Call for Proposals: The Neuro Open Science Grants 2024Ěý
**ĚýNEW DEADLINE: Sunday, November 17th at 11:59 pm (ET). Please note that no applications will be accepted after the deadline. **
The Tanenbaum Open Science Institute (TOSI) is requesting proposals from members of the Neuro community with the goal of identifying and supporting initiatives that facilitate opening the practice of research and the sharing and reuse of scientific outputs with other researchers, patients, policy makers and the public.Ěý
Proposals should be submitted in PDF format via email to TOSI at tosi [at] mcgill.ca. Please use the 
Open Science Grants Application TemplateĚýto submit your application.
| Do you have any questions regarding eligibility or the application process? Unsure whether your project qualifies for The Neuro Open Science Grants?Ěý to attend our info session on October 25Ěýat noon. Registration is required. |
2024 Call Theme: Facilitating the Implementation of Open Science in every labĚý
The specific objectives of this year’s funding call are to:Ěý
- Increase the adoption of Open Science practices by research teams who are less familiar with them,Ěý
- Fill the gaps in Open Science by encouraging practices that have received less attention at The Neuro, andĚý
- Facilitate the dissemination of existing Open Science expertise to more research teams at The Neuro and beyond.Ěý
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While we welcome submissions for all Open Science projects, the 2024 competition will prioritize submissions that fall into one of the following three broad categories:Ěý
NewcomersĚý
We encourage applications from research teams that have not previously received TOSI support (i.e. awards, grants, etc.) and who are seeking to implement or expand their Open Science practices.Ěý
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Pairing for SuccessĚý
We encourage joint applications from members of a research team already implementing a given Open Science practice (previously funded by TOSI or not), paired with members of another research team who will benefit from the previous team's expertise to implement the given practice in their own lab, group or initiative.Ěý
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Ongoing and SpreadingĚý
We encourage submissions from existing Open Science projects (previously funded by TOSI or otherwise) that require funding for their sustainability and growth, with the express intention of spreading the adoption of Open Science to other research teams at The Neuro.Ěý
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What we are looking forĚý
We recognize that Open Science is multifaceted. We welcome projects that aim to facilitate, implement or expand one or more Open Science practices, such as:Ěý
- Open-source software toolsĚý
- Data management, standardization and sharingĚý
- Open methods (e.g., open lab notebooks, video protocols)Ěý
- Open educational material, guides, tutorialsĚýĚý
- Peer support for Open Science practicesĚý
- Community development and events (e.g., hackathons, forums, etc.)Ěý
- Science communication and outreachĚý
- New methods of scholarly communication (e.g., micropublications, reproducible pre-prints, open peer review)Ěý
- Patient partnership and outreach (e.g., co-design)Ěý
- Participatory/community/citizen scienceĚý
This list is intended to be illustrative but not exhaustive.ĚýĚý
Important note: This funding opportunity is not primarily intended to support the generation of research outputs (e.g., data collection or procurement of materials/reagents). Proposals should primarily aim to facilitate the sharing of research through the development of infrastructure, workflows, and pipelines, produce educational materials, or enable research communication with key stakeholders (e.g., researchers, patients, policymakers, and the public).Ěý
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Eligibility and Conditions
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All applicants must be from the Neuro community (i.e., trainee, researcher, project coordinators, clinician, and/or research associate).
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At least one PI must be part of the application.
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All outputs of initiatives supported by TOSI funds must be released as openly as practically possible. Video recordings and educational materials, for example, may be publicly accessible and distributed under a license and appear on Neuro channels and websites whenever possible. Software may be publicly shared under a license approved by the
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All outputs of TOSI-supported initiatives must acknowledge TOSI support in all communications and report progress to TOSI through a brief report to be submitted at the end of the project.
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Recipients must agree to present at the annual Neuro Open Science In Action symposium, or any other OS-related event, if requested.
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Amount
The total TOSI funding for this call is $100,000 CAD, and the goal is to fund 2-4 projects at up to $50,000 CAD per project.
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Key Dates
- Proposals may be submitted to TOSI starting on: Tuesday, October 8, 2024
- Info session: Friday, October 25, 2024, from noon to 1 pm
- Submission deadline: Sunday, November 17, 2024, at 11:59Ěýpm (ET).ĚýPlease note that no applications will be accepted after the deadline.
- Applicants will be informed as to whether their initiative has been chosen to receive funding within a month following the submission deadline.
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Submission
Proposals must be submitted in PDF format via email to TOSI at tosi [at] mcgill.ca. The proposal should be no longer than 2 pages and should be in 12-point font. The page limit includes figures, images, and/or tables. Please use this application template to submit your proposal.
- Identify the people involved and their roles.
