CLIP

QBRC Galaxy

RDF2Graph

RDF2Graph using Reactome

SIFTED

SIFTED

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):

Vinther Lab

Vinther Lab: User-Friendly Tools for Sequencing-Based RNA Structure Probing Data

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/.

Galaxy@PRABI Tool Shed

Galaxy@PRABI

Tool Shed backing the Galaxy@PRABI server. DEfines bioinformatics tools developed by the research teams working in the perimeter of the PRABI core facility, including kissplice/kissDE, TETools, SexDetector, and priam.

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.

GUGGO ToolShed

The GUGGO public ToolShed contains over 160 valid tools in 132 repositories in 16 categories. GUGGO Tool Shed is at http://toolshed.genouest.org/.

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