Notice of Special Interest (NOSI): Administrative Supplements to Support Enhancement of Software Tools for Open Science

Notice Number: NOT-OD-20-073

Key Dates
Release Date: March 3, 2020
First Available Due Date: May 15, 2020
Expiration Date: May 16, 2020

Related Announcements

PA-18-591Administrative Supplements to Existing NIH Grants and Cooperative Agreements (Parent Administrative SupplementClinical Trial Optional)

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

National Eye Institute (NEI)

National Heart, Lung, and Blood Institute (NHLBI)

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 of Nursing Research (NINR)

National Institute on Minority Health and Health Disparities (NIMHD)

National Library of Medicine (NLM)

Fogarty International Center (FIC)

National Center for Complementary and Integrative Health (NCCIH)

National Center for Advancing Translational Sciences (NCATS)

National Cancer Institute (NCI)

Purpose

This Notice announces the availability of administrative supplements to active grants 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 in software development and advances in 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 and making data FAIR (findable, accessible, interoperable, and reusable) with high impact for open science. The supplements are intended to support 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 tools sustainable, contribute to open science, and take advantage of new data science and computing paradigms.

Background

As part of their research projects, investigators often produce innovative, scientifically valuable software tools. The tools have enabled scientists to efficiently process and manage data, mine, analyze, visualize, and interpret results. However, much of this valuable software has been built and supported under conditions that are no longer optimal in a rapidly changing landscape. Additionally, investigators lack the resources to adapt and revise the software to take advantage of new computing paradigms and to be robust, sustainable, and accessible to a broader community. This opportunity is intended to help researchers redeploy these research software tools to be robust and sustainable in a shared data ecosystem envisioned by the NIH ODSS.

The challenges are considerable. For example, many tools were developed and customized for data held on-premises, often optimized for local computing platforms (including the supporting libraries) and cannot be readily scaled or applied to open science data, such as those stored in a cloud environment. Software tools have most often been developed in academic settings in absence of input from research software engineers who can aid in this transition to operational efficiency and sustainability. There have been few practical ways to support joint efforts between researchers and software engineers with skills to develop and revise research tools for robust design, accessibility and scalability on modern computing platforms. The traditional grant funding process has emphasized innovation for research progress over the use of software engineering best-practices and design principles, which are essential for reliability and sustainability in an era of large-scale, integrated data.

It is the NIH vision to establish a modernized and integrated biomedical data ecosystem that adopts the latest data science technologies, including cloud computing, and best practice guidelines arising from community consensus, such as the FAIR principles and open-source development. This effort is described in the NIH Data Science Strategic Plan and led by the newly established ODSS. In addition to major efforts in IT infrastructure, data resources, workforce development, and policy considerations, the data science strategic plan includes goals to enhance software and workflows for the modern data ecosystem.

Research Objective

The goal of this Notice of Special Interest (NOSI) is to encourage researchers to engage in new types of collaborations that focus on research software. Supplements will support efforts that address robustness, sustainability, reusability, and scalability of existing biomedical research software tools and workflows of recognized scientific value. These efforts are expected to adhere to software engineering best practices and design principles and take significant steps toward sustainability in open source cloud-based environments. A broad range of projects that have significant biomedical research software or workflow development components are eligible, regardless of the scientific area of emphasis. The scope of each proposed project is defined by and limited to the aims of the funded project for which the supplement is being sought. Significant software engineering skills are expected to be needed to develop robust implementations and to adapt the software to changing computing paradigms. Thus, the supplements are primarily intended to provide support for software engineering staff and storage and computing costs that are required to test software revisions.

Delivering reliable, sustainable, and reusable software across multiple platforms is a whole-lifecycle effort, as illustrated in the following examples. Software development can be improved with enhancements to the development environment, including resources for building, testing, and community contribution. Engaging the community can improve robustness by making code available with appropriate open source licensing. Compliance with open interfaces and data formats can be added to enhance interoperability and reusability. Refactoring can be performed to take advantage of new hardware or compute environments (e.g., parallelizing a process or using a standard workflow language that can run in cloud environments). 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 by refinement of operating manuals.

Projects can propose to test cloud-readiness in a local, commercial, or public cloud environment. Working with the NIH STRIDES initiative (https://datascience.nih.gov/strides) is strongly encouraged. Cloud readiness is a blanket term that can encompass a range of activities. In this announcement cloud readiness refers to adapting to cloud architecture and extending the usefulness of software.

Examples to produce robust, sustainable or cloud-ready research software include, but are not limited to:

  • Adding APIs and services and reducing coupling and complex shared state
  • Decomposing and decoupling services from explicitly encoded data sources
  • Employing standard security that relies on cloud Identity and Access Management (IAM) models
  • Improving architecture to reduce chattiness over the network and to minimize data ingress/egress charges in cloud environments
  • Adopting standard input and output data formats
  • Factoring configuration of services into environment variables and configuration properties for deployment
  • Implementing standard logging models
  • Converting tools to provide clean input, output, and configuration that make them more usable in composition via workflow languages such as CWL and WDL
  • Enhancing source code 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

The supplement application must demonstrate the use of best software engineering practices and design principles. Examples of relevant projects that address one or more of the challenges toward becoming ready for open science and cloud environment include, but are not limited to:

  • Provisioning of standard source code structure, documentation, version management, build and test support in codebases that promotes community open source enhancement.
  • Refactoring of software to incorporate standard interfaces and data formats, replacement of built-in dependencies with standard and hardened libraries.
  • Adding APIs and services to software, especially when compliant to community standards
  • Refactoring software to scale efficiently on the cloud.
  • 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.
  • Enhancing data security and privacy protection.

Projects involving significant new scientific features as opposed to software engineering are NOT appropriate for this NOSI. Possible exceptions include enhanced data security and privacy functions.

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 FY2020 (Oct. 1, 2019 - Sept. 30, 2020) and not be in the final year or in a no-cost extension period at the time of the award.

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 6-10 awards will be made.

Eligible Activity Codes:

Administrative supplement requests may be submitted for the following activity codes: R01, U01, R03, R00, R21, R33, R35, R37, R61

Centers and multi-project grant mechanisms are not eligible.

Additional Information

Applications for this initiative must be submitted using PA-18-591 - Administrative Supplements to Existing NIH Grants and Cooperative Agreements (Parent Admin Supp Clinical Trial Optional) or its subsequent reissued equivalent.

All instructions in the SF424 (R&R) Application Guide and PA-18-591 must be followed, with the following additions:

  • Application Due Date(s) – May 15, 2020 by 5:00 PM local time of applicant organization.
  • For funding consideration, applicants must include "NOT-OD-20-073" (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 Research Strategy section of the application is limited to 3 pages. Research Strategy should include justification for significant user base and ‘cloud readiness’, timelines for activities proposed, indication of how supplement uses best software engineering practices and design principles.
  • Electronic submissions are required for this funding opportunity. The process for Streamlined Submissions using the eRA Commons cannot be used for this initiative.

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?
  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 or reliability, community engagement, sustainability, and adoption?

Other Information:

It is strongly recommended that the applicants contact their respective program officers 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:

Jessica Mazerik, Ph.D.
Office of Data Science Strategy
Division of Program Coordination, Planning, and Strategic Initiatives
Office of the Director
Jessica.mazerik@nih.gov