Agency	Mechanism	Key Format
NIH	R01	1p aims + 12p strategy
NIH	R21	1p aims + 6p strategy
NIH	R03	1p aims + 6p strategy (2 years, $50K/year)
NIH	DP2	10p essay (no aims page)
NIH	K99/R00	1p aims + 12p strategy + 6p candidate + 6p mentoring
NIH	K08/K23	1p aims + 12p strategy + candidate section + career goals + mentoring plan
NIH	F31/F32	1p aims + 6p strategy + applicant background + sponsor info + training plan
NIH	R24	1p aims + 12p strategy (resource-focused)
NIH	R43/R41 (SBIR/STTR Phase I)	1p milestone-driven aims + 6p strategy; no Commercialization Plan allowed
NIH	R44/R42 (SBIR/STTR Phase II, Fast-Track, Direct to Phase II)	1p milestone-driven aims + 12p strategy + 12p Commercialization Plan
NSF	Standard	1p summary + 15p project description
NSF	CAREER	Integrates research + education (see `references/career-award-guide.md`)

Core Workflow

Step 0: Parse the NOFO/FOA

Before writing anything, read the Notice of Funding Opportunity (NOFO) or Funding Opportunity Announcement (FOA) thoroughly. Extract and record:

Mechanism and agency: Determines page limits, required sections, and review criteria
Specific objectives: Many NOFOs list required research areas, populations, or methods
Page limits: Verify per-section limits (they vary by mechanism and can change between cycles)
Review criteria and weights: Identify how the review panel will score the application
Special requirements: Data sharing plans, milestones, letters of support, human subjects provisions
Eligible PIs: Career stage, citizenship, institutional requirements
Budget constraints: Direct cost caps, duration limits, cost-sharing restrictions
Submission deadline and receipt date: Plan backward from the deadline

Store the NOFO URL and key extracted details in NOFO.md within the proposal directory. Flag any requirements that deviate from the standard mechanism template.

Step 1: Plan the page budget

Before drafting, allocate pages across sections. Staying within limits while giving each section adequate space is a critical constraint. Use these as starting points and adjust based on the specific aims and preliminary data available:

R01 (12 pages total strategy):

Significance: ~2 pages
Innovation: ~1.5 pages
Approach: ~8.5 pages (including ~1.5-2p preliminary data, ~5-6p aims, ~1p rigor, ~0.5p timeline)

R21 (6 pages total strategy):

Significance: ~1 page
Innovation: ~0.75 pages
Approach: ~4.25 pages

R03 (6 pages total strategy):

Significance: ~1 page
Innovation: ~0.5 pages
Approach: ~4.5 pages (focus on methods; preliminary data less critical)

K99/R00 (12 pages strategy + 6p candidate + 6p mentoring):

Research strategy follows R01 proportions
Candidate section: training background, career trajectory, independence plan
Mentoring plan: structured activities, timeline, evaluation

F31/F32 (6 pages strategy):

Follows R21 proportions for strategy
Applicant background and goals: training rationale, career objectives
Sponsor and institutional environment: mentor qualifications, training plan, resources

Step 2: Draft the Specific Aims page (NIH) or Project Summary (NSF)

Branch first: is this a small-business application?

If the mechanism is SBIR or STTR (R41, R42, R43, R44), stop and use examples/sbir-specific-aims-template.md instead of the hypothesis-driven template below. Small-business aims are milestone-driven: each aim carries a month window and closes with a quantitative acceptance threshold, with go/no-go conditions where one aim gates the next. Using the hypothesis-driven structure on a small-business application loses points on Approach. See references/sbir-sttr-requirements.md.

NIH Specific Aims (1 page, <650 words):

Opening (2-3 sentences): State the problem and critical gap concisely
Bold overarching goal: One sentence in bold stating the ultimate objective, followed by innovation/methodology explanation
Brief scope statement: Recruitment/context (can merge with goal if space is tight)
Aims (2-3): Each titled in bold with an action verb
- Sub-hypotheses: Italic labels (Hypothesis 1A:), one sentence each
- After each hypothesis: "We will..." with bold key methodological innovations
Expected Impact: Bold header, numbered list of concrete deliverables

See examples/specific-aims-template.md for an annotated template.

NSF Project Summary (1 page):

Overview paragraph
Intellectual Merit paragraph
Broader Impacts paragraph

Step 3: Draft the Research Strategy (NIH) or Project Description (NSF)

NIH Research Strategy (Significance -> Innovation -> Approach):

Significance (~2p for R01): Problem -> Gap -> Why it matters -> What success enables
Innovation (~1.5p for R01): What is new -> Why current approaches fail -> Field advancement. Distinguish conceptual, technical, and methodological innovations
Approach (~8.5p for R01): Preliminary data -> Aim-by-aim breakdown (Rationale -> Methods -> Hypothesis -> Analyses -> Expected outcomes -> Problems/Alternatives) -> Rigor & Reproducibility -> Timeline

Consult references/research-strategy-guidelines.md for detailed section guidance.

