The Tanenbaum Open Science Institute (TOSI) is requesting proposals from Neuro community members to identify and support Open Science initiatives at the Neuro.
Proposals should be submitted in PDF format via email to TOSI at tosi [at] mcgill.ca
You can find a proposal here: funding_call_proposal_template_1.docx.
Goal: Supporting Open Science Community Initiatives
The purpose of this funding call is for TOSI to support initiatives emerging from within the Neuro community that facilitate open sharing of scientific outputs with key stakeholders, including other researchers, patients, policymakers, and the public.
Some examples of relevant initiatives include:
- Developing software tools
- Producing and disseminating guides and educational materials
- Organizing community development events (e.g., hackathons)
- Providing peer support for Open Science practices
- Hosting events and forums for communicating scientific results to non-researchers
- Creating online communities for open sharing
- Supporting patient partnership and outreach initiatives
- Exploring the use of new methods of scholarly communication (e.g., open lab notebooks or micropublications)
This list is meant to be illustrative but is not exhaustive. If you are part of an initiative aimed at promoting the open sharing of research or want to start one, TOSI invites you to submit a proposal.
Important note: This funding opportunity is not primarily intended to support the generation of research outputs (i.e., the collection of data or obtaining materials/reagents). Proposals should be primarily aimed at easing the sharing of research through developing infrastructure or educational materials, or the communication of research to key stakeholders (e.g., researchers, patients, policymakers, and the public).
Eligibility and Conditions
- At least one leading member of the initiative must belong to the Neuro community (i.e., trainee, researcher, clinician, and/or research associate working in Neuro-based labs).
- All outputs of initiatives supported by TOSI funds must be released as openly as practically possible. Video recordings and educational materials, for example, should be publicly accessible and apply for a Creative Commons license, and software should be publicly shared under an Open Source Initiative approved license.
- All outputs of initiatives supported by TOSI should acknowledge TOSI support in all communications and report progress to TOSI through a short report at the end of the project.
- Recipients must agree to present at the Neuro Open Science in Action annual symposium, or any other OS-related event, if requested.
The total TOSI funding for this call is CAD $50,000, and the goal is to fund 3-5 projects at CAD $5,000 - $20,000 per project.
Proposals may be submitted to tosi [at] mcgill.ca (TOSI) as of April 25th, 2022
The deadline for receiving proposals is May 25th, 2022.
Applicants will be informed as to whether their initiative has been chosen to receive funding within a month of submission. In the case of a decision not to fund an initiative, TOSI may provide brief feedback concerning how the proposal could be improved for possible resubmission if the funding total is not reached in the first round.
The proposal should be max. 2 pages, 12-point font, including any figures, images, or tables, and should:
- Identify the people involved, and clearly list members of the Neuro community
- Describe the initiative, highlighting its aims and how it advances the ability of researchers to practise open science at The Neuro
- List what concrete outcomes and outputs are expected
- Describe how and where the outputs will be shared
- Include a proposed budget outlining how much funding is requested (CAD $5,000 - $20,000), how the funds will be used, and other funding sources available to support the initiative
- Include a statement on how the initiative promotes Equity, Diversity, and Inclusion
Proposals will be evaluated by the Neuro’s Open Science Grassroots Initiatives Committee (GRC) at the GRC’s June meeting. If the $50,000 funding total is not reached another funding call will be made at a later date.
The GRC will assess proposals based on:
- The ability to promote open sharing of scientific outputs in line with The Neuro’s Open Science Guiding Principles,
- Feasibility is given the proposed budget, and
- Potential to make a concrete impact on the practice of Open Science at The Neuro.
Examples of Initiatives Funded in 2021 and Further Guidance
In 2021 TOSI, working with the GRC, identified and supported several Open Science initiatives arising from the Neuro community. The examples of funded initiatives below are provided to highlight some kinds of initiatives this funding call aims to support.
The Neurodegenerative Disease Knowledge Portal: An open-access genomics browser for neurodegenerative diseases
The Amyotrophic Lateral Sclerosis Knowledge Portal (ALSKP.org) is an open-access genomics browser composed of nearly 4000 ALS cases and 8000 ethnically matched controls that have been used by the community to access genomics data from ALS patients without the need for large, expensive computing resources.
