Related Announcements

PA-20-272- Administrative Supplements to Existing NIH Grants and Cooperative Agreements (Parent Admin Supp Clinical Trial Optional)

NOT-OD-21-091 - Notice of Special Interest (NOSI): Administrative Supplements to Support Enhancement of Software Tools for Open Science

NOT-OD-20-073- Notice of Special Interest (NOSI): Administrative Supplements to Support Enhancement of Software Tools for Open Science

Issued by

Office of The Director, National Institutes of Health (OD)

National Eye Institute (NEI)

National Human Genome Research Institute (NHGRI)

National Institute on Aging (NIA)

National Institute on Alcohol Abuse and Alcoholism (NIAAA)

National Institute of Allergy and Infectious Diseases (NIAID)

National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)

National Institute of Biomedical Imaging and Bioengineering (NIBIB)

Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)

National Institute on Deafness and Other Communication Disorders (NIDCD)

National Institute of Dental and Craniofacial Research (NIDCR)

National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)

National Institute on Drug Abuse (NIDA)

National Institute of Environmental Health Sciences (NIEHS)

National Institute of General Medical Sciences (NIGMS)

National Institute of Mental Health (NIMH)

National Institute of Neurological Disorders and Stroke (NINDS)

National Institute on Minority Health and Health Disparities (NIMHD)

National Library of Medicine (NLM)

National Center for Complementary and Integrative Health (NCCIH)

National Center for Advancing Translational Sciences (NCATS)

Purpose

This Notice announces the continuing availability of administrative supplements to active awards that focus on biomedical software development or have a significant software development component. The goal of these supplements is to invest in research software tools with recognized value in a scientific community to enhance their impact by leveraging best practices and design principles in software development and advances in technology including cloud computing. This initiative is part of a plan for implementing the NIH Strategic Plan for Data Science which describes actions aimed at modernizing the biomedical research data ecosystem to make data findable, accessible, interoperable, and reusable (FAIR) and provide robust, scalable, sustainable tools and workflows with high impact for open science. The supplements are intended to support and encourage collaborations between biomedical scientists and software engineers to enhance the design, implementation, and cloud-readiness of research software. Through these awards, the NIH Office of Data Science Strategy (ODSS) intends to help researchers who have developed scientifically valuable software to make their tools robust and sustainable, take advantage of new data science, software engineering, and computing paradigms, reach a broader community and contribute to open science.

Background

As part of their research projects, investigators often produce innovative, scientifically valuable software tools that are essential for scientists to make use of and interpret biomedical research data. However, much of this valuable software has been built and supported under conditions that are no longer optimal in a rapidly changing technical and scientific landscape. Additionally, investigators lack the resources to adapt and revise the software to take advantage of new technologies and computing paradigms.

The traditional grant funding process has emphasized innovation for research progress over the use of robust software engineering practices that have become essential for reliable software tools in an era of large-scale, integrated data. There have been few practical ways to support joint efforts between researchers and software engineers to develop and revise research tools according to well-recognized software engineering best practices and design principles. Thus, software tools for biomedical research to efficiently process, manage, mine, analyze, visualize, and interpret biomedical data have often been developed in academic settings in absence of input from software engineers or industry professionals that is needed for the transition to operational efficiency and sustainability that is envisioned by ODSS.

Two previous rounds of ODSS software supplements (supported by NOT-OD-20-073 and NOT-OD-21-091) have encompassed a wide range of research and translational projects reaching across NIH ICs and spanning many scientific domains. Building a robust software foundation is expected to speed progress across biomedical research and clinical translation and contribute towards the NIH vision to establish a modernized and integrated biomedical data ecosystem that adopts the latest data science technologies, including cloud computing, AI technology, and best practice guidelines for open science arising from community consensus, such as FAIR principles and open-source development.

Research Objective

The goal of this Notice of Special Interest (NOSI) is to encourage and enable researchers to engage in new types of collaborations that focus on improving the quality and sustainability of research software from a software engineering perspective. Supplements will support efforts that address robustness, sustainability, reusability, portability, and scalability of existing biomedical research software tools and workflows of recognized scientific value. The goal of the opportunity is to improve software engineering fundamentals, going beyond software hardening or high-level user interaction. These projects are expected to adhere to software engineering best practices and design principles and take significant steps toward open science and sustainability in modern computing environments such as cloud or hybrid, distributed computing, and workflow systems. Projects to improve software engineering of significant research tools are sought regardless of the scientific area of emphasis. However these projects should not direct effort towards new research functions and must be in scope of the funded grant for which the supplement is being sought.

