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Teach/Trainers

Galaxy Training Network

Galaxy Trainer Directory

The Galaxy Trainer Directory is a service of the Galaxy Training Network which aims to make it easy to share and find Galaxy training resources. This directory lists individuals and groups that do Galaxy training. The contacts listed here are willing to present Galaxy at meetings and workshops. The directory includes particular areas of expertise and how far the instructors are willing to travel.

If you offer Galaxy Training and want to be listed in this directory then see the Add a Trainer section below.


Trainers

Trainers are grouped by their reach. That is, by how far they are willing to travel and who they are eligible to teach.

  • Global: around the world

  • Continental: across their continent

  • Regional: Willing to travel beyond their local area, but not across their continent

  • Local: These trainers don't travel, but their workshops are open to researchers outside their institution.

  • Institution: Trainers that can only teach to researchers that are affiliated with their institution.

Global

Trainers are potentially willing to travel globally to present Galaxy Training.

The Centre for Bioinformatics and Computational Biology

The The Centre for Bioinformatics and Computational Biology, University of Pretoria

The FMI Bioinformatics Core Facilities

The FMI Bioinformatics and Functional Genomics Core Facilities
  • Description:

    • We mainly provide internal training for our local Galaxy server. However, we are also involved in training and consulting outside our institute.
  • Domains:

    • General usage
    • NGS analysis
    • Microarray analysis
  • Reach

    • Primarily central Europe, but available globally. Located in Basel, Switzerland.
  • Links & Contact

Freiburger Galaxy Project

Galaxy Project
  • Description:

    • The Freiburger Galaxy Project is led by Rolf Backofen from the University of Freiburg, Germany. The project is offerring Galaxy support and training for the University of Freiburg and beyond.
  • Domains:

    • General usage
    • Chip-Seq
    • RNA-Seq
    • Variant detection
    • Chemoinformatics
    • Genome annotation
    • Defining Tools in Galaxy
    • Installation and Administration
  • Reach

    • based in Freiburg (Germany), but used globally
  • Links & Contact

Galaxy Project

Galaxy Project
  • Description:

    • The Galaxy Project does training at events and institutions around the world. These cover the whole range of Galaxy related topics. Please contact Galaxy Outreach if you are interested in hosting training.

  • Domains:

    • General usage; several specific types of analysis
    • Galaxy on the cloud
    • Tool Development for Galaxy, including tool wrapping practices and the Galaxy ToolShed

    • Installation and Administration
  • GTN Training Resources:

  • Reach

    • Global
    • Project members are located in Pennsylvania, Maryland, Virginia, Georgia, California, and Oregon in the United States, and in Melbourne, Australia.

  • Links & Contact

GalaxyP Project

GalaxyP Project
  • Description:

    • Our training is part of the GalaxyP Project. We have training modules planned for using Galaxy for proteomics. This includes using ProteinPilot (licensed software) within Galaxy on our local server. We plan to develop tutorials for use of PeptideShaker, proteogenomics analysis and metaproteomics analysis.

  • Domains:

    • Proteomics tools within Galaxy.
  • Reach

    • Part of the University of Minnesota. Travel for Conferences, potentially around the world.
  • Links & Contact

Geneclat Technologies

Geneclat Technologies
  • Description:

    • We at Geneclat provide Training for individual or group of people who are interested in NGS and Bioinformatics

  • Domains:

    • General usage.
  • Reach

    • Based in Bengaluru, Karnataka, India; but available globally (and ready to travel!)
  • Links & Contact

Memorial Sloan Kettering Cancer Center, Rätsch Laboratory

Memorial Sloan Kettering Cancer Center, Rätsch Laboratory
  • Description:

    • We have efficient computational methods in modeling all processes involved in RNA expression, regulation and processing. Most of the trainings are based on Oqtans package.
  • Domains:

    • Deep Sequencing Data Analysis
  • Reach

    • Based in New York City, but willing to train around the world.
  • Links & Contact

MMG@IICT

MMG@IICT
  • Description:

    • Workshops and training about the Molecular Property Diagnostic Suite (MPDS).
  • Domains:

    • CADD
  • Reach

    • Based in Hyderabad, India, but willing to train around the world.
  • Links & Contact

Noor Biotechnologies Ltd.