This initiative will expand the ALSKP by building a larger Neurodegenerative Disease Knowledge Portal (NDKP) that contains genomics data from multiple neurodegenerative disease datasets such as Alzheimer’s disease (AD), and Parkinson’s disease (PD), frontotemporal dementia (FTD), and other allied neurological conditions. Users will be able to freely access genomic variants unique or common to all neurodegenerative diseases, as well as see their association metrics in each disease (e.g. significantly associated with a neurodegenerative disease or not.
NeuroLingo is a neuroscience outreach initiative founded and managed by graduate students in the Integrated Program in Neuroscience at McGill University. NeuroLingo helps guide IPN trainees in science communication, in part by running free public conferences where trainees give accessible TED-like talks about their research. TOSI Grassroots Funding in 2020 helped support the February 2021 Public Neuroscience Conference, as well as the summer conference in August 2021.
For more information about NeuroLingo, please see their website: https://www.neurolingo.org/
Four projects have been awarded funding through the Neuro Community Open Science Initiative call supported by the Tanenbaum Open Science Institute (TOSI). Proposals were submitted last fall to the Neuro’s Open Science Grassroots Initiatives Committee. Each of these funded projects facilitates the open sharing of scientific outputs with key stakeholders, including other researchers, patients, policymakers, and the public.
- The Neurodegenerative Disease Knowledge Portal
Sali Farhan (The Neuro), Mike Nalls (NIH - Center for Alzheimer’s and Related Dementias), Jason Flannick (MIT and Harvard)
- Video killed the written protocol: NeuroEDDU how-to vids
The Neuro Early Drug Discovery Unit (EDDU) team: Luisa Pimentel, Thomas Durcan, Paula Lépine, Meghna Mathur, Cecilia Rocha, and Sophia Penner
- Open Science Office Hours
Kendra Oudyk (The Neuro)
- Psychosis SpeechBank
Lena Palaniyappan (Douglas Mental Health University Institute)
To learn more about each of these Open Science initiatives, please see below.
Stay tuned for the next Neuro Community Open Science Funding Call announcement. Coming Soon!
The Neurodegenerative Disease Knowledge Portal: An open-access genomics browser for neurodegenerative diseases
The Amyotrophic Lateral Sclerosis Knowledge Portal (ALSKP.org) is an open-access genomics browser composed of nearly 4000 ALS cases and 8000 ethnically matched controls that have been used by the community to access genomics data from ALS patients without the need for large, expensive computing resources. In this project, we plan to continue to expand the ALSKP by building a larger Neurodegenerative Disease Knowledge Portal (NDKP) that contains genomics data from multiple neurodegenerative disease datasets such as Alzheimer’s disease (AD), Parkinson’s disease (PD), frontotemporal dementia (FTD), and other allied neurological conditions. Users will be able to freely access genomic variants unique or common to all neurodegenerative diseases, as well as see their association metrics in each disease (e.g. significantly associated with a neurodegenerative disease or not.
Video Killed the Written Protocol: The NeuroEDDU how-to-videos for working with iPSCs
At the Early Drug Discovery Unit (EDDU), we are active participants in fostering and practicing Open Science. As a result of our efforts, we have generated and published online a collection of 20+ openly available protocols ranging from handling induced pluripotent stem cells (iPSCs) to CRISPR editing, organoid generation and data analysis field. These protocols can be used by researchers and trainees across the globe and are openly available without restriction. These protocols, available on the Zenodo platform, have been viewed over 7000 times and downloaded more than 5,000 times within the past two years, ensuring what we do is getting into the hands of those that need it.
The pandemic has led researchers to become more visual, while at the same time putting technology at our fingertips to make our work more accessible. We propose to expand our portfolio of protocols by developing visual training guides. Our goal is a multi-language video collection—up to five of our written protocols will be converted to video format with closed captions. These videos will be available in a total of eight different languages for free and open access through our data portal, Vimeo channel and The Neuro’s YouTube channel. This material will be distributed through a Creative Commons license.
