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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, use "Edit on GitHub" link above, or [describe the server here](https://docs.google.com/forms/d/1KBkyhAPpgJLanRWBoIHmwtEJELDUifZLUixfoqZXXU4/viewform?usp=send_form) 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.

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](mailto: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](mailto: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
  • Link:
  • Domain/Purpose:
    • General purpose genomics analysis, featuring many standard tools plus many additional tools.
  • Comments:
    • This server supports a wealth of RNA-Seq tasks, including:
      • quantify gene expression (featureCounts, edgeR, experimental design module)
      • determine and prioritize fusion genes (star-fusion, Fuma, ifuse)
      • determine variants and annotate small variants (BAM to varscan2, Annovar)
      • detect small ncRNA derived RNAs in small RNA-seq alignments (Flaimapper)
      • Generate html user defined workflow (iReport)
    • All tools are also available in the Tool Shed.
    • See FuMa: reporting overlap in RNA-seq detected fusion genes, by Youri Hoogstrate, René Böttcher, Saskia Hiltemann, Peter van der Spek, Guido Jenster and Andrew P Stubbs, Bioinformatics (2015) doi: 10.1093/bioinformatics/btv721
  • User Support:
  • Quotas:
    • "This Galaxy instance may be used without registration, but guests' histories are deleted nightly. To request an account, please contact the Bioinformatics department."
  • Sponsor(s):

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](mailto: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:
  • 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](mailto: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](mailto: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@Pasteur

Galaxy@Pasteur
  • Link:
  • Domain/Purpose:
    • General purpose genomics analysis server.
  • Comments:
  • User Support:
  • Quotas:
    • Anonymous access is supported with a reduced quota; anyone can create an account.
  • Sponsor(s):
    • C3BI Insitute Pasteur

Galaxy Sigenae / BioInfo Genotoul

Galaxy Sigenae / BioInfo Genotoul

Galaxy Test

GigaGalaxy

GigaGalaxy

GVL QLD

Genomics Virtual Lab

GVL Tutorial

Genomics Virtual Lab

Insitut Curie

Institut Curie
  • Link:
  • Domain/Purpose: 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.
  • Comments:
  • User Support:
  • Quotas:
    • Requires that you create a login to access it.
    • Only 4 jobs can be run simultaneously for a single user. Other jobs will be put into queue.
    • Jobs running over than 72hrs (after the job actually runs on the server) will automatically been terminated.
    • Each user have a 400Gb quota.
    • Datasets and Histories will be automatically deleted after 10 weeks.
    • This service comes with absolutely no warranty. The data are not backed up.
  • 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](mailto: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

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-CEFAP

Galaxy-CEFAP

Galaxy Integrated Omics (GIO)

Galaxy Integrated Omics (GIO)

Galaxy-P

Galaxy-P

Galaxy PGTB (Virtual Biodiversity Lab)

PGTB Galaxy

Genomic Hyperbrowser

Genomic Hyperbrowser

Gene Ontololgy (GO)

GO Galaxy

GrAPPA

Graph Algorithms Pipeline for Pathway Analysis
  • Link:
  • Domain/Purpose:
    • 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.
  • Comments:
    • Efforts to increase GrAPPA’s functionality are underway. Features now being incorporated include:
      • a larger repertoire of pre-processing options, including Gaussian graphical models and an expanded set of correlation metrics such as mutual information
    • more powerful post-processing capabilities, for example, software tools for Bayesian analysis
    • links to related web-centric resources, e.g. GeneWeaver, so that users can seamlessly transfer data and results
  • User Support:
    • Email Support
    • Suggestions and feedback from the user community are encouraged.
  • Quotas:
    • You have to verify your email account before running jobs.
    • Quota: 5GB. To have more space, please contact grappa@utk.edu
    • Data will be kept 60 days after deletion from history or library.
    • FTP is not activated in this instance.
  • Sponsor(s):

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:
  • Sponsor(s):

ImmPort Galaxy

ImmPort Galaxy

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):

