Coming Soon: Essential Open Source Software for Science

The Chan Zuckerberg Initiative will soon invite applications for open source software projects that are essential to biomedical research. Applicants can request funding between $50k and $250k for one year. This RFA is the first of a series. CZI will invite applications during three distinct cycles, with rounds beginning June 18, 2019; mid-December 2019; and mid-June 2020. Read our Medium post to learn more.

Opportunity

The Chan Zuckerberg Initiative invites applications in support of open source software projects that are essential to biomedical research. The goal of the program is to support software maintenance, growth, development, and community engagement for these critical tools.

Overview

Open source software is critical to modern scientific research, advancing biology and medicine while providing reproducibility and transparency. Hundreds of software packages, libraries, and applications have become essential tools for research—so much so that many researchers could not continue their work without them. Despite its importance, a majority of research software is undervalued and lacks funding for maintenance, growth, development, and community engagement. Also, those who work on such software often lack credit and recognition.

In a new effort to support open source software for science, the Chan Zuckerberg Initiative (CZI) seeks applications for software projects that are essential to biomedical research, have already demonstrated impact, and can show potential for continued improvement. Grants will be for a one-year period with the potential to apply for renewal in future cycles.

With this program, we aim to provide projects with resources to support their tools and the communities behind them. Whether it’s hiring an additional developer, improving documentation, addressing usability, improving compatibility, onboarding contributors, or convening a community, we hope our support can help make the computational foundations of biological research more usable and robust.

Details

CZI currently supports several areas of basic science and technology with the goal of making it possible to cure, prevent, or manage all diseases by the end of this century. This program aims to support software tools that are essential to this mission. Applications for two broad categories of open source projects will be considered in scope:

  • Domain-specific software for analyzing, visualizing, and otherwise working with the specific data types that arise in biomedical science (e.g., genomic sequences, microscopy images, molecular structures). Software will be considered out of scope if it primarily serves domains outside biomedical science (e.g., physics, astronomy, earth sciences). While we appreciate that other communities may want to explore new extensions of their software to the life sciences, such applications are unlikely to be selected.
  • Foundational tools and infrastructure that enable a wide variety of downstream software across several domains of science and computational research (e.g., numerical computation, data structures, workflows, reproducibility). While foundational tools will be considered in scope for this program, they must have demonstrated impact on some area(s) of biomedical research.

Applications can request funding between $50k and $250k total costs (inclusive of up to 15% for indirect/overhead costs). Budgets will be evaluated for appropriateness relative to the scope of work proposed. Acceptable use of funds includes, but is not limited to:

  • Salary support for staff (full-time, part-time, or contract): developers, contributors, technical writers, community managers, product managers, project managers, user experience researchers, community educators, or other roles that directly support the project;
  • Hackathons, sprints, outreach, or other forms of community engagement and support for community participation;
  • Operational needs such as cloud computing, storage, networking, or continuous integration services; and
  • Support for work that bridges projects or ecosystems, including better coordination across projects that are similar, dependent on one another, or frequently used together.

CZI staff will further support awarded proposals by convening grantee meetings and helping connect open source software developers to scientists, including other CZI-funded grantees and members of the broader scientific community.

Eligibility
  • We welcome applications from any country, provided the proposed work is compliant with the US Treasury Department’s Office of Foreign Asset Control (OFAC) program. For additional information regarding OFAC sanctions, please refer to the US Treasury Department’s resources.
  • 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. Open source projects operating independently must be affiliated with an organization, as described below.
  • If an application does not come from an organization eligible to receive and distribute funds (e.g., an academic institution), the applicant may designate a fiscal sponsor (e.g., NumFOCUS, Code for Science & Society, or others). We encourage projects that require fiscal sponsorship to contact the appropriate organizations early in the application process. If your application requires a fiscal sponsor and you are unable to secure one by the application deadline, you may still apply, but your application should explain the financial situation of the project and how you are planning to receive and use the funds if successfully awarded. We will prioritize applications already able to receive and use funds at the time of application.
  • We will consider and potentially fund multiple applications from the same organization, multiple applications related to the same open source project(s), and multiple applications that include the same staff and/or project contributors. However, the proposed work in such applications must be distinct.
  • We encourage proposals supporting multiple open source projects. In the case of applications for work spanning multiple projects, one individual must complete the application and a single organization or fiscal sponsor must coordinate the dispersal of funds to the members of the collaboration. Note that foreign institutions may not subcontract to US institutions, so please be mindful when selecting the applicant organization.
  • We believe that the strongest teams incorporate a wide range of voices. Those underrepresented in science and technology are strongly encouraged to apply.
  • Facebook employees, including employees of any subsidiary Facebook entities, are not permitted to apply for this grant.
  • CZI reserves the sole right to decide if an applicant and applicant organization meet the eligibility requirements.

For questions about eligibility, please contact us in advance of the application deadline at sciencegrants@chanzuckerberg.com. Deadline extensions will not be granted.

Application Requirements

Key dates

We invite applications for consideration for funding during three distinct cycles, with rounds beginning June 18, 2019; mid-December 2019; and mid-June 2020.

All dates for the second and third cycles are subject to change. Please sign up for our mailing list to stay updated on these dates as they are announced and future funding opportunities.

