1 of 14

Reflections from an Open Science Initiative

Matthew Lewis, PhD

ASAP Program Officer – Open Science

​

12/13/2023

2 of 14

ASAP is a basic research initiative built upon strong open science policies

​

2

To accelerate the pace of discovery and inform the path to a cure for Parkinson’s disease through collaboration, research-enabling resources, and data sharing.

Our Mission

3 of 14

ASAP Programs

3

PARKINSONSROADMAP.ORG

4 of 14

Collaborative Research Network

4

PARKINSONSROADMAP.ORG

Key Scientific Themes

PD Functional Genomics

Neuro-Immune Interactions

Circuitry and Brain-Body Interactions

5 of 14

CRN Interaction at Various Nodes

5

Interest & Working Group Meetings

Interest Groups: Teams have been sorted into affinity groups for regular monthly meetings.

​

Working groups: Teams identify issues and come together to resolve them.

​

Annual Meetings: Bringing the Network together in person to share progress.

Compliance Review

Grantees receive feedback and training in open science best practices while registering their research outputs.

ASAP Hub

Virtual collaboration platform to facilitate communication & sharing across the CRN.

6 of 14

Our Open Science Policy

https://parkinsonsroadmap.org/open-access-policy/

​

Manuscripts posted in an OA preprint repository upon submission to a journal for review (or sooner).

Immediate free online access upon publication with grantees retaining copyright via CC BY 4.0 license (or equivalent) for unrestricted reuse.

All research outputs (data, code, lab materials, protocols) deposited in publicly accessible repositories and cited in the publication with their permanent identifier.

Appropriate attributions to ASAP funded work.

Utilizing our Research Output Management System (ROMS) to track research outputs within the ASAP virtual grantee platform known as the ASAP Hub.

6

7 of 14

Policy in Practice: Compliance Workflow

�

​

​

​

7

  • Workflow is a joint enterprise with DataSeer.

​

  • Compliance is a factor for future follow-on funding assessments

​

  • Iterative review allows researchers to increase compliance as manuscripts approach publication.

​

Dumanis and Ratan et al. 2023; DOI:10.1371/journal.pcbi.1011626

8 of 14

Open Science Experience

  • Current state: For many grantees, this is the first time they are sharing data and other outputs within their research publications.

​

  • Major focus: Grantee “User Experience” within the open science community
    • How can ASAP intervene to augment grantees’ experience and change research culture?

​

  • Top Questions from our Community:
    1. Where should I deposit my outputs?
    2. What should be included in the deposited materials?
    3. How should I do it?

​

​

​

​

8

9 of 14

Question 1: Where do I deposit?

  • Problem:
    • Not all datasets have a specific repository home
    • Siloed repositories

​

  • Solution:
    • Centralization of research outputs within a single repository increases the visibility of the research portfolio and aids future re-use by Parkinson’s Disease researchers
    • ASAP community on Zenodo (all purpose repository, where up to a certain file size, free to use)

​

  • Considerations:
    • Can share large files > 1TB, but cost associated (~4K) per data collection

​

9

10 of 14

Question 2: What should be deposited?

  • Problem:
    • CRN researchers are utilizing various experimental approaches and scientific instruments to perform their experiments.

​

  • Solution:
    • To maximize reproducibility, and re-use value, datasets require thorough documentation and methods for quality assessment
    • Create community-generated templates and standards (e.g., CRN Working Groups)
      • iPSC Working group – Developed QC data requirements when generating novel cell lines

​

  • Consideration:
    • Lots of communities working on same problem - hard to know what’s already been created and there is information overload
    • Different repositories/publishers have different requirements

​

​

10

11 of 14

Question 3: How should I do it?

  • Problem:
    • Not all datasets are created equally; sharing data becomes harder as datasets become larger and more complex.
    • Technical capacity is a significant factor in determining how and if a research group shares data (e.g., computer programming experience is essential to manipulating neurophysiology datasets)

​

  • Solution:
    • Providing training and curation support

​

  • Consideration:
    • Activation energy required to implement a new workflow
    • Cost associated with providing curation support
    • Scalability challenges – As new methods get developed, new tailored solutions are needed

​

​

11

12 of 14

Key Takeaways

  • “User Experience” of doing open science is a work in progress
    • Compliance reviews provide guidance and training in best practices

​

  • Knowledge Gap
    • Consistent interactions with grantees is necessary for changing researcher behavior

​

  • Need for greater integration within the community
    • A better connection between the open science community and researchers is paramount for changing culture

​

  • There is a cost to open science
    • Strong need to invest in open infrastructure that facilitates impact assessment of open science initiatives.

12

13 of 14

To Learn More

13

Blueprint for Collaborative Open Science

DOI:10.5281/zenodo.6979998

​

New Perspective Article:

From Policy to Practice

DOI:10.1371/journal.pcbi.1011626

ASAP’s Open Science Webpage

https://parkinsonsroadmap.org/open-science/#

14 of 14

Questions?

14

openaccess@parkinsonsroadmap.org