Visual Proteomics Imaging

Overview

The Chan Zuckerberg Initiative (CZI) seeks to support 2.5-year challenge grants in the field of visual proteomics. The ability to view protein molecules in cells and monitor changes in their structure, quantity, distribution, and interactions is key to understanding what causes diseases and finding treatments and cures. This grant program will advance technology development for the field of visual proteomics and aim to obtain near-atomic resolution readouts inside the cell. The funding mechanism will be targeted investments in the form of challenge grants with specified proof-of-concept milestones.

Scientific Scope

The long-term goal of this RFA, part of CZI’s Frontiers of Imaging effort, is to drive technology development aimed at visualizing proteins and their interactions inside the cell. This funding opportunity is explicitly aimed at technology development. It is not intended to support question-driven basic or translational research, clinical trials, or drug development. Preliminary data is encouraged but not required.

Examples of research themes:

• Hardware and software development to enhance contrast and resolution for electron tomography, high-resolution correlated light and electron microscopy (CLEM), and FIB-SEM. 
• Sample preparation improvements for electron tomography, or high-resolution correlated light and electron microscopy (CLEM) approaches, and FIB-SEM.
• Software development or development of new computational techniques and algorithms for identifying protein molecules inside cells or segmenting cellular sub-structures.

We particularly encourage applications from:

• Researchers in disciplines outside of biomedicine who bring new technology, resources, or frameworks to studying proteins and their interactions inside of cells; 
• Women, underrepresented minorities, and members of underserved populations; and
• Early-career investigators, defined as principal investigators who have been in an independent faculty role for less than six years at the time of application, i.e. starting after their first position after February 2015. 

Desired Outcomes 

Successful outcomes for this RFA could include:

• Development of hardware and software that will enhance contrast and resolution;
• Development of hardware, software, or methods that will improve sample preparation; and 
• Development of new computational techniques and algorithms for identifying protein molecules inside cells.

Collaboration and Open Science

CZI seeks investigators who will contribute to a collaborative interdisciplinary network and the advancement of the visual proteomics field.

• Investigators and members of their labs will participate in annual meetings of all funded groups, smaller meetings focused on specific biological or technical topics, and regular webinars.
• Investigators and CZI staff will work together to identify resources and technology that can drive the imaging field forward.

• Investigators will commit to rapid dissemination of all resulting data, protocols, code, reagents, and results prior to publication through resources such as protocols.io, GitHub, Addgene, and preprints. Please see the Policies section for additional details.

• Applications may be submitted by non-profit and for-profit organizations, public and private institutions, such as colleges, universities, hospitals, laboratories, units of state and local government, companies, and eligible agencies of the federal government. As part of the application process, for-profit organizations may need to provide additional information on the charitable purposes of the proposal. Grants are not permitted to individuals, only to organizations.
• Organizations may be based in any country.
• Each application should designate one principal investigator (PI) as the Coordinating Principal Investigator (Coordinating PI). The Coordinating PI will act as the administrative contact between CZI and all PIs on the grant (Co-PIs). The Coordinating PI must submit the application on behalf of all PIs. The Coordinating PI must be affiliated with the institution submitting the application, and grant funds will be awarded to that institution, which will take responsibility for distributing funds to any other institutions. Note that institutions outside the U.S. may not subcontract to U.S. institutions, so please be mindful when selecting the Coordinating PI/institution.
• Each application should have a minimum of one PI, but may designate up to three total PIs (one Coordinating PI and up to two Co-PIs).
• PIs may only serve as the Coordinating PI on one application, but may serve as a Co-PI on applications different from the one they submitted.
• Co-PIs may serve as a Co-PI on multiple applications.
• PIs/Co-PIs on one application may be employed at the same or at different institutions. 
• PIs and Co-PIs must hold a PhD, MD, or equivalent degree.
• PIs and Co-PIs must each run laboratories in which they control their budget, their space, and their research. Independence in an academic setting is typically demonstrated by a full-time faculty appointment, a tenure-track position, allocated space, a start-up package, and institutional commitment as defined or verified in a letter from a department chair or equivalent. Independence may be defined differently in other organizations. Note: an upload of the letter or proof of independence is not required at the time of application.
• CZI encourages applications from underrepresented minorities, women, and early-career scientists.
• All grants will be made in compliance with the US Treasury Department’s Office of Foreign Asset Control (OFAC) program. For additional information regarding OFAC sanctions, please refer to the U.S. Treasury Department’s resources.
• Facebook employees, including employees of any subsidiary Facebook entities, are not permitted to apply. 
• CZI reserves the sole right to decide if an applicant and applicant organization meet the eligibility requirements. 
• CZI reserves the right to request budget changes upon award.