Grant duration

Grants will be awarded for a one-year duration. The actual start date may vary based on specific needs (timing of hiring, etc.) and will be agreed upon after the grant is awarded. Successful awardees from the first cycle are eligible to apply for a renewal in the third cycle, with a budget and scope of work that can be either similar or altered depending on project needs. Renewals will be evaluated alongside new applications. No-cost extensions will be considered.

We will evaluate the success of this program during the initial cycles, with the possibility of extending it so that groups funded in the second and third cycles can apply for renewals in 2021, but no additional cycles are confirmed at this time.

Application specifics

All applications must be completed and submitted through the Chan Zuckerberg Initiative’s online grants management portal. We recommend that you familiarize yourself with this portal well in advance of the submission deadlines. Detailed application instructions, including required elements of the application, are available below in the Detailed Application Instructions section, as well as in the grants management portal.

Cycle
1
Portal opening date
June 18, 2019 by 9 am Pacific Time
Application due date
August 1, 2019 by 5 pm Pacific Time
Notification of decisions
Late October 2019
Earliest start date of grant
December 1, 2019
Cycle
2
Portal opening date
Mid-December 2019
Application due date
February 1, 2020
Notification of decisions
Late April 2020
Earliest start date of grant
June 1, 2020
Cycle
3
Portal opening date
Mid-June 2020
Application due date
August 1, 2020
Notification of decisions
Late October 2020
Earliest start date of grant
December 1, 2020
Detailed Application Instructions

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.

For the purpose of the application, we will use the following terms:

  • Applicant: The person submitting the application materials on behalf of the project(s)
  • Organization: The organization directly receiving and distributing funding
  • Project(s): The software project(s) that will be supported by the funding
  • Proposal: The proposed use of funding
  • Key Personnel: People involved in the project(s) described in the proposal and supported by the funding

The application consists of the following sections (called tasks in the grants portal): Applicant Details Part I, Applicant Details Part 2, Organization Details, Proposal Details, Number of Open Source Project(s), Open Source Project Details, Budget

