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ASAP CRN Cloud Overview

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Table of Contents

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Background:

  • ASAP CRN Background……………………. 4

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Product Overview:

  • Goals and Objectives……………………….. 6
  • First Release………………………………….7
  • Product Workflow…………………………….8
  • Product Architecture…………………….…...9
  • Data Overview………………………….......10

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Mockups:

  • UI Mockups……………………………...12-18
  • Verily Reference Space Mockups……. 19-20

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Timeline:

  • Timeline…………………………………….. 22

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BACKGROUND

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ASAP CRN | Background

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BACKGROUND

Aligning Science Across Parkinson’s (ASAP) is an organization dedicated to fostering “an environment that facilitates the rapid and free exchange of scientific ideas to spark new discoveries for Parkinson’s disease (PD).”1

To accomplish this goal, ASAP established the Collaborative Research Network (CRN).

“The CRN is an international, multidisciplinary, and multi-institutional network of collaborating investigators working to address high-priority basic science questions.”1

CRN HIGHLIGHTS

  • 35 Teams Funded
  • $290M+ in Grant Funding Awarded Over Four Years
  • 163 Investigators Total as Team Leaders
  • 14 Countries Represented Across Team Leadership
  • 80+ Institutions Across Team Leaders

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1https://parkinsonsroadmap.org/research-network/#

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PRODUCT OVERVIEW

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ASAP CRN Cloud | Goal and Objectives

GOAL

Increase collaboration and data sharing to accelerate the pace of discovery for PD.

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OBJECTIVES

  • Provide an environment for pre-publication collaboration and responsible data sharing within CRN.
  • Establish a scalable process for curation of CRN data.
  • Provide for secure data access across the neurodegeneration research community.
  • Enable meta-analysis and ensure that data disseminated by the CRN is reproducible.
  • Increase research potential by being interoperable with other ASAP program-specific cloud platforms (i.e., Accelerating Medicines Partnership Parkinson’s Disease (AMP PD) and Global Parkinson’s Genetics Program (GP2)).

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ASAP CRN Cloud | First Release

  • ASAP CRN Cloud will be released for use within the Collaborative Research Network in Q4 2023 with the following features:
    • Collection management through Explorer
    • Data access through Publisher
    • Data analysis through Verily Workbench
    • Harmonized PMDBS Collection and data from each contributing team

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  • In future releases we plan to add additional data generated by the ASAP CRN teams.

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Product Workflow

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Product Architecture

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Post-Mortem Derived Brain �Sequencing (PMDBS) Collection

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  • ~700 TB of post-mortem brain data will be collected from ASAP CRN teams.

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  • Data has been derived from 1,800+ brain samples

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      • Data will be available on ASAP CRN Cloud in two ways:
      • Individual teams in raw and processed forms
    • A smaller subset of data will be harmonized into the PMDBS Collection

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  • Brain samples include:
                  • Healthy Controls,
                  • Parkinson’s Disease,
                  • Alzheimer’s Disease, and
                  • Incidental Lewy Body Disease

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  • Types of sequencing include:
                  • Single-nucleus RNA-seq
                  • Single cell RNA-seq
                  • Bulk RNA-seq
                  • ATAC-seq
                  • Long read WGS
                  • Single-nucleus Multiome Sequencing (paired snRNAseq, snATACseq)

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  • Spatial transcriptomics and proteomics data from some of these brain samples will be made available in future releases.

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MOCKUPS

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Explorer | UI Mockups

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Explorer provides a unified user and programmatic interface to the universe of data registered to the network through Publisher. Each box represents a Collection, each potentially from a different data custodian, with data hosted from a different cloud and region.

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This product will be similar to Viral AI

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Explorer | UI Mockups

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Viewing a Collection in Explorer before being granted access. Users are able to review a description of the Collection (left image) and request access (top image). The Collection description can include rich text and reference additional external sources (e.g. journal publications, methods, data dictionaries).

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This product will be similar to Viral AI

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Explorer | UI Mockups

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Confirmation of Access Request sent to a user. An email is simultaneously sent to the appropriate data custodian.

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Explorer | UI Mockups

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Viewing a Collection in Explorer after being granted access. Users are able to view data within the Collection.

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Explorer | UI Mockups

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Browsing one of the tables within a Collection in Explorer.

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Explorer | UI Mockups

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Getting instructions from Explorer on how to query the data programmatically. For any search performed in Explorer, users can click the View Query button to show the corresponding query that can be issued via SQL and the Command Line Interface. 

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Publisher | UI Mockups

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Connecting a Google Cloud Storage bucket to Publisher.

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Verily Reference Space Mockups | UI Mockups

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Verily Reference Space Mockups | UI Mockups

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TIMELINE

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Timeline

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