Essential Open Source Software for Science (Cycle 5)

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, even the most widely-used research software often lacks dedicated funding for maintenance, growth, development, and community engagement. Also, those who work on such software often lack credit and recognition.

In an effort to support open source software for science, the Chan Zuckerberg Initiative (CZI) seeks letters of intent to apply for funding for software projects that are essential to biomedical research, have previously demonstrated impact, show potential for continued improvement, and expect to deliver added value to the biomedical research community through the proposed activities.

Grants will be for two years and can be used to fund a variety of eligible activities, as listed in the Use of Funds section below.

Note this is a two step application process: an initial Letter of Intent (LOI), which will be followed by invitations to a select number of applicants to submit a Full Application.

With this program, we aim to provide software 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.

For this Request For Applications, we seek to support software tools across a broad range of biomedical fields, including three areas of focus relevant to CZI Science: Infectious Disease, Imaging, and Single-Cell Biology.

Scope

Applications for two broad categories of open source software 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. Software will be considered out of scope if it primarily serves domains outside biomedical science without strong evidence of adoption in biomedicine. The Essential Open Source Software for Science (EOSS) program supports software tools across a broad range of biomedical fields. In this RFA cycle we will continue with this approach, including tools from three areas of focus relevant to CZI Science: Infectious Disease, Imaging, and Single-Cell Biology.
• Foundational tools and infrastructure that enable a wide variety of downstream software across several domains of science and computational research. While foundational tools will be considered in scope for this program, they must have demonstrated impact on some area(s) of biomedical research.

We strongly encourage proposals requesting funding for multiple related software projects (example here). For examples of open source projects we’ve previously funded through the EOSS program, we encourage you to check the list of proposals awarded in the previous cycles and our blog posts.

Examples of projects that are less likely to be successful:

• A project in its earlier stages that is not used extensively or known beyond the creator(s);
• A project that is focused on improving or supporting a database or knowledge base that has few community contributions or low adoption in the biomedical community;
• A project that is widely successful and adopted but has little or no applications to biomedicine; and
• A proposal for a research project to mine, publish, or analyze research results rather than a project that will support the biomedical research process itself.

Use of funds

Applications can request funding between $50,000 USD and $200,000 USD total costs per year for two years (inclusive of up to 15% for indirect/overhead costs) for an overall amount requested between $100,000 USD and $400,000 USD total costs for the two-year duration of the grant. Proposals will not need to provide a detailed budget or justification at the LOI stage. At the full proposal stage, budgets will be required and 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 software project(s);
• 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 software projects or ecosystems, including better coordination across software projects that are similar, dependent on one another, or frequently used together.

• 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 full 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 software 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), it may designate a fiscal sponsor (e.g., NumFOCUS, Code for Science & Society, or others). We encourage proposals that require fiscal sponsorship to contact the appropriate organizations early in the application process. If your application requires a fiscal sponsor, you must secure one by the full proposal application deadline.
• We will consider and potentially fund multiple applications from the same organization, multiple applications related to the same open source software project(s), and multiple applications that include the same staff and/or software project contributors. However, the proposed work in such applications must be distinct.
• We encourage proposals supporting multiple open source software projects. In the case of applications for work spanning multiple software 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 issue subcontracts to US institutions, so please be mindful when selecting the applicant organization.
• We encourage proposals that are currently funded from all four previous cycles of the EOSS RFA to submit an application to continue or build on the previously funded work.
• We believe that the strongest teams incorporate a wide range of voices. Those underrepresented in science and technology are strongly encouraged to apply.
• Meta employees, including employees of any subsidiary Meta entities, as well as employees of Chan Zuckerberg Initiative, LLC, are not permitted to apply.
• CZI reserves the sole right to decide if an applicant and applicant organization meet the eligibility requirements.
• We welcome applications from any country, provided the proposed work is compliant with the United States Treasury Department’s Office of Foreign Asset Control (OFAC) sanctions program. Prior to award, all grant applications will be reviewed for compliance with OFAC sanctions program, the United States Department of Commerce’s export administration regulations, the Foreign Corrupt Practices Act (FCPA), any other applicable U.S. laws and regulations, and any corresponding laws and regulations in the country where the applicant is based. All grant agreements will also require the grantee to comply with these laws and regulations. For additional information please refer to: the U.S. Treasury Department’s resources, the International Trade Administration’s website on US Export Controls, and the Department of Justice’s website on the FCPA.