  • Applicant Details Part 1: Complete all fields in this task; all fields are required. The information entered should be for the individual submitting the application who will act as the main person responsible for the application and as its point of contact. Information about other Key Personnel 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
    • Current Employer
    • Title/Position
    • CV of the Applicant (the person submitting the application): Upload in PDF format; font must be 11 points or larger and margins must be at least one-half inch (top, bottom, left, and right) (maximum of two pages)
      Include current and recent employment, education history, and references to any major publications and software authored.
  • Applicant Details Part 2: Complete all required fields in this task. The information entered should be for the individual submitting the application who will act as the main person responsible for the application and as its point of contact. Please note demographic information will not be used as a basis for review.
    • Work phone (required)
    • Highest degree (required) and year granted (optional)
    • Additional degrees and year granted (up to three) (optional)
    • Gender (optional)
    • Race/Ethnicity (optional)
    • Short narrative biography of the applicant (maximum of 100 words) (required)
  • Organization Details: Complete all sections in this task; all sections are required. The information entered should be for the organization that would be directly receiving and distributing funding if a grant is successfully awarded (e.g., academic institution, fiscal sponsor). Note that this may be different from the Applicant’s main affiliation.
    • Type of Organization: academic, other non-profit, industry/company, government, fiscal sponsor, fiscal sponsor not yet identified, or other (required)
    • Details:
      • Organization name, Address, City, State/Province and Country
      • Tax ID: If your organization has an Employer Identification Number (EIN), as assigned by the United States Internal Revenue Service, enter it in the 9-digit format (XX-XXXXXXX; 10 characters total). Organizations who do not have an EIN should enter 44-4444444
    • Institutional Approval Form: This form should be reviewed and signed by a person authorized to sign on behalf of your organization or fiscal sponsor (whichever organization that will be receiving the grant funds, if the application is selected for funding), agreeing to the stated institutional and applicant 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. Applicants may be asked to provide additional information on the governance of the proposal and its ability to receive and use the funds, if successfully awarded. If you do not have an organization identified to receive funds, the applicant should sign the form and note on the form that a fiscal sponsor has not been identified. Upload as a single PDF. This form is not set up to be completed online with a digital signature so you will need to print it, have it signed, and then upload as a PDF (required).
  • Proposal Details: Complete all required sections in this task.
    • Proposal Title: Auto filled. 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 (maximum of 75 characters, including spaces)
    • Proposal Purpose: One sentence (maximum of 255 characters including spaces)
    • Abstract/Proposal Summary: A short summary of the application ​(maximum of 250 words)
    • Proposal: Upload your proposal as a single PDF; font must be 11 points or larger and margins must be at least one-half inch (top, bottom, left, and right) for all pages. Include:
      • Body:​ (maximum of 2000 words). Should include the following parts:
        1. Goals
          • The objective and expected outcomes of the proposal
          • A description of how the applicant will determine if the goals of the proposal have been successfully met
        2. Work plan
          • A description of the proposed work the applicants are requesting funding for, including resources the applicants will provide that are not part of the requested funding. For software development related work (e.g., engineering, product design, user research), specify how the work fits into the existing project roadmap. For community outreach related activities (e.g., sprints, training), specify how these activities will be organized, the target audience, and expected outcomes
        3. Existing support
          • Current and recent financial support for the project(s), including duration, amount in USD, and source of funding
      • Figures (optional): Limit to one page, inclusive of legends
      • References cited in your proposal: No word/page limit
    • Milestones and Deliverables (required): List expected milestones and deliverables, and their expected timeline. Be specific and include (where possible) any goals for metrics the project(s) are expected to reach upon completion of the grant (maximum of 500 words)
    • Diversity and Inclusion Statement (optional): Upload as a single PDF; font must be 11 points or larger and margins must be at least one-half inch (top, bottom, left, and right) for all pages (one page maximum)
      • Describe what efforts the project(s) named in this proposal have undertaken to increase the diversity of contributors
  • Number of Open Source Project(s): Indicate the number of software projects involved in your proposal (up to five). Each proposal can request funding for work that includes up to five open source projects. If multiple projects are involved, details must be entered for all of them. If your proposal involves more than one project, mark this step as complete so you can fill in the details for additional projects. This section must be marked complete in order to proceed to the Open Source Project Details #2 – #5 tasks. To change the number of projects indicated after marking as complete, click the three dots in the upper right of the task and select edit, which will re-open the task.
  • Open Source Project Details #1 – #5: Depending upon your answer to the “Number of Open Source Project(s)” task above, the corresponding number of tasks—one for each project indicated above—will appear (Open Source Project Details #1 will appear by default). You may need to scroll down using the scroll bar in the task menu on the left side of the page to see these tasks. For each task/project in this section, please complete the following; all URLs should be in the format https://example.com:
    • Project Details: Complete the following for each software project that will be supported by the grant:
      • Project name (required)
      • Homepage URL (required)
      • Main code repository (e.g. GitHub URL) (required)
      • DOI of major publication(s) describing project (if applicable)
      • Social media handles (if applicable)
      • Short description of the project (maximum of 200 words) (required)
    • List of Known Key Personnel: Key personnel are people involved in the project who will be supported by the grant if the application is successful. Complete the following for each (up to 5) (required); enter n/a if any field is not applicable. Personnel to be hired that has not been identified at this time can be listed in the budget 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. To add another person/row (up to five), click the box at the end of the row.
      • Name
      • Email address
      • Current employer
      • Job title
      • Developer username if applicable (e.g., GitHub handle)
    • Project Metrics:
      • Quality (required)
        1. What is the project license?
          • Copyleft license (e.g. GPL, LGPL)
          • Permissive license (BSD 3-Clause, MIT, Apache 2.0)
          • Another OSI-approved license
          • Custom license/other (please specify)
        2. Does the project have a code of conduct? If yes, provide a link.
        3. Does the project have end-user documentation? If yes, provide a link.
        4. Does the project have an issue tracker? If yes, provide a link.
        5. Does the project have a community engagement/Q&A forum (self-hosted, on Stack Exchange, etc.)? If yes, provide a link.
        6. Does the project have contribution/coding guidelines? If yes, provide a link.
        7. Are there examples or demo notebooks, scripts, and datasets? If yes, provide a link.
        8. Is there a corresponding package available in a package manager (PyPi, CRAN, etc.)? If yes, provide names and links.
        9. Does the project use continuous integration for testing?
      • Impact (optional): Provide metrics for each open source project that will be supported by the grant to help us assess its impact and quality. Providing metrics is optional and metrics can be approximate. For each metric, provide a source, clarify how the metric was computed and/or provide any other comments. For monthly metrics, provide data from the most recent month for which the corresponding metric is available.
        1. List the number and explanation for each, if needed:
          • Number of scholarly paper(s) (including preprints) citing or mentioning the software project
          • Number of monthly users, if applicable (based on one or more of the following: monthly downloads from websites, monthly downloads from package managers, monthly unique requests for updates, actual tracked usage, etc.)
          • Number of software projects that depend on the project (if applicable)
          • Number of monthly visitors to project’s website, discussion forum (e.g. Stack Overflow, Discourse), or similar
        2. Size of the largest potential user base:
          • Estimate the potential number of unique users who could adopt this project in the relevant field/discipline and explanation, if needed. You can use as guidance the number of users of comparable projects, the number of papers published in the domain to which the project is applicable, number of labs able to adopt the project, etc.
            • ( ) 1-10;
            • ( ) 11-100;
            • ( ) 101-1,000;
            • ( ) 1001-10,000;
            • ( ) 10,001-100,000; or
            • ( ) over 100,000.
        3. List of upstream, downstream, or related software projects that the team is contributing to or receiving contributions from.
        4. Additional metrics from project code repositories and package managers:
          • Provide a short description of any considerations or caveats we should be aware of when computing metrics (e.g., a recent change in the name or hosting of the repository), or any additional information you would like to share about the project’s impact and quality (maximum of 500 words)
  • Budget
    • Amount Requested: Enter total budget amount requested in USD, including indirect costs; this number should be between $50k and $250k total costs and match total described in the Budget Description.
    • Budget Description: Upload in PDF format; budgets can be uploaded in a combined single PDF or one PDF for each software project; font must be 11 points or larger and margins must be at least one-half inch (top, bottom, left, and right) (one page per software project maximum)
      • 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).
      • Indirect costs are limited to up to 15% of direct costs and are included within the annual budget total. 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.
      • 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.

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.

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.

Selection Process

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.

Applications will be evaluated for their expected impact, the quality of the open source project(s) involved, and the feasibility of the proposal, each of which will be assessed through quantitative and qualitative factors. Relevant materials will be provided by the applicants and obtained by CZI from publicly available sources where possible (e.g., GitHub or other public code repositories). Quantitative metrics on projects will be optional in the application form. Independent expert review will be solicited, and final decisions will be made by CZI staff in consultation with our expert advisors.

