stanislavjiricek/phase-grant-proposal

phase-grant-proposal

The grant-proposal phase translates a defined research question into a competitive, funder-ready application. It begins with automatic discovery of ideation outputs and ends with a fully drafted, word-counted, reviewer-aligned document saved to .neuroflow/grant-proposal/.

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Phase entry checklist

Before drafting anything, verify:

• [ ] Researcher interview complete — answers saved to interview-[funder]-[date].md
• [ ] Objectives written to .neuroflow/objectives.md (one numbered sentence per objective)
• [ ] Ideation output discovered OR research question confirmed with user
• [ ] Funder and scheme identified
• [ ] Page/word limits per section confirmed
• [ ] Review criteria retrieved (from funder website or call document)
• [ ] Deadline confirmed and logged

Never skip the interview. Never draft without confirmed objectives.

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Interview protocol

Ask questions one or two at a time — conversational, not a form. Build context progressively.

Required questions:

1. Core research question (offer ideation summary if .neuroflow/ideation/ exists)
2. Funder and scheme (or URL to the call)
3. Budget ceiling and duration
4. Deadline
5. Specific objectives or aims — ask for 3–4 verb-led statements; these are the cornerstones
6. Preliminary data — what exists and how strong is the feasibility case?
7. Novelty — what does this do that current methods don't?
8. Team — PI and co-investigators with roles
9. Constraints — ethics status, required partnerships, pre-committed budget items
10. Previous grants for inspiration — if provided, build an inspiration map

After the interview:

• Save to .neuroflow/grant-proposal/interview-[funder]-[date].md
• Write objectives to .neuroflow/objectives.md (create or update)

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Objectives tracking

Objectives in .neuroflow/objectives.md are cornerstones for the entire grant. Rules:

1. Re-read objectives.md before drafting every section
2. For the Approach/Methodology section: verify all N objectives appear explicitly — flag any missing
3. For the quality checklist: verify all N objectives appear in both Aims AND Methodology
4. If the user adds or changes an objective mid-session: update objectives.md immediately and note the change in reasoning/grant-proposal.json

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Panel research protocol

When the user agrees to panel research:

1. Ask for the panel listing URL
2. Fetch the page (WebFetch)
3. For each panel member found: search their background (WebSearch — 2–3 key papers, primary topics, methodological focus)
4. Build a panel profile table: | Panel name | Member | Research background | Relevance to project |
5. Suggest top 2–3 panels with rationale (one sentence each)
6. Save to .neuroflow/grant-proposal/panels/panel-analysis-[funder]-[date].md
7. Use the preferred panel's terminology and methodological frame throughout the proposal — reviewers respond to language that mirrors their own thinking

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Inspiration map protocol

When the user provides previous grant documents:

1. Read each document in full
2. Build a cross-reference table:

| New grant section   | Grant A              | Grant B              |
|---------------------|----------------------|----------------------|
| Specific Aims       | Sec 1 (pp. 1–2)      | Introduction (pp. 1–3)|
| Background          | Lit Review (pp. 3–6) | Background (pp. 2–5) |
| Innovation          | Novelty (p. 7)       | Not present          |
| Approach            | Methods (pp. 8–14)   | Research Plan (pp. 6–12)|
| Budget              | Budget (pp. 15–16)   | Budget narrative (p.13)|

3. Save to .neuroflow/grant-proposal/inspiration-map-[date].md
4. Before drafting each section: reference the corresponding inspiration entry — adopt the structural approach and framing style while producing original content
5. When inspiration sections contain strong language or argument patterns: note them explicitly in the draft as structural guides

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Ideation discovery protocol

If ideation files exist (.neuroflow/ideation/*.md):

1. List all files
2. Read each and extract: research question, modality, population, preliminary data, key references
3. Present a 3–5 bullet summary during the interview
4. Ask: "Is this still the right question to build the grant around?"

If no ideation files exist: the interview questions cover everything needed.

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Funder knowledge base

Budget figures, page limits, and scheme names are approximate typical values as of 2024–2025. Verify against the current call document or funder website before advising a user — requirements change each cycle.