Significant software engineering skills are expected to be needed to develop robust tool implementations and to adapt software to changing computing paradigms. Thus, the supplements are primarily intended to provide support for software engineering staff with some allowance for other costs such as storage and computing that may be required to improve tools with significant user base or demonstrated potential for community adoption. New collaborations either within or across institutions are expected to be needed, which may include industry or academic partners. The notion of a research software engineer, or RSE, has been offered as an important enabler of sustainable research software in academic settings, both in the US-RSE and internationally. Developing these skills, enhancing team science, and building a supporting ecosystem, are understood to be other potential benefits of these collaborations, along with extending reach across boundaries to engage new diverse participants.

Delivering reliable, sustainable, and reusable software across multiple platforms is awhole-lifecycleeffort, as illustrated with a few instances. Software can be improved by enhancing the development process, including addition of resources for building, testing, and managing change in an open source community. Robustness and reliability can be improved through active community engagement to contribute to code made available with appropriate open source licensing. Reusability can be enhanced by improving dissemination channels for important algorithms and tools (e.g. inclusion in package distribution channels), by publication of tools in shared container registries, and with well-crafted operating manuals. Interoperability can be enhanced by incorporating open interfaces and data formats, especially through engagement in relevant communities and standards efforts. Refactoring can enhance portability and take advantage of new hardware or compute environments (e.g. parallelizing a process or using a standard workflow language that can run in cloud or hybrid environments).

Making software cloud ready can encompass the range of qualities of the ecosystem and software that allow it to be successfully adapted to environments (container, cloud/hybrid environments, distributed workflow systems) in a sustainable, secure, and scalable manner. Projects can propose to test software in a local, commercial, or public cloud and/or hybrid environments. Working with the STRIDES initiative is encouraged as relevant to the plan. It is further noted that portability of software tools across different cloud providers or environments is an important implication of the NIH Strategic Plan for Data Science, and interoperability across clouds to support distributed analysis is a key goal of this effort.

The supplement application must provide details of how the best software engineering practices and design principles will be employed in the supplement project, including a plan for how the software will be shared (see https://datascience.nih.gov/tools-and-analytics/best-practices-for-sharing-research-software-faq). The plan should also describe how the software will be improved for open science and community engagement.

Examples that address one or more challenges toward building robust software suitable for open science and modern computing include, but are not limited to:

• Adding APIs and services to software, especially when compliant to community standards
• Refactoring of software to incorporate standard interfaces and data formats, replace custom code with standard, hardened libraries where indicated
• Reducing coupling and complex shared state, allowing code to operate on diverse data sources and in collaboration with other services
• Adopting standard input and output data formats. Provide clean and well-documented input, output, and configuration that make software components more usable in composition via workflow languages. Ensure that data exchanged by services maximizes the use of open data formats
• Implementing standard logging models, improving performance through improved logging, monitoring, code profiling and optimization, taking advantage of parallelization, or use of GPUs
• Factoring configuration of services into environment variables and configuration properties for deployment
• Enhancing source code, documentation, version management and build/test tools to support community open source development
• Developing standard build and packaging tools to manage dependencies and produce containerized runtimes
• Formatting packages for sharing via common package management tools appropriate to the language and environment
• Enhancing standard unit and functional testing support and sample data sets for testing patches and upgrades
• Refactoring software for portability and to scale efficiently on the cloud or hybrid environments
• Improving architecture to reduce chattiness over the network and to minimize data ingress/egress charges in cloud environments
• Containerization of software and entry into a tool registry
• Enhancing usability, interoperability and scalability under increasing load, including making use of enhanced hardware and clustering technology
• Employing standard security that relies on cloud Identity and Access Management (IAM) models, and other improvements in privacy and security protection

Supplement applications must (1) demonstrate that to-be-improved software is being used by the scientific community by describing its user base or demonstrate clear potential for increased adoption by the user community and (2) discuss how the proposed improvements will help to increase the number of users and community diversity as well as the usage, and impact of the software for open science.

Projects involving significant new scientific features or developing new tools as opposed to software engineering are NOT appropriate for this NOSI.

Projects with no active software development components that would like to add one are NOT eligible for this NOSI.

Application and Submission Information

Budget

To be eligible, the parent award must be able to receive funds in FY2022 (Oct. 1, 2021 - Sept. 30, 2022) and not be in the final year or in a no-cost extension period as of July 1, 2022.

Projects that have already received awards under NOT-OD-20-073 or NOT-OD-21-091 are NOT eligible for this NOSI.

One-time supplement budget requests cannot exceed $150,000 direct costs. The number of awards will be contingent on availability of funds and receipt of meritorious applications. It is currently anticipated that 20 awards or more will be made depending on available funds.