Impact will assess the importance of the open source project(s) involved in the proposal to science and the open source ecosystem, in alignment with our mission to support the science and technology that will make it possible to cure, prevent, or manage all diseases by the end of the century. Reviewers will evaluate:

  • Demonstrated scientific impact of the project
  • The value to the project provided by the proposed scope of work
  • The role of the project in the scientific open source ecosystem
  • Alignment of the project to areas currently prioritized by CZI Science in accordance with our mission (e.g. imaging, cell biology, genomics)

Alongside qualitative materials, expert evaluation may utilize metrics such as:

  • Number of users and recent growth
  • Adoption within relevant communities
  • Number of citations or mentions of the project in scientific literature
  • Number of potential contributors and diversity of the organizations they represent
  • Number of past contributions to related projects in the relevant software stack (pushing changes upstream to dependencies, receiving changes from other nearby projects)

Quality will assess the maturity of the project(s), its compliance with best practices in open source development, and the existence of a healthy and diverse contributor community. It will again be assessed qualitatively and quantitatively. Reviewers will evaluate:

  • Composition and leadership of team
  • Governance structure of the project
  • Project communications and community engagement
  • Existence, clarity, and recency of project roadmap
  • Clarity of process for external contributions
  • Evidence of external contributions from outside of the core developer team (in the form of code, bugs/issue reports, documentation, etc.)
  • Availability of tutorials and examples
  • Quality and comprehensiveness of documentation

Alongside qualitative materials, evaluation may leverage metrics such as:

  • Frequency and growth trajectory of commits over time
  • Size and diversity of current developer team
  • Frequency of external contributions
  • Number of open issues, and rate of issues both opened and closed
  • Time between opening and closing of pull requests

Feasibility will assess the plan of work described in the proposal and whether it can be accomplished given the requested budget and key personnel involved. Reviewers will evaluate the following based on qualitative materials:

  • Specificity and clarity of plan of work to be accomplished
  • Proposed use of funds (relative to plan of work)
  • Likelihood of the work being accomplished
  • Plan for tracking and validating progress against goals
  • Degree of unmet need given existing resources
  • Future plans for sustaining or maintaining the work funded by the grant

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.

Reporting & Progress

Final reports, including a lay summary of the project progress that will be made publicly available, will be required from successful grantees to ensure that progress toward the deliverables described in the proposal is on track. Measures of progress will also include additional indicators on the growth and uptake of the project, as obtained from code repositories, issue trackers, package distribution systems, community forums, mailing lists, etc.

Policies
  • Funds from this award are intended to support specified grant activities. Grants are made to organizations on behalf of the named award recipients, and reasonable flexibility on how these funds are utilized is allowed, provided that the funds are used to support activities related to the proposal. Funded grantees will be asked to provide summary budgets at the time of award and during annual reporting.
  • For awarded proposals, financial statements and progress reports will be due at the conclusion of the grant. Specific deliverable requirements will be outlined in the award notification. Key personnel of funded proposals are expected to participate in regular grantee meetings, including annual meetings in the San Francisco Bay Area. Travel support for these meetings will be provided by CZI separately from the requested grant funds.
  • 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.
  • Grantees may obtain funds for the proposed work from other funding sources, provided that there is no conflict with meeting the terms of the CZI award.
  • Ethical conduct: CZI advocates the highest ethical standards for the conduct of research and for the professional and personal conduct of grantees. Grantee organizations must adopt appropriate procedures for examination of cases of scientific and personal misconduct, including harassment.
  • 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. Exceptions will be considered where there are situations that make this impossible or counterproductive.
    • 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.
    • 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, preferably CC0 or CC BY/CC BY SA for data that requires explicit attribution. This includes metadata, documentation, and intended use cases, as appropriate.
    • Publications:​ To encourage rapid dissemination of results, any publications related to this funded work must be submitted to a preprint server (such as bioRxiv, arXiv, or any appropriate preprint repository), at or before the first submission to a journal. CZI requests that scientific publications, preprints, and presentations that result from this award acknowledge support from this funding.
    • Intellectual property rights: CZI does not retain any rights, other than a use right, to data, published results, or any other intellectual property that results from the work funded by these grants. 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. Other technology and intellectual property rights (such as patents) should be made freely available for all academic and non-commercial use and where commercialized, it should generally be subject to non-exclusive commercial licenses that enable broad availability and dissemination.
  • Indirect costs cannot exceed 15% of direct costs and must be included within the annual budget total. Indirect costs may not be assessed on capital equipment or subcontracts, but subcontractors may include up to 15% indirect costs of their direct costs.
  • Applications selected through this process will either be funded by the Chan Zuckerberg Foundation or recommended for funding through the Chan Zuckerberg Initiative Donor-Advised Fund (DAF) at the Silicon Valley Community Foundation (SVCF).
Confidentiality

All submitted applications will be kept confidential, except as necessary for our evaluation or to comply with any applicable laws. Successfully funded proposals may be made publicly available and/or shared with other grantees or collaborators. Unfunded proposals will remain confidential. However, information on project metrics and types of organizations who have applied for funding may be made publicly available in aggregate form. Application materials will not be returned to applicants.

RFA Contact

For administrative and programmatic inquiries, technical assistance, or other questions pertaining to this RFA, please contact sciencegrants@chanzuckerberg.com.