NIH (USA)

• Mechanisms: R01 (5 yr, $500K DC/yr), R21 (2 yr, $275K total), R03 (2 yr, $50K/yr), K awards (career development), U01 (cooperative agreement)
• Key sections: Specific Aims (1 page — the most critical), Research Strategy (12p for R01: Significance, Innovation, Approach), Human Subjects, Authentication of Resources, Bibliography
• Review criteria (scored 1–9, lower = better): Significance (gap and impact), Investigators (team track record), Innovation (conceptual or methodological novelty), Approach (rigor, feasibility, power analysis), Environment (facilities, collaborations)
• Common weaknesses cited by study sections: insufficient power analysis, vague alternatives for failed aims, overambitious scope, lack of preliminary data, budget not justified
• Register on: NIH eRA Commons; submit via Grants.gov or ASSIST

ERC (EU)

• Mechanisms: Starting Grant (≤7 yr post-PhD, €1.5M), Consolidator (7–12 yr post-PhD, €2M), Advanced Grant (established PIs, €2.5M), Synergy Grant (2–4 PIs, €10M)
• Key sections: B1 Extended Synopsis (5p), B2 Full Proposal (Part B1 + B2 up to 15p for StG; 50p for AdG)
• Review criteria: Scientific excellence (primary), Impact (to science and society), Quality and efficiency of implementation (team, resources, management)
• Common weaknesses: proposal not ambitious enough for ERC standards, host institution not sufficiently described, no clear "frontier research" framing
• Note: ERC funds PI-driven curiosity research, not translational or applied work — frame accordingly

Wellcome Trust (UK)

• Mechanisms: Discovery Award (£3–5M, 5 yr), Investigator Award (£1–3M, 5 yr), Sir Henry Wellcome (4 yr postdoc award), Collaborative Award
• Key sections: Flexible — Wellcome provides a template; typically Summary, Scientific rationale, Approach, Impact, Team, Budget
• Review criteria: Scientific opportunity (is this the right question?), Team (can they deliver?), Delivery (is the plan achievable?)
• Note: Wellcome values interdisciplinary approaches and expects explicit attention to open science (data sharing, preregistration)

MRC (UK)

• Mechanisms: Programme Grant, Project Grant, Clinician Scientist Fellowship, Senior Research Fellowship
• Key sections: Case for Support (20p), Justification of Resources
• Review criteria: Importance (scientific and health impact), Quality and originality, Investigator capability, Resources

GAČR (Czech Republic)

• Mechanisms: Standard Project (3 yr, ~5M CZK/yr), Junior Star (5 yr, ~9M CZK/yr), EXPRO excellence (5 yr, ~10M CZK/yr), International bilateral projects
• Key sections: Project summary (Czech + English, 600 words), State of the art, Objectives and hypotheses, Methodology, Feasibility, Budget justification, Timeline
• Review criteria: Originality and scientific quality, Feasibility, Team qualification, Budget adequacy
• Note: Czech-language applications required for domestic funding; international projects use English

DFG (Germany)

• Mechanisms: Research Grants (Emmy Noether, Heisenberg, SPP priority programs, Collaborative Research Centres / SFB)
• Key sections: Work programme (10–15p), Preliminary work, Requested funds, Curriculum vitae (tabular, max 2p)
• Review criteria: Scientific quality, Originality, Feasibility, Training of junior researchers

Horizon Europe (EU)

• Mechanisms: EIC Pathfinder (€3M, 4 yr), EIC Transition, EIC Accelerator (SMEs), MSCA Fellowships, ERC (separate)
• Key sections: Excellence (concept, methodology), Impact (strategy, pathways to impact), Implementation (timeline, resources, team)
• Review criteria: Excellence (novelty, scientific quality), Impact (significance, dissemination), Implementation (coherence, resources)

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Neuroscience-specific grant writing tactics

Power analysis

• Always include a formal power analysis, even if approximate
• For EEG/ERP: reference pilot data or published effect sizes (Cohen's d for amplitude differences; cite the source)
• For fMRI: cite comparable studies for BOLD effect sizes; state voxel-wise threshold + cluster correction
• For behavioural measures: G*Power output with exact parameters (α, 1-β, effect size, allocation ratio)
• Reviewers from biostatistics panels will look for this — a missing power analysis is a common scoring weakness

Preprocessing and analysis plan

• Name the software pipeline explicitly (MNE-Python, EEGLAB, SPM12, FSL, Brainstorm, ERPLAB)
• State: sampling rate, bandpass filter cutoffs, epoch window, artifact rejection method (ICA, threshold)
• For fMRI: TR, slice timing, HRF model, motion scrubbing threshold
• Reference BIDS compliance if relevant

Participant recruitment

• State inclusion/exclusion criteria precisely
• Address any vulnerable populations explicitly (IRB / ethics committee considerations)
• If EEG: mention net type, cap system, electrode count
• Provide realistic recruitment numbers with dropout correction (plan for 20% attrition minimum)

