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.

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 The Centre for Bioinformatics and Computational Biology's function is training, support and research in the areas of Bioinformatics and Computational Biology. We function as part of The Genomics Research Institute and The African Centre for Gene Technologies.

Domains:

  • General usage
  • Analysing and comparing protein and nucleic acid sequences
  • Annotating genomes
  • Gene expression patterns
  • Investigating molecular structures
  • Simulating metabolic pathways

Reach: Most training is in southern Africa, but available globally. Located in Pretoria, South Africa.

Links & Contact:

The FMI Bioinformatics and Functional Genomics Core Facilities

The FMI Bioinformatics and Functional Genomics Core Facilities

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

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

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

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

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

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: GenEclat Technologies

Memorial Sloan Kettering Cancer Center, Rätsch Laboratory

Memorial Sloan Kettering Cancer Center, Rätsch Laboratory

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

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.

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 NGS and Bioinformatics including:

  • Library Preparation for DNA Sequencing on Illumina MiSeq and HiSeq
  • Illumina Library QC and Troubleshooting
  • Optimizing Cluster Densities on Illumina MiSeq and HiSeq
  • 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

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

QFAB Bioinformatics offers a range of Galaxy-based bioinformatics workshops run by their training manager Mark Crowe.

Domains:

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

Reach: Primarily Australia, but available globally

Links & Contact:

Stingray@Galaxy

Stingray@Galaxy

Stingray@Galaxy was developed by the Lab of Computational and Systems Biology (LBCS) of the Oswaldo Cruz Institute, FIOCRUZ. Rodrigo Jardim and Alberto Dávila (LBCS) offer training at Fiocruz (and more recently researchers based on universities of Rio de Janeiro state) and beyond on the usage of Stingray@Galaxy.

Domains:

  • NGS data manipulation
  • Genome assembly
  • Comparative genomics
  • Reach:* We are based at Rio de Janeiro (Brazil) but available globally.

Links & Contact:

University of Bradford, School of Medical Sciences, Krzysztof Poterlowicz

Krzysztof Poterlowicz, University of Bradford

Krzysztof Poterlowicz of The School of Medical Sciences of the University of Bradford offers a wide range of Galaxy-based trainings including (Assembly, RNAseq, ChIPseq, Hi-C, DNase-Seq, Pathway enrichment)

Domains:

  • General usage
  • Assembly
  • RNA-Seq
  • ChIP-Seq
  • Hi-C
  • DNase-Seq,
  • Ontology and pathway enrichment

Reach: Available Globally

Links & Contact:

Victorian Life Sciences Computation Initiative (VLSCI)

Victorian Life Sciences Computation Initiative (VLSCI)

VLSCI is a petascale facility incorporating the Life Sciences Computation Centre, led by Andrew Lonie and staffed with over 20 bioinformaticians. Amongst a suite of training courses on offer is a series of Galaxy-based bioinformatics workshops, each taught by an expert in that particular domain e.g. cancer genomics, microbial genomics etc. The materials are designed for both self-directed learning and as content for delivering workshops.

Domains:

  • General usage
  • Chip-Seq
  • RNA-Seq
  • Variant detection
  • Bacterial de novo genome assembly
  • 16S Metagenomics

GTN Training Resources:

Reach: Australian-based, but used globally

Links & Contact:

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

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

The GenoToul bioinformatics platform, Sigenae, NED (GenPhySE) and TWB offers a catalog of training sessions on Galaxy. Team members include Sarah Maman, Philippe Bardou, Sabrina Rodriguez, Celine Noirot, Cédric Cabau, Géraldine Pascal, Maria Bernard, Frederic Escudié, Laurent Cauquil, and Mahendra Mariadassou.

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

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

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

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 User Group Grand Ouest (GUGGO)

e-Biogenouest GUGGO Initiative

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

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

Bioinformatics groups at LUMC and 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:

Ruđer Bošković Institute (RBI)

Ruđer Bošković Institute (RBI)

The Ruđer Bošković Institute is Croatia’s leading scientific institute in the natural and biomedical sciences as well as marine and environmental research.

Domains:

  • General usage
  • Galaxy on the Cloud; CloudMan
  • Installation and Administration
  • RNA-Seq

Reach: We organize and contribute to training within Croatia.

Links & Contact:

South Green Platform

South Green Platform

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

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

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:

Texas A&M University/Center for Phage Technology

Texas A&M University/Center for Phage Technology

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

The UCD Bioinformatics Core offers Galaxy-based training using the Amazon Cloud, as well as command line training and project-based consulting and data analysis.

Domains:

  • General usage
  • Alignment
  • Variant Calling
  • Genome (DNA) Assembly
  • RNA-Seq
  • ChIP-Seq
  • miRNA-Seq

GTN Training Resources:

Reach: We teach on campus in Davis, California, USA - workshops are open to the public

Links & Contact:

University of Cambridge Bioinformatics Training Facility

University of Cambridge Bioinformatics Training Facility

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

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:

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

HBC's staff are available to help with the management, integration, and contextual analysis of high-throughput biological data, focusing on next-generation sequencing support. We provide consulting, training, tools, databases and best practices, while fostering collaboration and a community of bioinformatic activities. We also build unified infrastructure to support a diverse set of experimental systems and high-throughput biological data.

Domains:

  • General Introduction to Galaxy
  • RNA-Seq
  • ChIP-Seq
  • Exome-Seq

GTN Training Resources:

Reach: Limited to Harvard researchers with specific affiliations.

Links & Contact:

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.