CZI suggests that you consult your home institution to determine eligibility to apply for this grant and your institutional policy on indirect costs. For questions about eligibility for this award or the application process, please contact us in advance of the proposal deadline at sciencegrants@chanzuckerberg.com. Deadline extensions will not be granted. 

The Chan Zuckerberg Initiative uses SurveyMonkey Apply (SMApply) as its grants management portal. All applications must be submitted through this portal (https://apply.chanzuckerberg.com). SMApply is configured to work best using the Google Chrome browser. It is recommended that you familiarize yourself with this portal well in advance of any deadlines. Deadline extensions will not be granted.

Application Specifics:

• Eligibility: Please refer to the above Eligibility section of the RFA announcement.
• Award Period: Proposals should be 2.5 years (30 months) in duration with a project start date of no earlier than August 1, 2021. Actual start date may vary.
• Award amount: Because hardware, software, and protocol development projects that may be supported by this RFA likely require different resourcing levels, a budget limit has not been set on a per project basis. Award amounts will be project specific.
• Budgets for Full Applications will be evaluated for appropriateness relative to the scope of work proposed. Indirect costs cannot exceed 15% of direct costs. 
• Number of Principal Investigators (PI and Co-PIs): Each application should have a minimum of one PI, but may designate up to three total PIs (one Coordinating Principal Investigator and up to two Co-Principal Investigators (Co-PIs)).
• Institutional sign-off is required.

The application consists of the following sections (called tasks in the grants portal): Coordinating PI Details, Equal Opportunity & Diversity, Organization Details for Coordinating PI, Project Details, Project Proposal, Budget Description, Active Grant Support, Biosketches for Coordinating PI and Co-PIs, and Letters of Commitment.

• Coordinating PI Details: Complete all fields in this task; all fields are required. The information entered should be for the Coordinating Principal Investigator (Coordinating PI), who will be the person submitting the application on behalf of the team. The Coordinating PI will take responsibility for managing the group collaboration and be the administrative point of contact for CZI and any partners. Information about the Co-Principal Investigator(s) on the proposal should be entered where requested in the Project Details part of the application.
  • Name and email (auto-filled): To edit your name or email, please do so in your account information by clicking your name in the upper right corner and clicking My Account in the dropdown menu. 
  • Degrees.
  • Organization, Title/Position, Department or equivalent.
  • Career status: Select early-career (faculty 0 to 6 years), mid-career (faculty 6+ to 10 years), or neither. Note: Early- or mid- career status is not required to be eligible for this RFA.
    • Early-Career Definition: In the context of this RFA, an early-career investigator is someone who has been in an independent faculty position (or equivalent) for zero to six years at the time of application, i.e. have started their first independent position between February 17, 2015 and February 17, 2021. 
    • Mid-Career Definition: In the context of this RFA, a mid-career investigator is someone who has been in an independent faculty position (or equivalent) for more than six to 10 years at the time of application, i.e. have started their first independent position between February 17, 2011 and February 17, 2015. 
  • Short narrative biography of the Coordinating PI (maximum of 100 words).
  • ORCID iD: Enter in format XXXX-XXXX-XXXX-XXXX. ORCID iDs are unique, digital identifiers that distinguish individual scientists and unambiguously connect their contributions to science over time and across changes of name, location, and institutional affiliation. ORCID iDs will be used to streamline reporting in our applications and grant reports to reduce the burden on grantees. For more information, please visit https://orcid.org/register. (Please contact us at sciencegrants@chanzuckerberg.com if you wish to opt out).