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.

CZI 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.

Application specifics

• The application process is a two-stage process: Letter of Intent (LOI) and Full Application (if invited).
• Eligibility: Please refer to the Eligibility section.
• Award Period: Proposals should be two years in duration with a start date of November 1, 2022.
• Budget: Applications can request funding between $50,000 USD and $200,000 USD total costs per year for two years (inclusive of up to 15% for indirect/overhead costs) for a total amount requested between $100,000 USD and $400,000 USD for the two-year duration of the grant. A detailed budget is not required at the LOI stage.

GETTING STARTED

The applicant must first set up an account in the CZI online grants portal:

1. Go to https://apply.chanzuckerberg.com/.
2. Click the green Register button in the upper right corner.
3. Complete the requested fields and then click the green Create Account button.
4. Click the green Continue button to proceed to the site.
5. Verify your account via email.
6. Log in to the grants portal at https://apply.chanzuckerberg.com/. Using the links in the upper right corner, you can access available programs (which includes RFAs for all CZI areas) and any applications you have in preparation or previously submitted.

SUBMITTING THE LETTER OF INTENT

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

• Application: At this stage, the “application” refers to the Letter of Intent
• Applicant: The person submitting the application materials on behalf of the software project(s)
• Software project(s): The open source software project(s) that will be supported by the funding
• Proposal: The proposed use of funding

Process

The application (Letter of Intent) consists of the following sections (called tasks in the grants portal): Applicant Details, Proposal Details, Equal Opportunity & Diversity (optional).

1. Log into https://apply.chanzuckerberg.com.
2. Click the green View Programs button. Find the program/RFA you may need to scroll down. Click the green More button.
3. Click the green Apply button in the upper right and complete all sections.
4. Enter the title of your application. Proposal title is limited to 60 characters, including spaces. If you need to edit your proposal title, click on the My Applications link in upper right and click the green Continue button on the application you wish to edit. Once the application page opens, click on the three dots to the right of the application title and select Rename from the dropdown menu.
5. Task 1: Applicant Details. 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.
   1. Name and email are 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.
   2. Institution/Affiliation: Add your home institution, company, or organization. This does not need to be the organization to which a grant would ultimately be awarded, if selected for funding.
6. Task 2: Proposal Details. All sections are required.
   1. Proposal Title: Auto-filled; Maximum of 60 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; and select Rename from the dropdown menu.
   2. Amount Requested: Total budget amount requested in USD, including indirect costs; this number should be between $100,000 USD and $400,000 USD total costs over a two-year period.
   3. Proposal Summary/Scope of Work: Provide a short summary of the work being proposed (maximum of 500 words).
   4. Value to Biomedical Users: Describe the expected value of the proposed work to the biomedical research community (maximum of 250 words).
   5. Open Source Software Projects: Indicate the number of software projects involved in your proposal (up to five). Complete the table with the following information for each software project.
      • Software project name
      • Main code repository (e.g. GitHub URL)
      • Homepage URL (if none, re-enter the main code repository URL)
   6. Landscape Analysis: Briefly describe the other software tools (either proprietary or open source) that the audience for this proposal primarily uses. How do the software project(s) in this proposal compare to these other tools in terms of user base size, usage, and maturity? How do existing tools and the project(s) in this proposal interact? (maximum of 250 words)
   7. Category: Choose the two categories that best describe the software project(s) audience:
      • Bioinformatics
      • Single-cell biology
      • Structural biology
      • Clinical research
      • Genomics
      • Neuroscience
      • Infectious disease
      • Imaging
      • Data management and workflows
      • Machine learning and data analysis
      • Visualization
   8. Previous CZI funding:
      • Did you previously apply for funding for this or a related proposal under the CZI EOSS program? Select Yes or No.
      • Have you previously received funding for this proposal under the CZI EOSS program? Select Yes or No.
7. Task 3: (Optional) 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 backgrounds, 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 request demographic information associated with applications submitted to CZI in response to our open calls. This information helps us learn from the RFA process, as well as improve our strategies to help ensure members of underrepresented or marginalized groups in science are aware of and able to apply to CZI opportunities. 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 Applicant. Please note that completing the below is voluntary, and demographic information will not be used to make final grant funding decisions.

