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National Institutes of Health (NIH) - Preparing Proposals

NIH Resources - Find links to information about working with the National Institutes of Health (NIH) when preparing proposals.

  • Grants Overview- Learn from NIH about funding, grant programs, how the grants process works, and how to apply. 
  • NIH Guide for Grants and Contracts - NIH's official publication of notices of grant policies, guidelines and funding opportunity announcements (FOAs) 
  • Standard Due Dates - Learn about application cycles and their relationship to due dates, review and council dates, and earliest possible start dates. 
  • NIH Grants Basics - Learn why it is important to understand the structure of NIH and how they approach grant funding, what types of organizations and people are eligible to apply, what they look for in a research project, and the types of grant programs they offer 
  • Table of Page Limits - Follow the page limits for the attachments in your grant application, unless otherwise specified in the funding opportunity announcement 
  • Research Training and Career Development Programs – Learn more about programs to help prepare individuals for careers in biomedical, behavioral, social, and clinical research. 
  • Notices of Policy Changes – Learn about selected policy notices that supersede information in the NIH Grants Policy Statement. 
  • Application Guide – Learn about the application instructions and guidance outlined in the funding opportunity announcement to submit grant applications to NIH 
  • How to Apply Video Tutorials 

Proposal Development using UC San Diego’s Kuali Research 

Refer to Kuali Research Training Guides for preparing and routing proposals in campus enterprise system.  Proposals must be created and processed through Kuali Research in order for the designated Sponsored Research Office to review and submit to the sponsor.   

To ensure researchers have the best chance of having their research projects funded, we need to ensure compliance with ever changing regulations and identify inaccuracies or errors that can be fixed before proposals are reviewed by funding agencies.  Refer to important proposal timeliness requirements to ensure your proposal receives institutional review by the SPO and is submitted accurately and by the sponsor deadline.

Additional Information important for NIH Proposal Preparation

  • Data Management PlansRefer to information about NIH Data Sharing including full policies, data sharing plan examples, and extensive resources 


The Just-in-Time (JIT) feature of the eRA Commons is available for applications that meet established business criteria and fall within a certain percentile or priority scoring range. The JIT feature allows a Signing Official to electronically submit additional grant application information that qualifies for submission and is requested by the grantor agency.

The additional information is requested after a peer review of a grant application has been completed and prior to funding. Requests may come in the form of eRA system-generated emails or contact made directly from the awarding agency via e-mail and/or phone. Applicants should not submit any JIT information until it is requested by the grantor agency.

Who can use the Just-in-Time feature?

  • Signing officials from applicant organizations can provide information and submit to the agency.
  • Principal Investigators can upload JIT information into the Commons for the Signing Official to submit.

** As with use of all eRA Commons-based features, a Commons username and password are needed to log in.

eRA Commons

Registration in eRA Commons 

To be able to use the NIH eRA Commons you must be registered as a user. 

Principal Investigators and postdoctoral personnel funded by NIH are required to be registered with the Commons, and to include their Commons user name in their proposals. 


All non-competing continuation applications subject to the Simplified Non-competing Award Process (SNAP) must be submitted electronically via the Commons as eSNAP proposals. The UCSD Signing Officials (SOs) have delegated "submit" authority for eSNAPS to UCSD Principal Investigators (PIs). 

Who needs to be registered 

The Office of Contract and Grant Administration (OCGA) is responsible for registering Principal Investigators (PI)s, Training Grant Business Officials (BO), Postdoctoral Staff (POSTDOC), Mentors of Fellows (SPONSOR), and Assistants (ASST), who are affiliated with UCSD. 

  • Only PD/PIs are required to have a Commons User Name for competing proposal submission. 
  • PostDocs need a Commons User Name for continuations. 

Co-Investigators or other Key Personnel are not required to have a Commons User Name. There are currently no Commons roles appropriate for personnel in those positions. Do not request registration for Co-Investigators or other Key Personnel.