• Equal Opportunity & Diversity: CZI Science supports the science and technology that will make it possible to cure, prevent, or manage all diseases by the end of this century. Everyone is affected by disease, yet different communities are affected by or experience disease in different ways. Moreover, due to systemic barriers, the scientific enterprise itself is not a place where all voices and talents thrive. We believe the strongest scientific teams — encompassing ourselves, our grantees, and our partners — incorporate a wide range of lived experiences and perspectives that guide them to the most important unsolved problems. To enable our work, we incorporate diverse perspectives into our strategy and processes, and we also seek to empower community partners to engage in science.

We track demographic information associated with applications submitted to CZI in response to our open calls. Based on our learnings, we take steps to broaden or adjust our strategies to improve our reach and to help ensure members of underrepresented or marginalized groups in science are aware of CZI opportunities and able to apply. Please note that answering all questions below is voluntary, and demographic information will not be used to make final grant funding decisions. All responses will be shared only with limited personnel, who will use that information only for the purposes described in this paragraph. 

If you have any additional questions about why we ask this, what we do with the data, or to share suggestions for improvement, please reach out to sciencegrants@chanzuckerberg.com.

The information below may be entered for the Coordinating PI, who will be submitting the application on behalf of the team. Please note that completing the below is voluntary, and demographic information will not be used to make final grant funding decisions.

• What is your race/ethnicity? (optional)
• What is the year of your last academic degree? (optional)
• What is your gender? (optional)
• Are you transgender? (optional)
• Are you a member of the LGBTQ community? (optional)

The information below may be entered for the Co-Principal Investigators listed in the Project Details section. Please note that completing the below is voluntary, and demographic information will not be used to make final grant funding decisions. Please also let your Co-Principal Investigators know if you choose to enter the below in case they object to your providing that information to CZI.

• Do any of the Co-Principal Investigators self-identify as one of the following? Woman, Man, Non-binary/Third gender, Prefer not to state, Prefer to describe (optional)
  • If yes, how many of the listed Co-Principal Investigators self-identify as one of the above gender identities? Please do not include requested information on a per person basis; we are looking for aggregated information (optional)
• Do any of the Co-Principal Investigators self-identify as one of the following? Two or More Races, Black and/or African American, Asian, White, Hispanic or Latinx, Middle Eastern or North African, Native Hawaiian or Other Pacific Islander, American Indian or Alaska Native, Prefer not to state, Prefer to describe (optional)
  • If yes, how many of the listed Co-Principal Investigators self-identify as one of the above race/ethnicities? Please do not include requested information on a per person basis; we are looking for aggregated information (optional)
• Organization Details for Coordinating PI: Complete all fields in this task; all fields are required. The information entered should be for the organization of the Coordinating Principal Investigator (Coordinating PI), who will be the person submitting the application on behalf of the team. The Coordinating PI must be affiliated with the organization listed, and grant funds will be awarded to this organization, which will take responsibility for distributing funds to the institutions of the other team members.
  • Organization name/Street address/City/State/Country/Website.
  • Type of organization (academic/non-profit, industry/company, government, other).
  • Tax ID: Enter your organization’s Employer Identification Number (EIN), as assigned by the Internal Revenue Service in the 9-digit format (XX-XXXXXXX; 10 characters total). Foreign organizations or others who do not have an EIN should enter 44-4444444. 
  • Organizational/Administrative Contact: List the name and contact information for the administrative contact to discuss additional information needed, if selected for award.
    • First name, Last name, Title/Position, Email.
  • Signing Official: List the name and contact information for the person authorized to sign on behalf of your organization.
    • First name, Last name, Title/Position, Email.
  • Press Contact / Public Relations Official: List the name and contact information for the person to discuss press releases and media.
    • First name, Last name, Title/Position, Email.
  • Institutional Approval Form: Upload as a single PDF. This form should be reviewed and signed by a person authorized to sign on behalf of your organization agreeing to the stated institutional and investigator requirements and commitments on data, resource sharing, and publication policies, as well as endorsing/verifying your application materials and confirming their ability to receive funding for the proposal. In the event of an award, all funds will be awarded to the Coordinating PI institution as the prime institution, and the Coordinating PI institution will be responsible for ensuring compliance of all of the terms, including compliance of all partners/subcontract institutions. These policies are non-negotiable so this form should only be signed if the organization is able to comply with the terms as stated. While CZI does not require sign-off by all of your partner institutions, please refer to what your institution requires. Note: digital signatures are permitted as long as the document is not encrypted or password-protected.