   1. What is your race/ethnicity? (optional)
   2. What is the year of your last academic degree? (optional)
   3. What is your gender? (optional)
   4. Are you transgender? (optional)
   5. Are you a member of the LGBTQ community? (optional)
   6. Do you have one or more disabilities? Please specify (optional)
8. Mark all tasks as complete.
9. Submit your application: Once all required tasks are completed, click the green Review & Submit button. Note that once your application has been submitted, it cannot be edited.
   1. If the Submit button is grayed out, it means your application is not yet complete— check that all required fields are entered and you have clicked the Mark as Complete button within each task.
   2. Click the green Submit Your Application button on the left side of the window. Confirm your submission by clicking the Submit button in the pop up window.
10. Once your application is submitted, you will receive an email confirming submission. If you do not receive a confirmation email within a few minutes, please check your spam folder. If you still did not receive your confirmation email, please email sciencegrants@chanzuckerberg.com.

FULL APPLICATION

Applicants will be notified by email by May 5, 2022 if they have been invited to submit a Full Application. Detailed application instructions will be provided at that time. The Full Application will require additional materials such as a budget description, biosketches, software project metrics, and a detailed project proposal. Full Applications will require institutional sign-off (see Institutional Approval Form for details), so please be sure that your institution is able to comply with all requirements before submitting a Letter of Intent. Please also review the Full Application submission timeline before submitting a Letter of Intent; deadline extensions will not be granted. Full Applications (if invited) must be submitted by 5 pm Pacific Time on June 2, 2022.

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.

Applications will be evaluated for their existing impact, the quality of the open source software project(s) involved, the feasibility of the proposal, the expected value of the funded work to the biomedical community, and their diversity, equity, and inclusion statement — 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).

For those applicants asked to submit a Full Application, additional quantitative metrics on software projects will be requested. 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 software 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 and adoption of the software project, with a particular focus on its use in biomedicine
• The role of the software project in the scientific open source ecosystem

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

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

Quality will assess the maturity of the software 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 software project
• Software project communications and community engagement
• Existence, clarity, and recency of software 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 make-up 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.

In addition to the above criteria, reviewers will evaluate the value to the biomedical community of the proposed work, in particular:

• How the output of the proposal will advance project(s) adoption among biomedical researchers or produce value to their work
• Biomedical user needs that are unmet by the software project(s) in their current state and that will be addressed through the proposal
• Any improvement or integration with other tools that will improve the adoption, usability, functionality, extensibility, ease of use, or performance of the project in the context of the biomedical research community.

Lastly, all applicants invited to submit a Full Application must include in their proposal a Diversity, Equity, and Inclusion (DEI) statement, describing (a) any efforts the software project(s) named in this proposal have undertaken to increase diversity, equity, and inclusion with respect to their contributors and audience; and (b) the results of such efforts, if applicable. This statement will be reviewed alongside the above criteria. Please see examples of DEI statements from successful proposals funded in previous cycles.

There is no expectation of any specific number of awards for this RFA program, however this grant program operates within a budget which will inform the overall number of awards that are recommended for funding. The Chan Zuckerberg Initiative reserves the sole right to not recommend the funding of any applications.

REPORTING & PROGRESS

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

• Funds from this award are intended to support specified grant activities. Grants are made to organizations to support the work of the named grant lead, 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 annually and 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 (which may be in person or virtual). 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) must 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: Any software code developed by CZI grantees through the proposal shall generally be made publicly available on GitHub (or a similar public service). All newly developed code must be released under a permissive open source license (MIT, BSD 2-Clause, BSD 3-Clause, or Apache v2.0). All related pre-existing and derivative code shall 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 while respecting applicable laws and privacy rights of individuals. Any datasets either curated or generated through the proposal shall be made publicly available and easily accessible through an appropriate data repository, when applicable, under an Open Definition conformant license, preferably CC0. 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 shall be made available through permissive open source licenses. Other technology and intellectual property rights (such as patents) shall be made freely available for all academic and non-commercial use, and where commercialized, should generally be subject to non-exclusive commercial licenses that enable broad availability and dissemination.
• Unused research funds may be carried over to the following year, and requests for no-cost extensions will be considered at the end of the overall project period upon receipt of an annual report.
• 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. Non-charitable entities must include a clear allocation and explanation for any indirect costs included in a proposed budget.
• 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 (CZI 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.