Register as a user for UC San Diego

Health Sciences: email Nicole Foshey at
General Campus: Online Form

  • Next Steps:
    • Once registration information has been submitted by OCGA or HS SPPO, NIH will contact the newly registered user and provide a temporary password.
    • The user must then choose a personal password, using NIH's specific guidelines. NIH requires that a new Commons password be selected every six months.
  • Trainees are automatically invited to register (as TRAINEES) once the PI begins an appointment screen for them. Their eRA Commons registration will be initiated by NIH via a special mechanism. The trainee completes the registration process after being contacted by NIH.

Resources for eRA Commons

Grant Transfers

Grant Transfers take at minimum six months of planning and prescribed steps before the transfer is complete. The three institutional parties involved in agreeing to transfer a grant/contract from one institution to another include 1) the NIH Institute Program Officer and Grants Management Specialist, 2) the institution accepting the project(s) and 3) the institution relinquishing the project(s). All three parties must mutually agree to transfer the grant. The lead Principal Investigator must ensure that all cognizant institutional and NIH officials are informed months prior to the transfer, including the confirmation of the timing of the transfer (mid-year or anniversary).

At first knowledge of a NIH funded PI transferring from another institution to UC San Diego, or from UC San Diego to another institution, please read the following guidance:

Outgoing Grant Transfers (From UC San Diego to another institution)

Incoming Grant Transfers (From another institution to UC San Diego)

Public Access Policy/Publications

NIH Public Access Policy –To advance science and improve human health, NIH makes the peer-reviewed articles it funds publicly available on PubMed Central. The NIH public access policy requires scientists to submit final peer-reviewed journal manuscripts that arise from NIH funds to PubMed Central immediately upon acceptance for publication. Compliance with NIH policy is a statutory requirement and a term and condition of the grant award,cooperative agreement, and contracts.  For further assistance, visit the UCSD Biomedical and Medical Center Libraries.

Address Copyright

In order to comply with this requirement, University of California Investigators should enclose this letter signed by the Executive Provost and Executive Vice President, Academic and Health Affairs , University of California, Office of the President, with any articles submitted to publishers for possible publication. This letter gives notice to the publishers that if accepted for publication the article will be required by law to be posted on PubMed Central. If this letter is not submitted to the publisher at the time the article is sent in for review, it must be submitted along with any publication agreement signed by a University of California Investigator.

Submit Manuscripts

Certain publishers have agreed to automatically submit articles to PubMed Central on behalf of the authors. However, the Investigator should always verify that their published article is submitted to PubMed Central in compliance with this law.

If an Investigator's publisher is not on NIH's list of publishers that automatically submit articles to PubMed Central, then it is the Investigator's responsibility to submit their article to PubMed Central and verify that their article was received.

To facilitate the submission of articles to PubMed Central (PMC), NIH has developed the NIH Manuscript Submission (NIHMS) System. There are also detailed Online Instructions that are available for users.

NIH Resources regarding Policy on Public Access and Publications

Research Performance Progress Report (RPPR)

Research Performance Progress Report (RPPR) - The RPPR is used by grantees to submit progress reports to NIH on their grant awards. Refer to this overview of the annual RPPR, the final RPPR and the interim RPPR and provides resources to help you understand how to submit a progress report.  Refer to the Guide Notice - NIH Requires Use of RPPR for All SNAP and Fellowship Progress Reports, and Expands RPPR Functionality for more detailed information.

Resource Sharing

NIH Data Sharing Policy Review highlight selected NIH policies and related guidance on sharing of research resources developed with NIH funding.

It is NIH policy that the results and accomplishments of the activities that it funds should be made available to the public.  Principal Investigators (PIs) and funding recipient institutions are expected to make the results and accomplishments of their activities available to the research community and to the public at large. 

Sharing Model Organisms

NIH Requirements for Proposed Human Fetal Tissue Research

Human Fetal Tissue (HFT) Research

NIH defines Human Fetal Tissue (HFT) Research as research involving the study, analysis, or use of primary HFT, cells, and derivatives, and human fetal primary cell cultures obtained from elective abortions.

Changes to NIH Requirements Regarding Proposed HFT Research

For competing applications and competing revisions submitted after September 25, 2019, NIH will require applicants/contract offerors to address HFT requirements by providing the following:

  1. a justification of the use of HFT
  2. details regarding procurement and costs, and
  3. information about how the applicant/contract officer will use HFT

Applications that do not address all of the required information, including the detailed (non-modular) budget as specifically instructed, will be administratively withdrawn and not reviewed.