• Project Details: Complete all fields in this task; all fields are required. 
  • Project Title: Project title is limited to 75 characters, including spaces. If you need to edit your proposal title, navigate to your application summary page, click on the three dots to the right of the application title (next to the Preview link) and select Rename from the dropdown menu.
  • Project Purpose: Summarize your research project; limited to one sentence (maximum of 255 characters including spaces). Please use a third-person voice.
    • Example: To develop a comprehensive, validated atlas of the human kidney at single-cell resolution open to the entire scientific and clinical community.
  • Abstract/Project Summary: Describe your project in brief (maximum of 250 words). Please use a third-person voice (example). 
  • Milestones: Summarize the main milestones for your project (list format, maximum of 250 words). 
  • Diversity, Equity, and Inclusion (DEI) Statement: Advancing DEI is a core value for CZI, and we are requesting information on your efforts in this area. Please describe how your proposal or your team seek to promote diversity, equity, and inclusion in this project (maximum of 250 words). 
  • Type of Project: Designate if the project is a hardware, software, and/or protocol development project. Check all that apply.
  • Amount Requested: Enter total budget amount requested in USD, including indirect costs; this number should match the total described in the Budget Description. Enter whole numbers only (no dollar signs, commas, or cents).
  • Co-Principal Investigators: Indicate the number of Co-Principal Investigators, not including the Coordinating PI. Complete the table with the following information for each Co-PI (maximum of two). Do not include the Coordinating PI in this section. You may need to use the scroll bar at the bottom of the table to scroll right to view and to complete all fields. Alternatively, you can tab to move through and complete the fields. For each Co-PI, please provide:
    • Co-PI name, Title/Position, Degrees, ORCiD ID (format: XXXX-XXXX-XXXX-XXXX), Email, Career status 
      • In the context of this RFA, an early-career investigator is someone who has been in an independent faculty position (or equivalent) for zero to six years at the time of application, i.e. have started their first independent position between February 17, 2015 and February 17, 2021, and mid-career as someone who has been in an independent faculty role (or equivalent) for more than six to 10 years at the time of application, i.e. have started their first independent position between February 17, 2011 and February 17, 2015. 
    • Organization Name, Country, Website
    • Type of organization (drop down menu: academic/non-profit, industry/company, government, other).
    • Tax ID: Enter your organization’s Employer Identification Number (EIN), as assigned by the Internal Revenue Service in the 9-digit format (XX-XXXXXXX; total of 10 characters). Foreign organizations or others who do not have an EIN should enter 44-4444444.