Key Dates
JUNE 18, 2019
Application portal opens
AUG 1, 2019
Applications due by 5:00 PM PT
OCT 2019
Earliest notification of decisions (subject to change)
DEC 1, 2019
Earliest start date of project (subject to change)

Award period and start date: Proposed projects should be one year in duration with a projected start date no earlier than December 1, 2019. Actual start date may vary.

Successful awardees from the first cycle are eligible to apply for a renewal in the third cycle. Renewals will be evaluated alongside new applications.

Opportunity

The Chan Zuckerberg Initiative invites applications in support of open source software projects that are essential to biomedical research. The goal of the program is to support software maintenance, growth, development, and community engagement for these critical tools.

Overview

Open source software is critical to modern scientific research, advancing biology and medicine while providing reproducibility and transparency. Hundreds of software packages, libraries, and applications have become essential tools for research—so much so that many researchers could not continue their work without them. Despite its importance, a majority of research software is undervalued and lacks funding for maintenance, growth, development, and community engagement. Also, those who work on such software often lack credit and recognition.

In a new effort to support open source software for science, the Chan Zuckerberg Initiative (CZI) seeks applications for software projects that are essential to biomedical research, have already demonstrated impact, and can show potential for continued improvement. Grants will be for a one-year period with the potential to apply for renewal in future cycles.

With this program, we aim to provide projects with resources to support their tools and the communities behind them. Whether it’s hiring an additional developer, improving documentation, addressing usability, improving compatibility, onboarding contributors, or convening a community, we hope our support can help make the computational foundations of biological research more usable and robust.

Details

CZI currently supports several areas of basic science and technology with the goal of making it possible to cure, prevent, or manage all diseases by the end of this century. This program aims to support software tools that are essential to this mission. Applications for two broad categories of open source projects will be considered in scope:

  • Domain-specific software for analyzing, visualizing, and otherwise working with the specific data types that arise in biomedical science (e.g., genomic sequences, microscopy images, molecular structures). Software will be considered out of scope if it primarily serves domains outside biomedical science (e.g., physics, astronomy, earth sciences). While we appreciate that other communities may want to explore new extensions of their software to the life sciences, such applications are unlikely to be selected.
  • Foundational tools and infrastructure that enable a wide variety of downstream software across several domains of science and computational research (e.g., numerical computation, data structures, workflows, reproducibility). While foundational tools will be considered in scope for this program, they must have demonstrated impact on some area(s) of biomedical research.

Applications can request funding between $50k and $250k total costs (inclusive of up to 15% for indirect/overhead costs). Budgets will be evaluated for appropriateness relative to the scope of work proposed. Acceptable use of funds includes, but is not limited to:

  • Salary support for staff (full-time, part-time, or contract): developers, contributors, technical writers, community managers, product managers, project managers, user experience researchers, community educators, or other roles that directly support the project;
  • Hackathons, sprints, outreach, or other forms of community engagement and support for community participation;
  • Operational needs such as cloud computing, storage, networking, or continuous integration services; and
  • Support for work that bridges projects or ecosystems, including better coordination across projects that are similar, dependent on one another, or frequently used together.

CZI staff will further support awarded proposals by convening grantee meetings and helping connect open source software developers to scientists, including other CZI-funded grantees and members of the broader scientific community.

Eligibility
  • We welcome applications from any country, provided the proposed work is compliant with the US Treasury Department’s Office of Foreign Asset Control (OFAC) program. For additional information regarding OFAC sanctions, please refer to the US Treasury Department’s resources.
  • 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. Open source projects operating independently must be affiliated with an organization, as described below.
  • If an application does not come from an organization eligible to receive and distribute funds (e.g., an academic institution), the applicant may designate a fiscal sponsor (e.g., NumFOCUS, Code for Science & Society, or others). We encourage projects that require fiscal sponsorship to contact the appropriate organizations early in the application process. If your application requires a fiscal sponsor and you are unable to secure one by the application deadline, you may still apply, but your application should explain the financial situation of the project and how you are planning to receive and use the funds if successfully awarded. We will prioritize applications already able to receive and use funds at the time of application.
  • We will consider and potentially fund multiple applications from the same organization, multiple applications related to the same open source project(s), and multiple applications that include the same staff and/or project contributors. However, the proposed work in such applications must be distinct.
  • We encourage proposals supporting multiple open source projects. In the case of applications for work spanning multiple projects, one individual must complete the application and a single organization or fiscal sponsor must coordinate the dispersal of funds to the members of the collaboration. Note that foreign institutions may not subcontract to US institutions, so please be mindful when selecting the applicant organization.
  • We believe that the strongest teams incorporate a wide range of voices. Those underrepresented in science and technology are strongly encouraged to apply.
  • Facebook employees, including employees of any subsidiary Facebook entities, are not permitted to apply for this grant.
  • CZI reserves the sole right to decide if an applicant and applicant organization meet the eligibility requirements.

For questions about eligibility, please contact us in advance of the application deadline at sciencegrants@chanzuckerberg.com. Deadline extensions will not be granted.

Application Requirements

Key dates

We invite applications for consideration for funding during three distinct cycles, with rounds beginning June 18, 2019; mid-December 2019; and mid-June 2020.

All dates for the second and third cycles are subject to change. Please sign up for our mailing list to stay updated on these dates as they are announced and future funding opportunities.