Open Science Office Hours (OSOH)
The goal of Open Science Office Hours (OSOH) is to empower students and researchers to make their work more open. We plan to do this by sharing Open Science resources, facilitating discussion, and offering individual assistance. We will start by engaging the neuroscience community at McGill University, and perhaps increase the scope in the future.
Many students learn Open Science skills at events like summer schools and hackathons, but might not have in-lab support for using what they have learned in their everyday research. Even principal investigators may need extra support to transition to a more open workflow. In 2020, we did a survey to assess the need for OSOH, and over half of our respondents listed “limited support” and “limited skills” as barriers to doing Open Science. OSOH aims to remove these barriers at the Neuro.
There will be two organizers consistently involved throughout the year. Each month will have a theme, such as “Open data” or “Open hardware”. At the beginning of the month, we will share resources on the theme, and people can sign up for help during office hours. At the end of the month, we will hold a live virtual discussion on the theme.
Psychosis SpeechBank: A collaboration for clinical linguistic research in psychiatry
Many adolescent onset mental disorders have a chronic intermittent course, with frequent and disabling relapses. We urgently need reproducible markers to track the illness course and enable wider implementation of early intervention at every stage of disorders such as psychosis. The form and content of speech provide the primary diagnostic and prognostic information for psychiatric practice. Our speech tracks our mental state; it remains the most accessible, remotely generated, inexpensively acquired, objectively recorded, and automatically analyzed digital health marker. There is a need for clinically validated longitudinal, patient-generated (i.e., not health-records based) speech data in psychosis for large-scale sustainable deployment of speech in digital healthcare.
The Diverse International Consortium of Research in Thought/Language & Communication in Psychosis has 110 international members with 26 sites across the world expressing interest in collecting speech samples using a uniform protocol. One of the main aims of this consortium is to create an open source SpeechBank for Psychosis. This project will generate the infrastructure to host this first-ever effort to create an open-access repository for speech data collected during clinical visits. As we develop project-specific funding applications, TOSI’s support will enable us to (1) create a secure cloud space to hold anonymized audio data from participating sites (2) disseminate a protocol (already developed by our Steering Committee) for harmonized speech sampling across sites that will contribute data to this SpeechBank, and (3) develop a pipeline for uniform pre-processing of audio data for computational analysis by the user community.
Furthermore, this will provide the first crucial step to create a repository for clinical linguistic data in the domain of mental health—an area where open clinical data is difficult to obtain.
Summary: As a memorial prize to honor Dale Hatrock's openness to methods development, the Hatrock Award for Open Methods Development is given annually by the Tanenbaum Open Science Institute to an outstanding trainee at The Neuro.
Background: Dale Hatrock was a graduate student in the Integrated Program in Neuroscience who passed away in 2021. Dale was passionate about developing methods and experimental protocols that enabled others to answer their research questions using the most advanced and technically-sound approaches. Dale was also highly committed to openly communicating his ideas so that his colleagues could learn, replicate, and build upon his rigorous methods.
Amount: $2000 CAD cash prize
Eligibility: Trainee (Undergraduate, Graduate or Postdoctoral Fellow) who is undertaking full-time research at The Neuro.
Requirement: The applicant must have a proven record in sharing openly to be considered for the award. Sharing can be done via an open access online methods portal (eg. protocols.io), or via pre-prints, or other open access publications. In addition, the applicant must provide a lay summary (200 words max) describing the relevance of the methods to the open study of neurological diseases.
Nomination: A call will be communicated annually, and applicants will be reviewed and ranked by the Awards & Prizes Team of the Open Science Grassroots (GRC) Committee.
2021 Award Winner: JUSTINE HANSEN
- Lead an open science effort to map neurotransmitter receptors to the human brain
- Developed methods for detecting gene expression and cognitive specialization across the brain
- Developed tools for brain map annotations (NeuroMaps)
- Teaching materials, tools, methods, atlases and publications are open access
*The inaugural award was made possible by a generous contribution from Ben Stecher, Patient Advocate and speaker at the 2021 Open Science in Action Symposium.