NSF Project Description (15 pages):

Results from Prior NSF Support (within the 15 pages)
Research Plan
Broader Impacts activities

NSF CAREER: Research and education plans must be bidirectionally integrated. See references/career-award-guide.md.

Step 4: Draft supporting sections

After the core strategy is drafted, prepare the remaining required documents:

Facilities & Other Resources: Describe lab space, equipment, computational infrastructure, core facilities, and collaborating sites. Emphasize resources that directly enable the proposed work.
Equipment: List major equipment available for the project. Distinguish from equipment requested in the budget.
Data Management & Sharing Plan (DMS, typically 2 pages): Describe what data will be generated, how it will be stored, standards for formatting, timeline for sharing, and any access restrictions. Follow the 2023 NIH DMS Policy or NSF DMP requirements.
Budget Justification: Justify every budget category. See references/budget-justification-guide.md and examples/budget-justification-template.md.
Letters of Support: Request from collaborators, consultants, and core facility directors. Each letter should confirm the specific contribution described in the proposal.

For fellowship and career development mechanisms (F31, F32, K08, K23, K99):

Candidate/Applicant Section: Training history, skills acquired, career goals, and how this award fills gaps
Mentoring/Training Plan: Structured mentoring activities, timeline, and evaluation criteria
Sponsor Statement: Mentor's qualifications, commitment, and training record

Step 5: Apply writing style

Consult references/writing-style-guide.md and references/tone-guide.md for established voice conventions. Key principles:

Direct, active voice ("We will demonstrate" not "It will be demonstrated")
Strategic bolding: overarching goal, aim titles, one key innovation per aim, memorable phrases
Italic hypothesis labels
No em-dashes (PI style preference, not a universal standard); use commas, semicolons, or parentheses
Define abbreviations on first use (once per document)
Quantify when possible (N=24, 6-month, etc.)
Bold claims backed by technical precision
First person for vision ("I propose"), "we" for team work

After drafting, invoke the fully qualified manuscript:humanizer skill through the host's skill-invocation mechanism as a final natural-writing pass. Pay particular attention to:

Pattern 1 (significance inflation): strip filler ("pivotal moment", "evolving landscape") but keep evidence-backed importance ("affects 1.2M patients annually").
Pattern 4 (promotional language): "groundbreaking", "transformative", "paradigm-shifting" read as red flags in Innovation sections. Let the methods carry the claim.
Pattern 24 (excessive hedging): tighten stacked hedges, but keep appropriate uncertainty in Approach risks/alternatives.
Patterns 17 and 19 (title case, curly quotes): for NIH/NSF, defer to mechanism formatting in Step 6.

Step 6: Format for submission

NIH LaTeX formatting:

Arial 11pt body, 12pt title. Note: Arial is not available in standard LaTeX distributions; use the helvet package for Helvetica, which is an accepted substitute.
0.5in margins all sides
No indentation; 4pt space between paragraphs
Justified text
Fit within page limits by trimming content, not reducing spacing

NSF formatting:

Arial/Helvetica 10pt+, Times New Roman 11pt+, or Palatino 10pt+
1 inch margins minimum
Single-spaced

Step 7: Pre-submission checklist

Before submitting, verify every item:

Content completeness:

All required sections present per the NOFO
Page limits respected for every section
All aims referenced in both the Specific Aims page and the Approach
Rigor and reproducibility addressed (biological variables, authentication, blinding)
Timeline with milestones included
All abbreviations defined on first use
All figures referenced in text and legible at printed size
Citations complete and formatted per agency requirements

Budget and administrative:

Budget matches the narrative (effort levels, equipment, travel consistent with text)
Budget justification covers every line item
Biosketches current and formatted correctly (SciENcv for NIH)
Letters of support included for all named collaborators and consultants
Data Management and Sharing Plan included
Facilities and Equipment documents included
Human subjects or vertebrate animals sections complete (if applicable)

Formatting:

Font, margins, and spacing meet agency requirements
No text extends beyond page limits
PDF renders correctly (no font substitution, no clipped figures)
File naming follows agency conventions

For resubmissions (A1):

Introduction page present and within 1-page limit
All reviewer critiques addressed
Changes marked in the body of the application
See references/resubmission-guide.md for detailed guidance

Special Cases

DP2 (New Innovator Award)

NO specific aims page; write a 10-page essay instead
Emphasize PI creativity and innovation
Written for broad audience
Use catchy component names
Include "What If" contingency section

Fellowship Mechanisms (F31/F32)