Noor Biotechnologies Ltd.
  • Description:

    • In collaboration with a number of research scientists with hands on experience in genomics and bioinformatics, Noor Biotechnologies offer consultancy services and onsite practical training in:

      • Next Generation Sequencing:
        • Next Generation Sequencing Technologies
        • Library Preparation for DNA Sequencing on Illumina MiSeq and HiSeq

        • Illumina Library QC and Troubleshooting
        • Optimizing Cluster Densities on Illumina MiSeq and HiSeq

      • Bioinformatics:
        • Next Generation DNA Sequencing Technologies and Data Management
        • Basic Concepts in Bioinformatics and Making Sense of Data
        • Using Galaxy for Analysis of High Throughput Sequence Data
  • Domains:

    • De novo assembly
    • Small genome annotation
    • Mapping and variant calling
    • Multiple sequences alignment
    • Phylogeny
    • Multi Locus Sequencing Typing
    • Microbial species identification (16S and 18S metagenomics)
    • Antibiotics resistance predictions
  • Reach

    • Based in Malaysia and Saudi Arabia. We are available to train around the world.
  • Links & Contact

OpenHelix

OpenHelix
  • Description:

    • OpenHelix specializes in end-user training on a wide range of bioinformatics databases and software tools. Our goal is to reach new users with introductory information that can get them started using tools that are new to them, or to build their confidence by improving their grasp of the foundational features of the tools. We offer workshops or online training.

  • Domains:

    • General usage
  • Reach

    • It is easiest for us to travel in North America, but we have also delivered training in Europe, Asia, South America, and Africa. We can also do webinar format training. We are limited to delivering training in English, however.
  • Links & Contact

QFAB Bioinformatics

QFAB Bioinformatics
  • Description:

  • Domains:

    • General usage
    • RNA-Seq
    • Variant detection
    • Bacterial de novo genome assembly
  • Reach

    • Primarily Australia, but available globally
  • Links & Contact

Stingray@Galaxy

Stingray@Galaxy

University of Bradford, School of Medical Sciences, Krzysztof Poterlowicz

Krzysztof Poterlowicz, University of Bradford

Victorian Life Sciences Computation Initiative (VLSCI)

Victorian Life Sciences Computation Initiative (VLSCI)

Continental

Trainers that are potentially willing to travel, roughly within their home continent.

CRS4 - Centre for Advanced Studies, Research and Development in Sardinia

CRS4
  • Description:

    • The CRS4's Bioinformatics Laboratory offers bioinformatics training and project-based data analysis. The training is based on Orione, our Galaxy-based platform for NGS analysis. CRS4 is at the forefront in the research, development and application of technology for acquisition, processing, distribution, and visualization of massive data (Big Data) with a special emphasis on bio-medical and healthcare applications.

  • Domains:

    • General usage
    • Variant detection
    • RNA-Seq
    • Metagenomics
    • Microbiology
    • Data visualization
    • Installation and administration
    • Tool Development
  • Reach

    • Regional. Trainings are offered primarily in Italy, but available in Europe.
  • Links & Contact

EMBL-ABR

EMBL-ABR
  • Description:

    • EMBL Australian Bioinformatics Resource is a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. EMBL ABR aims to provide new opportunities and harmonise existing training efforts across Australia to maximise the reach and scope of bioinformatics training, as well as to share experience and best practice from Australia with international initiatives. The EMBL ABR Training programme comprises a series of focal topics to tackle training gaps with the aim of enabling sustainable and scalable bioinformatics use by life scientists across Australia. There are three main factors contributing to training gaps among life science researchers:

      1. insufficient exposure to the principles and application of bioinformatics;
      2. the speed at which technologies, data analysis practices and tools develop and the lag in how these are incorporated into the current undergraduate and postgraduate curricula
      3. a lack of support within some research groups or institutions for students and postdoctoral researchers to learn bioinformatics skills and tools.
  • Domains:

    • Currently, in terms of topics we offer training on:
      • Introduction to Galaxy
      • Galaxy Workflows
      • Using Histories and Workflows
  • Reach

    • Primarily Australia, but we welcome opportunities to contribute when invited to training efforts world wide.
  • Links & Contact

GenoToul bioinformatics platform, Sigenae, NED (GenPhySE) and TWB

GenoToul Training
Sigenae
  • Description:

  • Domains:

    • Galaxy : First steps (1 day)
    • Galaxy: Reads alignment and SNP calling (1,5 days)
    • Galaxy : RNAseq alignment and transcripts assemblies (1.5 days)
    • Metagenomics: amplicon analysis (4 days)
  • Reach

    • Based in Toulouse, France; potentially willing to present across Europe
  • Links & Contact

Regional

Regional is roughly defined as "willing to travel beyond my local area, but not across the continent."

Alberta Children's Hospital Research Institute

Alberta Children's Hospital Research Institute
  • Description:

    • ACHRI has three research foci, with one being The Molecular and Genetic Basis of Child Health. With $5M in funding from the Alberta Children's Hospital Foundation, next-generation sequencing and bioinformatics platform was established in 2011 to advance personalized medicine and basic science research at the University of Calgary. Bioinformatics efforts have largely centered around new tools and workflows for optimizing exome genotyping, quality control and variant triage based on clinical symptoms.

  • Domains:

    • Exome and whole genome variant analysis
    • RNASeq
    • General usage
    • Developing tool wrappers
  • Reach

    • Have taught for the local Calgary community only so far, but would be willing to do roadshows globally on exome analysis using Galaxy and our custom tools as we roll out a public version of the portal.
  • Links & Contact

Bioinformatics.ca

Bioinformatics.ca
  • Description:

    • Bioinformatics.ca through its Canadian Bioinformatics Workshops (CBW) series began offering one and two week short courses in bioinformatics, genomics and proteomics in 1999. In the fall of 2007, bioinformatics.ca moved to its new host at the Ontario Institute for Cancer Research and the CBW initiated development of a new format and series of exciting workshops. It was recognized that with the introduction of new technologies and scientific approaches to research, having the computational biology capacity and skill to deal with this new data has become an even greater asset. This new series of workshops focuses on training the researchers of these advanced technologies on the latest approaches being used in computational biology to deal with the new data. In one of the workshops we teach, Informatics on High Throughput Sequencing Data, we teach 1/2 day on use of Galaxy in NGS analysis. We cover an overview of Galaxy as well as an example of RNA-Seq and SNP-calling (lab).

  • Domains:

    • Alignment (lab)
    • SNP-calling (lab)
    • RNA-Seq (lecture)
  • Reach

    • Courses are in Toronto (Canada), and are open to all world-wide.
  • Links & Contact

Galaxy @ PRABI Project

Galaxy@prabi Project
  • Description:

    • The galaxy@prabi project is led by Vincent Navratil from the University of Lyon, France. The project is offerring Galaxy service, support and training for and with research teams working in the perimeter of the PRABI core facility (Rhône Alpes Region, mainly Lyon and Grenoble) but also beyond the Alps montains.

  • Domains:

    • General usage
    • RNA-Seq, Differential Expression, Variant calling and functional impact prediction
    • PRABI tools (kissplice, kissDE, discoSNP, priam)

    • Defining Tools in Galaxy
    • Installation and Administration
  • Reach

    • Rhône Alpes regions (France), beyond the Alps montains if requested.
  • Links & Contact

    • galaxy.prabi.fr and toolshed.prabi.fr soon available in production
    • galaxy@prabi user list <galaxy-user AT listes DOT univ-lyon1 DOT fr> (in french)

    • galaxy@prabi support <galaxy-support AT listes DOT univ-lyon1 DOT fr>

Galaxy User Group Grand Ouest (GUGGO)

e-Biogenouest GUGGO Initiative
  • Description:

    • GUGGO is a working group gathering 6 Western France Life Sciences Computation Centre. From West to East:

      • Cellule Bioinformatique-Ifremer Ifremer/U.B.O./CNRS/ (Brest/Plouzane, contact: Laure Quintric <bioinfo-contact AT ifremer DOT fr>)

      • ABiMS IFB core facility UPMC/CNRS (Roscoff, contact: Christophe Caron <christophe DOT caron AT fr>)

      • GenOuest IFB core facility Rennes1 University/CNRS/INRIA (Rennes, contact: Yvan Le Bras <yvan.le_bras AT irisa DOT fr>)

      • BIPAA INRA (Rennes, contact: Anthony Bretaudeau <anthony DOT bretaudeau AT irisa DOT fr>)

      • BIRD IFB core facility Nantes University/INSERM (Nantes, contact: Audrey Bihouée <audrey DOT bihouee AT univ-nantes DOT fr>)

      • IRHS BioInformatics team Angers University/Agrocampus Ouest/INRA (Angers, Jean-Pierre Renou <jean-pierre DOT renou AT angers DOT inra DOT fr>).

  • Domains:

    • Life science
      • General usage
      • DNA-seq, RNA-seq, RAD-Seq
      • Without assembly NGS data treatment
      • Metagenomics
      • Transcriptomics
      • Phylogeny
    • Bioinformatics
      • Galaxy tools development, integration and sharing
      • Galaxy on the Cloud
  • Reach

    • Primarily (western) France but available globally
  • Links & Contact

LUMC, ErasmusMC, DTL Learning Programme

LUMC

ErasmusMC

Dutch Techcentre for Life Science Learning Programme
  • Description:

    • Bioinformatics groups at LUMC & ErasmusMC contributed to several courses on using Galaxy for NGS data analysis. We also plan to sustain those courses on a yearly base. The organization of these courses is supported by the DTL learning program.

  • Domains:

    • General usage
    • RNA-seq
    • Assembly
    • Variant calling and filtering
    • Building tools in Galaxy
    • Interaction with other workflow systems
  • Reach

    • We organize and contribute to courses within the Netherlands.
  • Links & Contact

    • DTL Learning Programme

    • Contacts: Leon Mei <h DOT mei AT lumc DOT nl>, Andrew Stubbs <a DOT stubbs AT erasmusmc DOT nl>

Ruđer Bošković Institute (RBI)

Ruđer Bošković Institute (RBI)

South Green Platform

South Green Platform
  • Description:

    • South Green is a bioinformatic platform, studying tropical crops. It uses Galaxy for a large panel of bioinformatic analyses, from RNA-seq to phylogeny and 3D protein structure prediction.

  • Domains:

    • RNA-seq
    • assembly
    • mapping
    • SNP calling
    • annotation
    • phylogeny
    • 3D protein structure
  • Reach

    • We teach mainly in Montpellier (France), but also anywhere in France in collaboration with the IFB (Bioinformatic French Institut).
  • Links & Contact

Local

These trainers don't travel, but their workshops are open to researchers outside their institution.

Earlham Institute

Earlham Institute
  • Description:

    • The Earlham Institute's Scientific Training team work with content experts from EI and across the world to create hands-on training courses and workshops in cutting edge genomics, bioinformatics and high-performance computing.

  • Domains:

    • General usage and many specialisations
  • Reach

    • Workshops are held in Norwich, United Kingdom, and are open to all researchers and students.
  • Links & Contact

Peter Mac

Peter MacCallum Cancer Center
  • Description:

    • Peter Mac is one of the world’s leading cancer research, education and treatment centres globally and is Australia’s only public hospital solely dedicated to caring for people affected by cancer. We have over 2,500 staff, including more than 580 laboratory and clinical researchers, all focused on providing better treatments, better care and potential cures for cancer.

  • Domains:

    • General usage, cancer genomics
  • Reach

    • Training is held at Peter Mac in Melbourne, Australia, and are open to all researchers and students.