Preliminary data

• Show it early — link pilot data to feasibility
• If no preliminary data exists: substitute published proof-of-concept studies with your team's commentary
• Use figures — a single figure showing pilot ERP or BOLD effect is worth 200 words

Budget granularity

• Break personnel costs to FTE fractions (PI 20%, postdoc 100%, RA 50%, etc.)
• List equipment by model number and price if >$5K items
• Consumables: EEG gel/electrode replacement, MRI contrast agents, participant payment
• Travel: conference attendance, site visits (justify each)
• Indirect costs: confirm the correct rate for your institution

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Review criteria alignment checklist

For each major funder, map every section of the proposal to the review criterion it addresses:

| Section | NIH criterion | ERC criterion | Wellcome criterion | |---|---|---|---| | Specific Aims | Significance + Innovation | Scientific excellence | Scientific opportunity | | Background | Significance | Scientific excellence | Scientific opportunity | | Innovation | Innovation | Scientific excellence | — | | Approach | Approach + Environment | Quality of implementation | Delivery | | Team | Investigators | Quality of implementation | Team | | Budget | — | Quality of implementation | Delivery | | Preliminary data | Approach | Scientific excellence | Delivery |

Use this mapping to ensure reviewer criteria are explicitly addressed in the text — never assume reviewers will infer alignment.

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Common fatal weaknesses (avoid these)

1. Overambitious scope — three aims that cannot be done in the funded period
2. No power analysis — instant credibility loss with quantitative reviewers
3. Vague alternatives — "if Aim 1 fails, we will modify our approach" is not acceptable
4. Hypothesis-free Approach — methods with no testable prediction attached
5. Budget not justified — line items without rationale
6. Ignoring funder priorities — NIH wants disease relevance; ERC wants frontier science; these are different framings
7. Insufficient preliminary data — especially for NIH R01; reviewers score feasibility based on prior work
8. Poor Specific Aims page — the single most influential page in a US grant; if reviewers are not sold after 1 page, scores suffer

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Workflow integration

Reads from

• .neuroflow/ideation/ — research question, literature, study design drafts
• .neuroflow/project_config.md — team, institution, phase, modality
• .neuroflow/objectives.md — project objectives cornerstones (re-read before every section)
• .neuroflow/grant-proposal/flow.md — prior grant context if resuming
• Previous grant documents (provided by user) — for inspiration map

Writes to

• .neuroflow/objectives.md — written/updated after interview confirms objectives
• .neuroflow/grant-proposal/interview-[funder]-[date].md — interview transcript
• .neuroflow/grant-proposal/inspiration-map-[date].md — cross-reference table (if previous grants provided)
• .neuroflow/grant-proposal/panels/panel-analysis-[funder]-[date].md — panel profiles (if panel research done)
• .neuroflow/grant-proposal/draft-[funder]-[date]-[section].md — per-section drafts
• .neuroflow/grant-proposal/grant-[funder]-[date].md — full consolidated draft
• .neuroflow/grant-proposal/flow.md — funder, scheme, deadline, section status
• .neuroflow/sessions/YYYY-MM-DD.md — session log (using ## milestone headers)
• project_config.md — funder and deadline (with user confirmation)

Connects to

• /ideation — if no research question exists, redirect the user there first
• /experiment — paradigm details flow into the Approach section
• /preregistration — registered analysis plan can be referenced in the Approach
• /write-report — funder progress reports use the same structure

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Output format standard

Each drafted section is presented as a standalone block:

## [Section name]  ([page limit] page / [word limit] words)

[Drafted content]

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Word count: NNN / NNN limit    ✅ within limit  /  ⚠️ over by NNN words

After each section, offer:

• "revise" — rework the current section
• "next" — proceed to the next section
• "expand [topic]" — add depth to a specific part of the current section
• "save" — write current section to the draft file
• "checklist" — run the quality checklist against the current section

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Relevant skills

• neuroflow:neuroflow-core — lifecycle and .neuroflow/ write rules (read first)
• neuroflow:phase-ideation — if user needs to define the research question first
• neuroflow:phase-experiment — paradigm design details for the Approach section
• neuroflow:phase-preregistration — link registered analysis plan
• neuroflow:humanizer — apply to every drafted section to strip AI signatures, fix rhythm, and calibrate register so the prose reads as genuinely human-authored
• sequentialthinking MCP — invoke before drafting Innovation and Approach sections to build a rigorous logical argument chain

Slash command

/neuroflow:grant-proposal — runs this workflow as a slash command.