Grant duration

Grants will be awarded for a one-year duration. The actual start date may vary based on specific needs (timing of hiring, etc.) and will be agreed upon after the grant is awarded. Successful awardees from the first cycle are eligible to apply for a renewal in the third cycle, with a budget and scope of work that can be either similar or altered depending on project needs. Renewals will be evaluated alongside new applications. No-cost extensions will be considered.

We will evaluate the success of this program during the initial cycles, with the possibility of extending it so that groups funded in the second and third cycles can apply for renewals in 2021, but no additional cycles are confirmed at this time.

Application specifics

All applications must be completed and submitted through the Chan Zuckerberg Initiative’s online grants management portal. We recommend that you familiarize yourself with this portal well in advance of the submission deadlines. Detailed application instructions, including required elements of the application, are available below in the Detailed Application Instructions section, as well as in the grants management portal.

Cycle
1
Portal opening date
June 18, 2019 by 9 am Pacific Time
Application due date
August 1, 2019 by 5 pm Pacific Time
Notification of decisions
Late October 2019
Earliest start date of grant
December 1, 2019
Cycle
2
Portal opening date
Mid-December 2019
Application due date
February 1, 2020
Notification of decisions
Late April 2020
Earliest start date of grant
June 1, 2020
Cycle
3
Portal opening date
Mid-June 2020
Application due date
August 1, 2020
Notification of decisions
Late October 2020
Earliest start date of grant
December 1, 2020
Detailed Application Instructions

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.

For the purpose of the application, we will use the following terms:

  • Applicant: The person submitting the application materials on behalf of the project(s)
  • Organization: The organization directly receiving and distributing funding
  • Project(s): The software project(s) that will be supported by the funding
  • Proposal: The proposed use of funding
  • Key Personnel: People involved in the project(s) described in the proposal and supported by the funding

The application consists of the following sections (called tasks in the grants portal): Applicant Details Part I, Applicant Details Part 2, Organization Details, Proposal Details, Number of Open Source Project(s), Open Source Project Details, Budget