  • Links & Contact

    • Peter Mac

    • E-mail contact Maria Doyle <Maria DOT Doyle AT petermac DOT org>

Texas A&M University/Center for Phage Technology

Texas A&M University/Center for Phage Technology
  • Description:

    • The TAMU Galaxy offers access a local Galaxy instance for TAMU Staff, faculty, and researchers. The CPT@TAMU offers a Galaxy instance catering to Bacteriophage Research.
  • Domains:

    • General usage
    • Variant detection
    • Genome/Transcriptome Assembly
    • Genome annotation
  • Reach

    • Based in College Station, Texas.
  • Links & Contact

UC Davis Genome Center's Bioinformatics Core Facility

UC Davis Genome Center's Bioinformatics Core Facility

University of Aberdeen Centre for Genome Enabled Biology and Medicine

University of Aberdeen Centre for Genome Enabled Biology and Medicine
  • Description:

    • The Centre for Genome Enabled Biology and Medicine organises and runs workshops in order to help aid researchers in analysis of next generation sequencing data. We offer workshops covering both Galaxy and command line approaches to make computational analysis accessible to all.

  • Domains:

    • Next Generation Sequencing specific workshops including:
      • Quality Control of NGS data
      • Genome Assembly and Annotation
      • RNA Sequencing and Differential Expression
      • Alignment, Visualisation and Variant Calling
      • ChIP Sequencing
  • Reach

  • Links & Contact

University of Cambridge Bioinformatics Training Facility

University of Cambridge Bioinformatics Training Facility
  • Description:

    • The Bioinformatics Training Facility of the School of Biological Sciences of the University of Cambridge offers a wide range of bioinformatics training courses, including Galaxy-based training.

  • Domains:

    • General usage
    • Alignment
    • Variant Calling
    • RNA-Seq
    • ChIP-Seq
  • Reach

    • Workshops take place at the University of Cambridge, and are open to people outside the University of Cambridge.
  • Links & Contact

University of Minnesota Minnesota Supercomputing Institute Research Informatics Solutions

University of Minnesota Minnesota Supercomputing Institute Research Informatics Solutions
  • Description:

    • RIS is a group of experienced bioinformatics experts within the Supercomputing Institute at the University of Minnesota.

  • Domains:

    • General usage
    • RNA-Seq
    • ChIP-Seq
  • Reach

    • Workshops take place at the University of Minnesota, and are open to people outside the University of Minnesota.
  • Links & Contact

    • Access all MSI tutorials

    • Contact Lauren Mills <ljmills AT umn DOT edu> for more info.

Institution

Trainers that can only teach to researchers that are affiliated with their institution.

HSPH Bioinformatics Core (HBC)

HSPH (Harvard School of Public Health) Bioinformatics Core

Add a Trainer

Do you or your organization do Galaxy training? Then please tell the Galaxy Community! You can either edit this wiki page directly (you will need to create a login), or submit the information through this online form.

Frequently Asked Questions

Q: Have instructors in this directory been vetted in any way?

No, not in any rigorous or official way. However, trainers listed here are well-known in their communities.

Q: What does it cost to bring a trainer to my institution or event?

That depends entirely on who does the training. Most/All of these groups are not specifically funded to do Galaxy Training outside their home organization. It may require creative funding and/or a nearby trainer to get Galaxy Training at your institution or event. The trainer location map can help you identify nearby trainers.

Q: Where can I find other non-Galaxy specific bioinformatics training?

Global Organisation for Bioinformatics Learning, Education & Training (GOBLET)

Most of the members of the GTN also do bioinformatics training that isn't Galaxy-based. If you want training that involves both Galaxy-based and non-Galaxy-based material than the GTN membership is the best place to start. For general bioinformatics training a great place to look for trainers is the Global Organisation for Bioinformatics Learning, Education & Training (GOBLET). GOBLET was founded in 2012 by a group of international & national societies & networks to offer an umbrella for bioinformatics, biocuration, biocomputing & computational biology learning, education & training. It has online resource directories, very similar to what the GTN has.

And, as of 2015 the Galaxy Training Network is a proud member of GOBLET.