Eligible Activity Codes:

Additional funds may be awarded as supplements to parent awards using any Activity Code, with the following exceptions: Small business activity codes (e.g. R41, R42, R43, R44, U44, and Fast Track), as well as G20, PS1, P60, R13, U13, U42, UG1, and S10 are NOT ELIGIBLE. Note that not all participating NIH Institutes and Centers (ICs) support all the activity codes that may otherwise be allowed. Applicants are therefore strongly encouraged to consult the program officer and the grant management officer of the parent grant to confirm eligibility.

Centers and multi-project grant mechanisms are eligible but must provide a strong justification for why existing funds cannot be reallocated toward the proposed project and clearly demonstrate benefit to open science and a broader community.

For awards that are already primarily funded to deliver software resources to the community (e.g., R24, U24, P41), applicants should provide strong justification for why additional funds are needed to support software enhancement and best practices, given that these activities could already be supported through the parent award.

Additional Information

Applications for this initiative must be submitted using the following opportunity or its subsequent reissued equivalent.

• PA-20-272- Administrative Supplements to Existing NIH Grants and Cooperative Agreements (Parent Admin Supp Clinical Trial Optional)

All instructions in the SF424 (R&R) Application Guide and PA-20-272 must be followed, with the following additions:

• Application Due Date(s) April 12, 2022 by 5:00 PM local time of applicant organization.
• For funding consideration, applicants must include "NOT-OD-22-068" (without quotation marks) in the Agency Routing Identifier field (box 4B) of the SF424 R&R form. Applications without this information in box 4B will not be considered for this initiative.
• Requests may be for one year of support only.
• The supplement should be given a title separate from the parent grant.
• The Project Summary should briefly summarize the parent grant and describe the goals of the supplement project.
• Biosketches for additional staff may be included beyond the Key Personnel in order to document the strength of the software engineering staff.
• The Introduction page should succinctly describe the parent grant goals that provide relevant background for the project and indicate how the proposed supplement is in scope of the parent grant.
• The Specific Aims page should provide the name or clearly identify the software that is the subject of the supplement project.
• The Research Strategy section of the application is limited to 3 pages. This section should succinctly justify the value of the software to the scientific community such as significant user base or clear potential for increased adoption and community access. Research Strategy should describe the approach to enhancing the software, clearly indicate how supplement uses best software engineering practices and design principles, and provide a software engineering plan with timelines for the activities proposed. The section should also address how the proposed work contributes to open science, community engagement, outreach, building diverse collaborations and workforce development.
• The Budget Justification should clearly specify team member contributions to the proposed work with roles and responsibilities, and indicate the software engineering team skills and expertise.

Administrative Evaluation Process

Submitted applications must follow the guidelines of the IC that funds the parent grant. Administrative Supplements do not receive peer review. Each IC will conduct administrative reviews of applications submitted to their IC separately. The most meritorious applications will be evaluated by a trans-NIH panel of NIH staff and supported based upon availability of funds. The criteria described below will be considered in the administrative evaluation process:

1. Is the work proposed within the scope of the active award?
2. Is the active award to be supplemented focused on software tool/workflow development, or is it a significant component of the award?
3. Does the user base justify this additional support? Will the proposed improvements help to increase the number of users and the impact of the software significantly?
4. Is the proposed project technically feasible within the supplement's funding period?
5. Are the proposed timelines adequate and realistic?
6. Is the proposed supplement project focused on software engineering for robust, sustainable software that is cloud ready (as opposed to enhancing scientific value)?
7. Does the project demonstrate sound software development practices, improve performance, interoperability, portability, reliability, community engagement, sustainability, and adoption?

Other Information:

It is strongly recommended that the applicants contact their respective program officers and grant management officer at the Institute supporting the parent award in advance to:

• Confirm that the supplement falls within scope of the parent award
• Request the requirements of the IC for submitting applications for administrative supplements

Investigators planning to submit an application in response to this NOSI are also strongly encouraged to contact and discuss their proposed research/aims with the scientific contact listed on this NOSI in advance of the application receipt date.

Following submission, applicants are strongly encouraged to notify the program contact at the IC supporting the parent award that a request has been submitted in response to this FOA in order to facilitate efficient processing of the request.

Inquiries

Please direct all inquiries to:

Scientific/Research Contact(s)

Fenglou Mao

Office of Data Science Strategy
Division of Program Coordination, Planning, and Strategic Initiatives
Office of the Director
Telephone: 301-451-9389
[email protected]

Heidi Sofia

Division of Genomic Medicine
National Human Genome Research Institute
Telephone: 301-480-3424
[email protected]