• Project Proposal: Upload your project proposal as a single PDF; font must be Arial 11 points or larger and margins must be at least one-half inch (top, bottom, left, and right) for all pages (letter size required). Include the following sections:
  • Proposal Body: (maximum of 2500 words, which includes 250 words for the Abstract)
    • Abstract: Copy your Abstract/Project Summary entered in the Project Details section here. 
    • Background: Describe the current state-of-the-art technology you are working on. 
    • Project Goals: Detail the technology goals of the project.
    • Significance: Describe the scientific significance if the technology goals are met.
    • Project Plan: Describe clearly the research and development strategy to be employed, main milestones, expected outcomes, deliverables, and associated timeline.
  • Figures (optional): Limited to two pages, inclusive of legends. Figure legends do not count towards the word count.
  • References Cited in your proposal: No word/page limit; include complete source references.
• Budget Description: Upload in PDF format; font must be Arial 11 points or larger and margins must be at least one-half inch (top, bottom, left, and right) for all pages (letter size required); no page limit. Provide a detailed description of the costs to be funded by this grant at a high level and in narrative or tabular form, outlining costs for personnel (including names, if known), supplies, equipment, travel, meetings/hackathons/sprints, subcontracts, other costs, and up to 15% indirect costs (excluding equipment and subcontracts). Tabular format preferred.
  • Indirect costs are limited to up to 15% of direct costs. Indirect costs may not be assessed on capital equipment or subcontracts, but subcontractors may include up to 15% indirect costs of their direct costs.
  • Budget should be requested in US dollars. 
  • International grantees must use all grant funds exclusively for activities conducted outside the United States of America. Travel expenses to the United States (including round-trip tickets) should not be covered from the requested grant funds. Any attendance at CZI meetings in the US will be covered by CZI outside of requested grant funds.
  • Application budgets must reflect the actual needs of the proposal. The Chan Zuckerberg Initiative will work closely with successful applicants to arrive at a mutually acceptable budget after review.
• Active Grant Support: Upload in PDF format; font must be Arial 11 points or larger and margins must be at least one-half inch (top, bottom, left, and right) for all pages (letter size required); no page limit. List all active grant support for Coordinating PI and Co-PIs (source, project title, description, dates of funding, amount per year (directs + indirects)). 
• Biosketches for Coordinating PI and Co-PIs: Upload the biosketches in PDF format for the Coordinating PI and for each of the Co-PIs. Biosketches can be uploaded in a combined single PDF or one PDF for each Co-PI; maximum of five pages per biosketch; NIH format or similar. Do not include any biosketches for any additional collaborators beyond the Coordinating PI and Co-PIs, as listed.
• Letters of Commitment: Upload a signed letter from each Co-PI briefly describing the role and contribution of the Co-PI to the overall team and project. Letters should be in PDF format (letter size) and can be uploaded in a combined single PDF or one PDF for each Co-PI. A letter is not needed from the Coordinating PI, but since this section is required, please upload a blank sheet if there are no Co-PIs in order to complete this section and submit your application. Note: digital signatures are permitted as long as the document is not encrypted or password-protected.

The formatting and component requirements, including word and page limits indicated above, will be enforced by the review team. Any submitted materials that exceed the word and page limits or do not follow the requirements will not be considered during the application review process.

QUESTIONS?

For administrative and programmatic inquiries pertaining to this RFA, please contact sciencegrants@chanzuckerberg.com. For technical assistance with SMApply, please contact support@smapply.io or while logged into SMApply, click on the information ”i” link in the upper right corner and submit a help request ticket.

The Chan Zuckerberg Initiative’s core values center around people, technology, collaboration, and open science. We adhere to those values in both proposal selection and evaluation of progress.

CZI will evaluate all applications for scientific merit through independent expert review. Final decisions will be made by CZI staff in consultation with our scientific advisors. There is no expectation of any specific number of awards, and the Chan Zuckerberg Initiative reserves the sole right to not recommend the funding of any applications. CZI does not provide feedback on decisions for unfunded proposals.

Selection of awardees will be based on:

• The quality of the proposal, and the expertise and capacity of the group for addressing the proposed project.
• Significance and potential impact of the project.
• Potential of the awardee to contribute to and benefit from a collaborative interdisciplinary network.