MetaDP

MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets
  • Links:
  • Domain/Purpose:
    • "a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets"
  • Comments:
    • "for 16S rRNA sequencing data analysis, including data quality control, operational taxonomic unit clustering, diversity analysis, and disease risk prediction modeling."
    • See MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets by Xilin Xu, Aiping Wu, Xinlei Zhang, Mingming Su, Taijiao Jiang, Zhe-Ming Yuan. Biophys Reports (2017). doi:10.1007/s41048-016-0033-4
    • This is perhaps the first Galaxy-based server on this list with a user interface that does not resemble Galaxy in any way.
  • User Support:
    • User Guide
  • Quotas: * Sponsor(s):
    • Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
    • Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing; Suzhou Institute of Systems Medicine, Suzhou, China
    • Suzhou Geneworks Technology Company Limited, Suzhou, China
    • Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China

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](mailto: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](mailto: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.
    • 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

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
  • 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](mailto:lxue AT uga DOT edu).
  • Quotas:
  • Sponsor(s):

APOSTL

Automated Processing of SAINT Templated Layouts
  • Link:
  • Domain/Purpose:
    • Automated Processing of SAINT Templated Layouts (APOSTL) is a freely available software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data.
  • Comments:
    • APOSTL is an evolving software project with the potential to customize individual analyses with additional Galaxy tools and widgets using the R web application framework, Shiny. The source code, data and documentation are freely available from GitHub and other sources.
    • APOSTL utilizes Significance Analysis of INTeractome (SAINT), a popular command-line software for analyzing AP data. APOSTL can process AP results from MaxQuant, Scaffold, PeptideShaker, or any software that can export mzIdentML.
    • APOSTL can create a number of publication-quality visualizations including interactive bubble plots, protein-protein interaction networks through Cytoscape.js integration, and pathway enrichment/gene ontology plots.
    • APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data, Brent M. Kuenzi, Adam L. Borne, Jiannong Li, Eric B Haura, Steven A Eschrich, John M Koomen, Uwe Rix, and Paul A Stewart. J. Proteome Res., DOI: 10.1021/acs.jproteome.6b00660
    • An Interactive Tool for Reproducible Analysis of Affinity Proteomics Data, presented by Paul A Stewart at GCC2016.
  • User Support:
  • Quotas:
  • Sponsor(s):

ARGs-OAP

Structured ARG reference database Online Analysis Platform

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](mailto:bruno DOT fosso AT gmail.com) and/or to [Giacinto Donvito](mailto: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:
  • Quotas:
    • Supports anonymous access and creation of user logins.
  • Sponsor(s):

Chemical Annotation Retrieval Toolkit (CART)

Chemical Annotation Retrieval Toolkit (CART) Galaxy
  • Link:
  • Domain/Purpose:
    • Retrieves annotations on biological effects of chemicals and determines which ones are enriched.
  • Comments:
    • From "CART – a chemical annotation retrieval toolkit" by Samy Deghou, Georg Zeller, Murat Iskar, Marja Driessen, Mercedes Castillo, Vera van Noort, and Peer Bork. Bioinformatics (2016), doi: 10.1093/bioinformatics/btw233 "it matches an input list of chemical names into a comprehensive reference space to assign unambiguous chemical identifiers. In this unified space, bioactivity annotations can be easily retrieved from databases covering a wide variety of chemical effects on biological systems. Subsequently, CART can determine annotations enriched in the input set of chemicals and display these in tabular format and interactive network visualizations, thereby facilitating integrative analysis of chemical bioactivity data."
    • Source code and an easy-to-install command line tool are also available.
  • User Support:
    • See the "Tutorial" and "Contact" tabs on the website.
  • Quotas:
    • Supports anonymous access and creation of user logins.
  • Sponsor(s):

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):

IBERS @ Aberystwyth

IBERS @ Aberystwyth Galaxy

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:
    • InMoDe is a collection of Tools for learning and visualizing inhomogeneous parsimonious Markov models (iPMMs).
    • 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](mailto: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](mailto: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."

Osiris

Osiris

Palfinder

Galaxy Palfinder Service

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):

VarCap

VarCap

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.