- Describe the initiative, highlighting its goals and how it advances researchers' ability to practice Open Science in The Neuro.
- Describe whether and how the proposal is aligned with the strategic priorities of the 2024 funding call.
- List what concrete outcomes and outputs are expected. Include how and where the outputs will be shared.
- Include a proposed budget outlining how much funding is requested (up to $50,000 CAD/per project or initiative), how the funds will be used, and other funding sources available to support the initiative.
- Include a sustainability plan detailing how the initiative/project will be sustainable beyond this grant, if applicable.
- Explain how your initiative/project will recognize or promote support from TOSI.
- Include a statement about how the initiative/project promotes Equity, Diversity, and Inclusion (EDI).
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Evaluation process
Proposals will be evaluated by Neuro PIs and external members based on:
- Alignment with the strategic priorities of the 2024 funding call
- Alignment with The Neuro’s Open Science Guiding Principles
- Potential to make a concrete impact on the practice of Open Science at The Neuro
- Feasibility given the proposed budget
- The promotion of Equity, Diversity and Inclusion
- The sustainability plan and potential for continued impact beyond grant funding.
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Selection committee
Ed Ruthazer, Professor, The Neuro
JĂ©rĂ´me Fortin, Assistant Professor, The Neuro
Yang Zhou, Assistant Professor, The Neuro
Agah Karakuzu, Postdoctoral research fellow, UniversitĂ© de MontrĂ©alĚý
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The final decision will be made by the Neuro director, Dr Rouleau.Ěý
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Previous funding recipients
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2021 TOSI Neuro Community Open Science Initiative call
Four projects have been awarded funding through the 2021 Neuro Community Open Science Initiative call supported by the Tanenbaum Open Science Institute (TOSI). 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 LĂ©pine, 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
Summary
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
Summary
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 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)
Summary
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 Â鶹AV, 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
Summary
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.
2022 TOSI Neuro Community Open Science Initiative call
Four projects have been awarded funding through the 2022 Neuro Community Open Science Initiative call supported by the Tanenbaum Open Science Institute (TOSI). Each of these funded projects facilitates the open sharing of scientific outputs with key stakeholders, including other researchers, patients, policymakers, and the public.
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DĂ©jĂ vu: Development of an openly available knowledge portal for epilepsy presurgical evaluation
John Thomas (The Neuro), Birgit Frauscher (The Neuro), Jean Gotman (The Neuro) -
The White Matter Rounds: From monthly meetings to Open Science Network
Roberta La Piana (The Neuro), Sunita Venkateswaran (Children’s Hospital of Eastern Ontario), Ruwan Bedeir (The Neuro), Stephane Mukunzi (The Neuro) -
Open-source software to automatically detect epileptic spikes on EEG and MEG signals with AI
Sylvain Baillet (The Neuro), Julien Cohen-Adad (Polytechnique Montreal, CRIUGM, Mila) -
The PynaSuite, open-source software for neural data analysis
Guillaume Viejo (The Neuro), Adrien Peyrache (The Neuro)
To learn more about each of these Open Science initiatives, please see below.
DĂ©jĂ vu: Development of an openly available knowledge portal for epilepsy presurgical evaluation
Up to 40% of patients with epilepsy do not respond to anti-seizure medication, and this group requires up to 80% of the resources available for epilepsy care. The only possibility to cure drug-resistant focal epilepsy is surgery. The use stereotactic-EEG (SEEG) for pre-surgical planning has gained increasing popularity but remains limited, and clinicians rarely have access to a large number of patient case studies to optimize SEEG surgery planning and maximize surgical outcomes. This project aims to augment our limited knowledge on SEEGs and create an open, multicenter, Pan-Canadian directory of patients that could optimize pre-surgical planning for focal drug-resistant epilepsy.
The aims of the project are the following: (1) Develop a repository of epilepsy surgery patients based on patient clinical and investigation characteristics; (2) Implement a portal to retrieve information regarding patients with similar characteristics to a new surgical candidate; (3) Disseminate the portal description and details through open access publications; (4) Expand the database by recruiting additional patients through our collaborators from the Pan-Canadian epilepsy network.
The White Matter Rounds: From monthly meetings to Open Science Network
The White Matter Rounds Network is a one-of-a-kind initiative that brings together clinicians and scientists from 16 centers around the world interested in rare and atypical white matter disorders. The WM Rounds were initially local monthly meetings between MS specialists, radiologists, and geneticists to discuss clinical cases of rare white matter disorders that could be amenable for genetic testing, and involve colleagues from 16 centers in North and South America, Europe, and the Middle East. The overarching goal of this project is to formalize and extend the WM rounds in an international network to advance the quality of research in the field of rare white matter disorders by creating an Open Bioregistry of adult genetic white matter disorders that will accelerate the diagnosis of these rare patients. The synergy with patients’ associations enhances these collaborative efforts and facilitate access to rare patients’ populations.