• Funds from this award are intended to support research activities. Grants are made to institutions on behalf of the named award recipients, and reasonable flexibility on how these funds are utilized is allowed, provided that funds are used to support research activities related to the project. A detailed budget is required.
• For awarded projects, financial statements and progress reports will be due at the conclusion of each grant year. Specific deliverable requirements will be outlined in the award notification. Grantees of funded projects will be required to participate in regular meetings, including annual scientist meetings. Travel support for these meetings will be provided by CZI separately from the requested grant funds. 
• Grantees may obtain funds for their research from other funding sources, provided that there is no conflict with meeting the terms of the CZI award.
• Unused research funds may be carried over to the following year, and requests for no-cost extensions will be considered.
• Indirect costs cannot exceed 15% of direct costs. Indirect costs may not be assessed on capital equipment or subcontracts, but subcontractors may include up to 15% indirect costs of their direct costs.
• International grantees must use all grant funds exclusively for activities conducted outside the United States of America. 
• Ethical conduct: CZI advocates the highest standards for the ethical conduct of research. In addition to requirements of their own countries, grantees should adopt procedures for the use of animals in research and for the ethical treatment of human subjects and tissue donors, including obtaining their written informed consent. CZI regards the policies of the National Institutes of Health as a strong model for such procedures.
• Data, publication, and dissemination policies:​ To accelerate scientific discovery and collaboration, CZI supports a consent, sharing, and publication policy for open and rapid dissemination of proposal results, including methods, data and reagents, and a policy for software development that maximizes accessibility, reuse, and shared development. Under rare circumstances, exceptions to the above may be considered where there are specific situations that make meeting these goals impossible or counterproductive to the project. 
  • Software code: CZI requires sharing of software code developed by its grantees generally to be made publicly available on GitHub (or a similar public service). All new code must be released under a permissive open source license (MIT, BSD 2-Clause, BSD 3-Clause, or Apache v2.0). All pre-existing and derivative code should be licensed under the most permissive license possible, given the licensing terms of the pre-existing code. All analysis packages must be released through the appropriate language-specific package manager (e.g., PyPi for Python, Bioconductor and CRAN for R) with documentation, example data, and interactive demos (e.g., Jupyter notebooks), and the use of Docker or similar container technologies to ensure portability and reproducibility. Software code supported by CZI should be archived for long-term digital preservation and citability, when applicable.
  • Content and data sharing: ​CZI is committed to developing and using platforms that disseminate data openly and freely. Any datasets either curated or generated through the proposal should be made publicly available and easily accessible through an appropriate data repository, when applicable, under an Open Definition conformant license. Ideally data sets would not include personally identifiable information, but if they do, consent to sharing the data should be obtained. Metadata, documentation, and intended use cases, as appropriate should be made available under an Open Definition conformant license, preferably CC0 or CC BY/CC BY SA for content that requires explicit attribution. 
  • Publications:​ To encourage rapid dissemination of results, any publications related to this funded work must be submitted to a preprint server (such as bioRxiv, medRxiv, arXiv, or any appropriate preprint repository), at or before the first submission to a journal. Experimental protocols should be made publicly available through a protocol sharing service, such as protocols.io. CZI requests that scientific publications, preprints, and presentations that result from this award acknowledge support from this funding.
  • Reagent sharing: Resources and reagents developed with this funding support should be available for rapid dissemination to the community, where possible in an accessible community repository, such as Addgene (for plasmids/DNA reagents/viruses) and Jackson Labs (for model systems lines), etc. This requirement applies to cell lines, transgenic organisms, plasmids/clones, antibodies, and other reagents. 
  • Consent: All human tissues should be adequately and fully consented to permit full sharing of the resulting data and any resulting tools, in accordance with laws and regulatory requirements. Any desired exceptions to this policy must be identified at the time of application, and such requests may affect the application’s chance of success. We are aware that there may be circumstances where broad consent may be challenging, and in some cases consent may be subject to revocation; we encourage investigators to discuss these cases with CZI scientific staff.
  • Intellectual property rights: CZI does not require assignment of ownership to any data, published results, or any other intellectual property that results from the work funded by these grants, but will have the same rights generally granted to others in the permissive licenses described above. CZI supports and promotes policies that enable results and technologies to have the broadest reach and impact. To this end, all newly developed software should be made available through permissive open source licenses as described more fully above. Other technology and intellectual property rights (such as patents) should be made freely available for all academic and non-commercial use, and where intellectual property rights are commercialized, they should generally be subject to non-exclusive commercial licenses that enable broad availability and dissemination. 

• Applications selected through this process will either be funded by the Chan Zuckerberg Initiative Foundation (CZIF) or recommended for funding through the Chan Zuckerberg Initiative Donor-Advised Fund (DAF) at the Silicon Valley Community Foundation (SVCF).

All submitted applications will be kept confidential, except (1) as necessary for our evaluation or to comply with any applicable laws; and (2) to the extent that the application is made public or available to others without a duty of confidentiality through no fault of CZI. Notwithstanding, successfully funded proposals may be made publicly available and/or shared with other grantees or collaborators. Unfunded proposals will remain confidential as provided herein; however, information, including brief summaries of the proposed projects, project metrics, and the types of organizations that have applied for funding, may be made publicly available in aggregate form. Application materials will not be returned to applicants.