Specific guidelines for information and forms that must be included in applications are specified in the Guide Notices:

Compliance Requirements

Refer to the comprehensive links for UC San Diego Compliance Offices and requirements that must be followed for preparing proposals. 


NIH Budgets

For detailed information about preparing NIH budgets, refer to this comprehensive overview published and updated by NIH.

NIH Salary Cap

Effective January 3, 2021, the salary limitation for Executive Level II is $199,300.

For issued awards that were restricted to Executive Level, including competing awards already issued in FY2021, if adequate funds are available in active awards, and if the salary cap increase is consistent with the institutional base salary, recipients may re-budget funds to accommodate the current Executive Level II salary level.

For historical rates and more information on the current NIH salary cap, go to Salary Cap Summary (FY 1990 - Present)

Salary Waiver for Health Sciences Investigators

A salary waiver is an approval obtained by a Health Sciences investigator and his/her department prior to submission of a proposal for extramural support allowing a waiver of salary for effort devoted to the project.

Salary Waiver Requests are memos written by the PI’s home department Chair, addressed to Erika Wilson, Senior Director of HS SPPO. This request consists of an explanation on why salary has not been budgeted and what fund source(s) the department will use to cover that salary. Salary Waiver Requests are not automatically approved and should be requested with sufficient lead-time so that if turned down, the budget can be revised to include the required salary.


The Health Sciences policy for sponsored projects requires that commensurate salary is requested for effort applied on all extramurally funded research projects.

In the event a Health Sciences application proposes unfunded effort, a salary waiver request must be approved by the appropriate Dean's Office, either in the School of Medicine or Skaggs School of Pharmacy and Pharmaceutical Sciences. Contact the Health Sciences Sponsored Project Pre-Award Office (HSSPPO) for instructions.


  • NIH will not pay for stipends on a research grant because only compensation (i.e., salary) for effort can be paid on a research grant.
  • Postgraduates who are to be paid on a research grant should be budgeted as Postgraduate Researchers (PGRs), not as postdoctoral fellows, postgraduate fellows, etc.
  • Graduate students who are to be paid, should be budgeted as Graduate Student Researchers (GSRs). Payments to these individuals should not be referred to as stipends in the Budget Justification.

Graduate Student Compensation

Maximum Compensation

The maximum amount allowed by NIH for the support of a graduate student employed on a research grant or a cooperative agreement is equal to the amount paid to a first-year postdoctoral scientist at the same institution performing comparable work.

  • UC San Diego interprets this to be the postdoctoral National Research Service Award (NRSA) Stipend Level zero plus benefits.
  • For NRSA Levels, see the current NIH Notice: Ruth L. Kirschstein National Research Service Award (NRSA) Stipends, Tuition/Fees and Other Budgetary Levels Effective for Fiscal Year 2020 - NOT-OD-20-070

Total Compensation for "full-time" Work

Total compensation represents compensation for "full-time" graduate student work, which is the maximum the University will allow students to work outside their studies. Total compensation includes: salaryemployee benefits, and tuition remission

Depending on the graduate program, "full-time" means:

  • 50% (4.5 person months) during the academic year
  • 50–100% (1.5–3 person months) during the summer months

For students working less than "full-time," the NRSA level zero ceiling should be prorated.

Patient Care Costs

Refer to the NIH Grants Policy Statement on Research Patient Care Costs for more detailed information:

Indirect Costs (IDC)

  • Refer to updated information on UC San Diego’s IDC rates.
  • Special rates may apply for clinical space. Contact or 858-822-4109 (HSSPPO) for questions regarding locations that might be considered clinical.
  • NIH limits IDC on training grants and career awards to 8%.
  • No IDC is awarded on NIH conference grants.

Total Direct Cost of $500,000 or More

If total direct costs for any year are budgeted at $500,000 or more, excluding consortium IDC, written permission must be obtained from NIH at least 6 weeks prior to proposal submission. For further detailed information, see the following NIH Notices: NOT-OD-02-004 and NOT-OD-05-004.
For more information, contact our main desk at 858-534-3330 or email