The Galaxy project will team up with The Carpentries to create and deliver a genomics curriculum, starting from raw data and leading up to the production of publication-ready visualizations of the analysis results.
The proposed curriculum will be built around reproducing published research using the publicly available data and will comprise the following two parts:
- The data analysis steps leading from the raw sequencing data to the downstream count tables, using Galaxy tools relying on both their wide use as well as the standardization they offer.
- Manipulation and visualization of the results using R as the data science programming language of choice, including an introduction to R using RStudio inside a Galaxy Interactive Environment (GIE).
In order to ensure the quality of the material, we will be leveraging the knowledge and materials currently offered by the Carpentries and the Galaxy community. All training material produced in the project will be developed in an open collaborative environment in adherence to the Open Science principles. Specifically, the training material on the data analysis steps leading from the raw sequencing data to the downstream count tables will be hosted in the Galaxy Training Material website using the provided template as the driving structure. The material focusing on the introduction to R using RStudio inside a Galaxy Interactive Environment will be hosted on the Carpentries Lesson Incubator and will rely on the lesson template provided by The Carpentries. The complete curriculum will be provided here, with complete bidirectional linking to both websites, and acts as a representation of the virtual bridge between the two communities.
The produced training materials will be delivered during two three days workshops with one occurring as a satellite event of the Galaxy Community Conference in 2019. Each workshop will include both a physical and a virtual aspect; it will comprise of multiple sites delivering the same content at the same time across multiple time zones and various locations, through online streaming. This is a very ambitious goal of the project, with significant importance to other communities and initiatives; as such we will document all the organizational and practical steps required in making this “hybrid” workshops happen, and provide this information as a resource for adoption, reuse and further improvement.
This project is supported by an Open Science Mini-Grants, from the Mozilla Foundation.