  • Applicant Details Part 1: Complete all fields in this task; all fields are required. The information entered should be for the individual submitting the application who will act as the main person responsible for the application and as its point of contact. Information about other Key Personnel 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
    • Current Employer
    • Title/Position
    • CV of the Applicant (the person submitting the application): Upload in PDF format; font must be 11 points or larger and margins must be at least one-half inch (top, bottom, left, and right) (maximum of two pages)
      Include current and recent employment, education history, and references to any major publications and software authored.
  • Applicant Details Part 2: Complete all required fields in this task. The information entered should be for the individual submitting the application who will act as the main person responsible for the application and as its point of contact. Please note demographic information will not be used as a basis for review.
    • Work phone (required)
    • Highest degree (required) and year granted (optional)
    • Additional degrees and year granted (up to three) (optional)
    • Gender (optional)
    • Race/Ethnicity (optional)
    • Short narrative biography of the applicant (maximum of 100 words) (required)
  • Organization Details: Complete all sections in this task; all sections are required. The information entered should be for the organization that would be directly receiving and distributing funding if a grant is successfully awarded (e.g., academic institution, fiscal sponsor). Note that this may be different from the Applicant’s main affiliation.
    • Type of Organization: academic, other non-profit, industry/company, government, fiscal sponsor, fiscal sponsor not yet identified, or other (required)
    • Details:
      • Organization name, Address, City, State/Province and Country
      • Tax ID: If your organization has an Employer Identification Number (EIN), as assigned by the United States Internal Revenue Service, enter it in the 9-digit format (XX-XXXXXXX; 10 characters total). Organizations who do not have an EIN should enter 44-4444444
    • Institutional Approval Form: This form should be reviewed and signed by a person authorized to sign on behalf of your organization or fiscal sponsor (whichever organization that will be receiving the grant funds, if the application is selected for funding), agreeing to the stated institutional and applicant 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. Applicants may be asked to provide additional information on the governance of the proposal and its ability to receive and use the funds, if successfully awarded. If you do not have an organization identified to receive funds, the applicant should sign the form and note on the form that a fiscal sponsor has not been identified. Upload as a single PDF. This form is not set up to be completed online with a digital signature so you will need to print it, have it signed, and then upload as a PDF (required).
  • Proposal Details: Complete all required sections in this task.
    • Proposal Title: Auto filled. 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 (maximum of 75 characters, including spaces)
    • Proposal Purpose: One sentence (maximum of 255 characters including spaces)
    • Abstract/Proposal Summary: A short summary of the application ​(maximum of 250 words)
    • Proposal: Upload your proposal as a single PDF; font must be 11 points or larger and margins must be at least one-half inch (top, bottom, left, and right) for all pages. Include:
      • Body:​ (maximum of 2000 words). Should include the following parts:
        1. Goals
          • The objective and expected outcomes of the proposal
          • A description of how the applicant will determine if the goals of the proposal have been successfully met
        2. Work plan
          • A description of the proposed work the applicants are requesting funding for, including resources the applicants will provide that are not part of the requested funding. For software development related work (e.g., engineering, product design, user research), specify how the work fits into the existing project roadmap. For community outreach related activities (e.g., sprints, training), specify how these activities will be organized, the target audience, and expected outcomes
        3. Existing support
          • Current and recent financial support for the project(s), including duration, amount in USD, and source of funding
      • Figures (optional): Limit to one page, inclusive of legends
      • References cited in your proposal: No word/page limit
    • Milestones and Deliverables (required): List expected milestones and deliverables, and their expected timeline. Be specific and include (where possible) any goals for metrics the project(s) are expected to reach upon completion of the grant (maximum of 500 words)
    • Diversity and Inclusion Statement (optional): Upload as a single PDF; font must be 11 points or larger and margins must be at least one-half inch (top, bottom, left, and right) for all pages (one page maximum)
      • Describe what efforts the project(s) named in this proposal have undertaken to increase the diversity of contributors
  • Number of Open Source Project(s): Indicate the number of software projects involved in your proposal (up to five). Each proposal can request funding for work that includes up to five open source projects. If multiple projects are involved, details must be entered for all of them. If your proposal involves more than one project, mark this step as complete so you can fill in the details for additional projects. This section must be marked complete in order to proceed to the Open Source Project Details #2 – #5 tasks. To change the number of projects indicated after marking as complete, click the three dots in the upper right of the task and select edit, which will re-open the task.
  • Open Source Project Details #1 – #5: Depending upon your answer to the “Number of Open Source Project(s)” task above, the corresponding number of tasks—one for each project indicated above—will appear (Open Source Project Details #1 will appear by default). You may need to scroll down using the scroll bar in the task menu on the left side of the page to see these tasks. For each task/project in this section, please complete the following; all URLs should be in the format https://example.com:
    • Project Details: Complete the following for each software project that will be supported by the grant:
      • Project name (required)
      • Homepage URL (required)
      • Main code repository (e.g. GitHub URL) (required)
      • DOI of major publication(s) describing project (if applicable)
      • Social media handles (if applicable)
      • Short description of the project (maximum of 200 words) (required)
    • List of Known Key Personnel: Key personnel are people involved in the project who will be supported by the grant if the application is successful. Complete the following for each (up to 5) (required); enter n/a if any field is not applicable. Personnel to be hired that has not been identified at this time can be listed in the budget 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. To add another person/row (up to five), click the box at the end of the row.
      • Name
      • Email address
      • Current employer
      • Job title
      • Developer username if applicable (e.g., GitHub handle)
    • Project Metrics:
      • Quality (required)
        1. What is the project license?
          • Copyleft license (e.g. GPL, LGPL)
          • Permissive license (BSD 3-Clause, MIT, Apache 2.0)
          • Another OSI-approved license
          • Custom license/other (please specify)
        2. Does the project have a code of conduct? If yes, provide a link.
        3. Does the project have end-user documentation? If yes, provide a link.
        4. Does the project have an issue tracker? If yes, provide a link.
        5. Does the project have a community engagement/Q&A forum (self-hosted, on Stack Exchange, etc.)? If yes, provide a link.
        6. Does the project have contribution/coding guidelines? If yes, provide a link.
        7. Are there examples or demo notebooks, scripts, and datasets? If yes, provide a link.
        8. Is there a corresponding package available in a package manager (PyPi, CRAN, etc.)? If yes, provide names and links.
        9. Does the project use continuous integration for testing?
      • Impact (optional): Provide metrics for each open source project that will be supported by the grant to help us assess its impact and quality. Providing metrics is optional and metrics can be approximate. For each metric, provide a source, clarify how the metric was computed and/or provide any other comments. For monthly metrics, provide data from the most recent month for which the corresponding metric is available.
        1. List the number and explanation for each, if needed:
          • Number of scholarly paper(s) (including preprints) citing or mentioning the software project
          • Number of monthly users, if applicable (based on one or more of the following: monthly downloads from websites, monthly downloads from package managers, monthly unique requests for updates, actual tracked usage, etc.)
          • Number of software projects that depend on the project (if applicable)
          • Number of monthly visitors to project’s website, discussion forum (e.g. Stack Overflow, Discourse), or similar
        2. Size of the largest potential user base:
          • Estimate the potential number of unique users who could adopt this project in the relevant field/discipline and explanation, if needed. You can use as guidance the number of users of comparable projects, the number of papers published in the domain to which the project is applicable, number of labs able to adopt the project, etc.
            • ( ) 1-10;
            • ( ) 11-100;
            • ( ) 101-1,000;
            • ( ) 1001-10,000;
            • ( ) 10,001-100,000; or
            • ( ) over 100,000.
        3. List of upstream, downstream, or related software projects that the team is contributing to or receiving contributions from.
        4. Additional metrics from project code repositories and package managers:
          • Provide a short description of any considerations or caveats we should be aware of when computing metrics (e.g., a recent change in the name or hosting of the repository), or any additional information you would like to share about the project’s impact and quality (maximum of 500 words)
  • Budget
    • Amount Requested: Enter total budget amount requested in USD, including indirect costs; this number should be between $50k and $250k total costs and match total described in the Budget Description.
    • Budget Description: Upload in PDF format; budgets can be uploaded in a combined single PDF or one PDF for each software project; font must be 11 points or larger and margins must be at least one-half inch (top, bottom, left, and right) (one page per software project maximum)
      • 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).
      • Indirect costs are limited to up to 15% of direct costs and are included within the annual budget total. 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.
      • 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.

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.

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.

Selection Process

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.