Applicant background and goals section replaces the standard biosketch narrative
Sponsor and co-sponsor statements are critical; coordinate closely with mentors
Training plan must describe specific skills to be acquired
Institutional environment section should demonstrate access to resources and training opportunities
See references/nih-requirements.md for page limits and section details

Career Development (K08/K23)

Candidate section describes prior training and career goals
Career development plan outlines specific training activities and timeline
Mentoring plan must name mentors and describe their expertise and roles
Research plan follows standard structure but is evaluated in the context of career development
See references/nih-requirements.md for details

SBIR/STTR (R41, R42, R43, R44)

Milestone-driven aims, not hypotheses: use examples/sbir-specific-aims-template.md
Reviewed on the five classic criteria (Significance, Investigator(s), Innovation, Approach, Environment), not the RPG Simplified Review Framework
Commercial potential is scored inside those criteria, in every phase, including Phase I
Write for a panel where only some reviewers know the field; all of them score
Restate every result that matters inside the Research Strategy; referenced manuscripts and preprints score nothing
Phase II, Direct to Phase II, Phase IIB, Fast-Track, and the Commercialization Readiness Pilot require a 12-page Commercialization Plan; a standalone Phase I cannot include one
Collect letters of interest from potential customers early, not only from academic collaborators
Phase I runs up to 2 years, so a 24 to 30 month scope is often Phase I plus Phase II rather than a Direct to Phase II
A Phase I may state an intent to join I-Corps at NIH for customer discovery, which strengthens a later Commercialization Plan
See references/sbir-sttr-requirements.md, references/commercialization-plan-guide.md, and references/niaid-sample-applications.md

Resubmissions

Address reviewer concerns point-by-point in an Introduction (1 page)
Bold changes or mark with change bars
Keep reviews in a reviews/ directory for reference
See references/resubmission-guide.md for detailed strategy

Proposal Directory Structure

When creating a new proposal, follow this structure:

proposals/{mechanism}/{year}-{short-name}/
├── README.md            # Proposal overview: title, mechanism, PI, deadline, status
├── NOFO.md              # Extracted NOFO requirements with URL link to the original
├── ideas.md             # Early brainstorming, concept development, design decisions
├── research.md          # Background research notes, key references, field context
├── lit-review/          # Literature review materials: search results, annotated bibliographies
├── submission/          # Final submission-ready documents
│   ├── specific-aims.md
│   ├── research-strategy/
│   │   ├── significance.md
│   │   ├── innovation.md
│   │   └── approach.md
│   ├── budget/          # Budget spreadsheets, justification narrative, subaward budgets
│   └── biosketches/     # PI and co-investigator biosketches (SciENcv exports)
├── drafts/              # Working drafts and intermediate versions (not submission-ready)
├── reviews/             # Summary statements, reviewer comments, resubmission notes
└── figures/             # All figures: conceptual diagrams, preliminary data, methods workflows

Additional Resources

Reference Files

For detailed guidance, consult:

references/nih-requirements.md - NIH mechanisms, page limits, review criteria, deadlines
references/nsf-requirements.md - NSF mechanisms, formatting, review criteria
references/research-strategy-guidelines.md - Detailed section-by-section writing guide for NIH research strategy
references/writing-style-guide.md - Comprehensive scientific writing style guide
references/tone-guide.md - Narrative tone patterns and voice conventions
references/budget-justification-guide.md - Budget categories, modular vs detailed, common pitfalls
references/career-award-guide.md - NSF CAREER award requirements and integration guidance
references/resubmission-guide.md - Resubmission strategy, Introduction page format, change marking
references/sbir-sttr-requirements.md - SBIR/STTR program structure, budgets, phase choice, Fast-Track, eligibility, and how small-business review differs
references/commercialization-plan-guide.md - The 12-page Commercialization Plan, section by section, with the criticisms weak plans draw
references/niaid-sample-applications.md - Curated index of the NIAID funded sample applications and summary statements, with what to study in each

Example Templates

examples/specific-aims-template.md - Annotated specific aims page with placeholders (hypothesis-driven; not for SBIR/STTR)
examples/sbir-specific-aims-template.md - Milestone-driven specific aims for SBIR/STTR, with a contrast table against the generic template
examples/budget-justification-template.md - Modular and detailed budget formats

Scripts

scripts/fetch-niaid-samples.sh - Downloads the NIAID small-business sample applications and summary statements, optionally converting them to markdown. The samples are copyrighted and licensed for nonprofit educational use only, so they are fetched on demand rather than bundled. Manifest: scripts/niaid-samples.txt.

Literature Search

Use the fully qualified opencite:opencite skill through the host's skill-invocation mechanism for literature searches to support proposals:

uvx opencite search "topic" --max 20 -f bibtex -o refs.bib
uvx opencite canonical "field" --max 10

grant-writing

Grant Writing Skill

Supported Mechanisms