An open-source software to automatically detect epileptic spikes on EEG and MEG signals with AI
Around 50 million people worldwide suffer from epilepsy, making it one of the most common neurological diseases globally. Epilepsy affects the central nervous system and prevents patients from living a normal life. Electroencephalography (EEG) and magnetoencephalography (MEG) recordings contain patterns of abnormal brain activity such as interictal epileptiform discharges (IEDs), also known as spikes, that are diagnosis signature neurologists are after when analyzing these long recordings. However, such signals are tedious and time consuming to manually analyze. The goal of this project is to create and distribute an open-source robust user-friendly AI-powered pipeline to epileptologists to study brain recordings and localize epileptic spikes.
To achieve the AI-powered analysis pipeline of EEG/MEG signals, we will create interoperability between Ivadomed and Brainstorm software. Brainstorm is a collaborative, open-source software dedicated to the analysis of brain recordings and Ivadomed is an open-source software toolkit allowing researchers to conveniently prototype deep learning models for applications in medical imaging. Physicians and researchers will be able to explore/analyse brain recordings signals (EEG and MEG) on the Brainstorm side, while leveraging powerful AI methods thanks to Ivadomed. This novel open-source software will be tailored to epileptologists and researchers enabling the study EEG/MEG brain recordings and automatic localization epileptic spikes without any programming knowledge.
The PynaSuite, open-source software for neural data analysis
An increasing number of laboratories are using simultaneous calcium imaging, electrophysiology and/or behavioral assays to address their scientific questions. The combination of multiple modalities results in complex data structures, increasing the difficulty of data analysis. Most data analysis toolboxes focus on a single modality. The aim of the project is to pursue the development of PynaSuite, a collection of open-source python software for cross-modal neural data analysis. This project has already been kickstarted with the creation and public release of Pynapple, a light-weight library for neurophysiological data analysis (). The data science ecosystem has widely adopted Python as a standard for programming and we are therefore using the same language.
The aims of this project are as follows: 1) Extend Pynapple and release a complete suite of software tools for the neuroscience community, openly and freely accessible. 2) Develop interactive tutorials and workshop hosted on an open platform and 3) Share knowledge through the organization of workshops to teach data analysis for the largest number.
2023 TOSI Neuro Community Open Science Initiative call
Two projects have been awarded funding through the 2023 Neuro Community Open Science Initiative call supported by the Tanenbaum Open Science Institute (TOSI). Each of these funded projects facilitates the open sharing of scientific outputs with key stakeholders, including other researchers, patients, policymakers, and the public.
- NeuroArch: A ParkCore initiative to support Open Science practices at NIMHANS, India through technology transfer and training in neuroinformatic toolkits
Nikhil Bhagwat (The Neuro), Sebastian Urchs, (The Neuro), JB Poline (The Neuro), Shweta Prasad (NIMHANS, Bangalore, India), Jitender Saini (NIMHANS, Bangalore, India)
- Â鶹AVXR – NeuroVR: Neuroscience and Virtual Reality Hackathon
​â¶Ä‹â¶Ä‹â¶Ä‹â¶Ä‹â¶Ä‹Mari Shishikura (The Neuro), Annabel Wing-Yan Fan (Montreal General Hospital), Daniel Gurman, (Montreal General Hospital), Eden Redman (CISSS Laval).
To learn more about each of these Open Science initiatives, please see below.
NeuroArch: A ParkCore initiative to support Open Science practices at NIMHANS, India through technology transfer and training in neuroinformatic toolkits
Currently the lack of diverse datasets has negatively affected the generalizability of our models and biomarkers. Particularly in neuroimaging, this has prevented adaptation of MRI-based measures in clinical practice due to poor reliability. This initiative aims at improving representation of diverse populations in neuroscience research by building collaborations in developing countries via Open Science, technology transfer, data harmonization, and training – starting with harmonization of Parkinson’s Disease datasets between The Neuro and NIMHANS, India.Ěý
Â鶹AVXR – NeuroVR: Neuroscience and Virtual Reality Hackathon
The NeuroVR Hackathon aims to foster a community within Â鶹AV to learn, experience, and share resources around extended reality (XR), including augmented, virtual, and mixed reality (AR, VR, and MR respectively). Â鶹AVXR promotes and organizes XR-related events for Â鶹AV graduate and undergraduate students to raise awareness and education on these emerging technologies and their intersection with neuroscience. They seek to provide a professional development platform for interested attendees to explore the
technologies, artworks, philosophies, and challenges of this new evolution in the technology space.