Applications will be evaluated for their expected impact, the quality of the open source project(s) involved, and the feasibility of the proposal, each of which will be assessed through quantitative and qualitative factors. Relevant materials will be provided by the applicants and obtained by CZI from publicly available sources where possible (e.g., GitHub or other public code repositories). Quantitative metrics on projects will be optional in the application form. Independent expert review will be solicited, and final decisions will be made by CZI staff in consultation with our expert advisors.

Impact will assess the importance of the open source project(s) involved in the proposal to science and the open source ecosystem, in alignment with our mission to support the science and technology that will make it possible to cure, prevent, or manage all diseases by the end of the century. Reviewers will evaluate:

  • Demonstrated scientific impact of the project
  • The value to the project provided by the proposed scope of work
  • The role of the project in the scientific open source ecosystem
  • Alignment of the project to areas currently prioritized by CZI Science in accordance with our mission (e.g. imaging, cell biology, genomics)

Alongside qualitative materials, expert evaluation may utilize metrics such as:

  • Number of users and recent growth
  • Adoption within relevant communities
  • Number of citations or mentions of the project in scientific literature
  • Number of potential contributors and diversity of the organizations they represent
  • Number of past contributions to related projects in the relevant software stack (pushing changes upstream to dependencies, receiving changes from other nearby projects)

Quality will assess the maturity of the project(s), its compliance with best practices in open source development, and the existence of a healthy and diverse contributor community. It will again be assessed qualitatively and quantitatively. Reviewers will evaluate:

  • Composition and leadership of team
  • Governance structure of the project
  • Project communications and community engagement
  • Existence, clarity, and recency of project roadmap
  • Clarity of process for external contributions
  • Evidence of external contributions from outside of the core developer team (in the form of code, bugs/issue reports, documentation, etc.)
  • Availability of tutorials and examples
  • Quality and comprehensiveness of documentation

Alongside qualitative materials, evaluation may leverage metrics such as:

  • Frequency and growth trajectory of commits over time
  • Size and diversity of current developer team
  • Frequency of external contributions
  • Number of open issues, and rate of issues both opened and closed
  • Time between opening and closing of pull requests

Feasibility will assess the plan of work described in the proposal and whether it can be accomplished given the requested budget and key personnel involved. Reviewers will evaluate the following based on qualitative materials:

  • Specificity and clarity of plan of work to be accomplished
  • Proposed use of funds (relative to plan of work)
  • Likelihood of the work being accomplished
  • Plan for tracking and validating progress against goals
  • Degree of unmet need given existing resources
  • Future plans for sustaining or maintaining the work funded by the grant

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.

Reporting & Progress

Final reports, including a lay summary of the project progress that will be made publicly available, will be required from successful grantees to ensure that progress toward the deliverables described in the proposal is on track. Measures of progress will also include additional indicators on the growth and uptake of the project, as obtained from code repositories, issue trackers, package distribution systems, community forums, mailing lists, etc.

Policies
  • Funds from this award are intended to support specified grant activities. Grants are made to organizations on behalf of the named award recipients, and reasonable flexibility on how these funds are utilized is allowed, provided that the funds are used to support activities related to the proposal. Funded grantees will be asked to provide summary budgets at the time of award and during annual reporting.
  • For awarded proposals, financial statements and progress reports will be due at the conclusion of the grant. Specific deliverable requirements will be outlined in the award notification. Key personnel of funded proposals are expected to participate in regular grantee meetings, including annual meetings in the San Francisco Bay Area. Travel support for these meetings will be provided by CZI separately from the requested grant funds.
  • 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.
  • Grantees may obtain funds for the proposed work from other funding sources, provided that there is no conflict with meeting the terms of the CZI award.
  • Ethical conduct: CZI advocates the highest ethical standards for the conduct of research and for the professional and personal conduct of grantees. Grantee organizations must adopt appropriate procedures for examination of cases of scientific and personal misconduct, including harassment.
  • 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. Exceptions will be considered where there are situations that make this impossible or counterproductive.
    • 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.
    • 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, preferably CC0 or CC BY/CC BY SA for data that requires explicit attribution. This includes metadata, documentation, and intended use cases, as appropriate.
    • Publications:​ To encourage rapid dissemination of results, any publications related to this funded work must be submitted to a preprint server (such as bioRxiv, arXiv, or any appropriate preprint repository), at or before the first submission to a journal. CZI requests that scientific publications, preprints, and presentations that result from this award acknowledge support from this funding.
    • Intellectual property rights: CZI does not retain any rights, other than a use right, to data, published results, or any other intellectual property that results from the work funded by these grants. 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. Other technology and intellectual property rights (such as patents) should be made freely available for all academic and non-commercial use and where commercialized, it should generally be subject to non-exclusive commercial licenses that enable broad availability and dissemination.
  • Indirect costs cannot exceed 15% of direct costs and must be included within the annual budget total. Indirect costs may not be assessed on capital equipment or subcontracts, but subcontractors may include up to 15% indirect costs of their direct costs.
  • Applications selected through this process will either be funded by the Chan Zuckerberg Foundation or recommended for funding through the Chan Zuckerberg Initiative Donor-Advised Fund (DAF) at the Silicon Valley Community Foundation (SVCF).
Confidentiality

All submitted applications will be kept confidential, except as necessary for our evaluation or to comply with any applicable laws. Successfully funded proposals may be made publicly available and/or shared with other grantees or collaborators. Unfunded proposals will remain confidential. However, information on project metrics and types of organizations who have applied for funding may be made publicly available in aggregate form. Application materials will not be returned to applicants.