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ELIXIR Workshop for Galaxy training material and skills imporovement
May 21, 2018 - May 23, 2018
Galaxy is an open-source, web framework for easy-to-use, reproducible and shareable computational life science research. There are around 50 public Galaxy servers in Europe, with many more private instances. Several of these installations are part of the national infrastructure of ELIXIR Nodes, which has recently been recognised by the establishment of Galaxy as one of the seven ELIXIR Use Cases/ELIXIR Communities.
Education and training is an integral part of the Galaxy community. The Galaxy Training Network (GTN) has been working for several years with GOBLET and the ELIXIR Training Platform to create material and deliver training for scientists, developers and system administrators.
One of the GTN recent efforts is to develop open, peer-reviewed and FAIR (Findable, Accessible, Interoperable and Reusable) training material following the example of Software/Data Carpentry (SDC). A selection of 72 tutorials, developed by more than 60 contributors, is already available at http://training.galaxyproject.org. The material is complemented by numerous metadata used to automatically populate the Training eSupport System (TeSS) training portal, to reference topics in the EDAM ontology, and to describe the technical infrastructure needed to run the tutorial (e.g. tools, data, workflows, etc.).
In this workshop, we intend to improve the participants’ understanding of learning principles, training techniques and best practices for materials preparation. We will then work together to expand the existing collection of Galaxy training materials by covering more topics relevant to the ELIXIR use cases, add missing annotation and metadata and make the materials easily accessible.
The aim of this workshop is to:
- Build on an existing collection of Galaxy training materials (https://github.com/galaxyproject/training-material), which was initiated at the 2016 Galaxy Community Conference. Materials are currently available for several topics (including Galaxy introduction, genome annotation, transcriptomics, proteomics, ChIP-seq, variant analysis, epigenetics, metagenomics, server administration, and development in Galaxy) with various degrees of completeness.
- Integrate the admin training slides and tutorials.
- Improve materials’ descriptions introducing full BioSchemas compliance.
- Extend the existing “curated” dataset collection, currently stored in Zenodo (an example is available at: https://zenodo.org/record/60520#.WIYKGd_RbmE), which will provide stable Digital Object Identifiers (DOIs) and reliable data hosting.
- Annotate each tutorial with the existing public Galaxy instances where it can be executed (i.e. where the necessary tools and genome indexes are installed), allowing users to immediately try it on the server of their choice.
- Increase the number of Docker/Virtual Machines available for easy installation of Galaxy training environments.
- Explore possible integration with the new TeSS workflow annotator (crosslinking, import/export).
The workshop will start with a 1-day “Train the Trainer” course, similar to the SDC “Instructor Training” (https://carpentries.github.io/instructor-training/) and the ELIXIR-EXCELERATE “Train the Trainer” (https://github.com/TrainTheTrainer/EXCELERATE-TtT). Here Galaxy trainers will develop an insight into different learning styles, understand what makes a good trainer, and learn new approaches to training from experienced trainers. This course will help them to better contribute and shape the materials during the hackathon.