Training & Development

Training is central to the GP2 effort, and throughout this project we will offer development opportunities on genetics of Parkinson’s disease and other related areas to everyone interested. Materials like these from different sources will be posted here, along with educational content produced by the GP2 team.

Please return to this page regularly for updates and contact us at if you have queries about training opportunities.

  • Using Terra to Access Data & Perform Analyses

    By Hampton Leonard | |

    Watch this video to learn how to access data from Accelerated Medicines Partnership Parkinson's Disease (AMP-PD) and perform analyses using the Terra platform. This training resource will walk you through notebook structure, the Google Cloud Platform, and Big Query functionality. It will introduce how to use the programming language SQL to write queries in order to access data. Access the resources for the practical here.

  • Beginner Bioinformatics for Parkinson’s Disease Genetics Course

    This series of training modules developed by the GP2 Training working group, provides a practical introduction to the process of genotyping quality control at a variant and sample level, genotype imputation, how to prepare for and run a GWAS versus PD risk and PD onset, polygenic risk score calculation and data visualization, hands-on examples on variant annotation, filtering and prioritization, the application of network analyses to translational genetics, and more. No previous coding experience is needed!

  • The process for GWAS/WGS

    By Jeff Leek | |

    Brief overview of GWAS and WGS including variant selection, populating stratification, statistical tests, examining locus/fine mapping, and annotation.

  • Part 4: NIH Strides Overview

    By Nick Weber | |

    Summarizes the advantages of cloud-based data handling and analysis and describes the STRIDES initiative which involves Google Cloud Platform and Amazon Web Services. The STRIDES program offers discounts, consultancy and professional services to NIH institutes and centers, or NIH-funded researchers.

  • Part 3b: AMP-PD Workspaces

    By Barry Landin | |

    Introduction to AMP-PR workspaces which exist within the Terra platform. These are organized by access level and consist of extensive notes and example scripts written in both Python and R script. Recaps a lot of the tools that have been mentioned in previous talks. Provides important information about how to link Terra to a Google billing account to pay for data usage and set up alerts.

  • Part 3a: Research Workbench (Terra)

    By Allie Hajiani and Barry Landin | |

    Introduction to the Terra platform and walkthrough of the website, including registration, using workspaces, and a bit of background on Hail, Cromwell, Jupyter notebooks. Covers the sub-menus in Terra and talks about the free credit program. Hands-on guide to using a ""workspace"" with a public data example