@pikaa-ai/pikaa 0.3.23 → 0.3.25

package/skills/relsa-severity-assessment/SKILL.md

@@ -1,354 +0,0 @@
----
-name: relsa-severity-assessment
-description: Multivariate severity assessment and humane endpoint prediction for laboratory animal studies using the RELSA (RELative Severity Assessment) score and ARIMA-based foRcast forecasting. Use when combining welfare readouts — body weight or weight loss, body temperature, clinical or nesting scores, biomarkers, activity, heart rate, burrowing, wheel running — into one severity score per animal per day, when asking which animals are at risk of reaching a humane endpoint or when one will be reached, when defining attention/danger zones or thresholds on a severity scale by kernel density estimation, or when reporting severity for a 3Rs, refinement, animal-welfare, or EU Directive 2010/63/EU severity-assessment context. Covers directionality ("turned" variables), baseline normalization, reference sets, RELSA weights, ARIMA prediction intervals, and RMSE/PICP/MPIW evaluation.
-license: MIT
-allowed-tools: Read Write Edit Bash
-compatibility: Requires Python >=3.10 with numpy, pandas, and scipy; statsmodels >=0.14 for forecasting and matplotlib for figures. Tested with numpy 2.5, pandas 3.0, scipy 1.18, statsmodels 0.14.6. No network access needed.
-metadata:
-  version: "1.0"
-  skill-author: K-Dense Inc.
----
-
-# RELSA severity assessment and humane endpoint forecasting
-
-## Overview
-
-Severity assessment in animal research is legally mandatory and scientifically load-bearing:
-it drives humane endpoint decisions, and poor welfare monitoring degrades reproducibility.
-The usual practice evaluates each readout in isolation — weight loss here, a clinical score
-there — which makes it hard to say how badly an individual animal is actually doing.
-
-This skill implements two published procedures that address that:
-
-- **RELSA** (Talbot et al., 2022) combines several outcome measures into one score per animal
-  per time point, expressed *relative to a reference set of known burden*. RELSA = 0 is
-  baseline; RELSA = 1 means the animal has reached the reference set's maximum deviation.
-- **foRcast** (Lutscher et al., 2026) fits an ARIMA model to an individual animal's RELSA
-  trajectory and forecasts the next score with a 95% prediction interval, so animals heading
-  for a humane endpoint can be identified before they get there. Kernel density estimation on
-  the RELSA scale supplies candidate *attention* and *danger* zones for interpretation.
-
-The point is **refinement**: give at-risk animals attention earlier, and avoid euthanising
-animals that would have recovered. Both procedures are aids to severity assessment, not
-decision rules — see [Boundaries](#boundaries-state-these-when-you-report).
-
-## When to use this skill
-
-- Combining weight loss, temperature, clinical scoring, biomarkers, or telemetry into a single
-  per-animal severity score
-- Asking which animals in a cohort are at risk of reaching a humane endpoint, or predicting
-  the severity score at a coming time point
-- Comparing severity between treatment groups, interventions, or animal models on a common
-  relative scale
-- Defining thresholds or zones on a severity scale from the data
-- Writing the severity-assessment section of an animal welfare report, a 3Rs/refinement
-  analysis, or an application under EU Directive 2010/63/EU
-
-For general forecasting of a time series that is not a severity score, use
-**timesfm-forecasting** or **statsmodels**. For study design and sample size, use
-**experimental-design** and **statistical-power**.
-
-## Installation
-
-```bash
-uv pip install "numpy>=1.26" "pandas>=2.0" "scipy>=1.11" "statsmodels>=0.14" matplotlib
-```
-
-`relsa_score.py` and `kde_thresholds.py` need only numpy/pandas/scipy; statsmodels is required
-for forecasting and matplotlib only for figures.
-
-## Data format
-
-One row per animal per time point, in a CSV:
-
-| id | treatment | condition | day | temp | weight | score | il6 |
-| --- | --- | --- | --- | --- | --- | --- | --- |
-| M01 | treated | endpoint | -1 | 37.15 | 25.17 | 0 | 35.1 |
-| M01 | treated | endpoint | 0 | 37.26 | 25.25 | 0 | 39.5 |
-| M01 | treated | endpoint | 1 | 35.83 | 23.12 | 4 | 162.0 |
-
-- `id` and a time column (`day`, `time`, `hour`, …) are required; `treatment` and `condition`
-  are optional labels used for grouping and for selecting the reference set.
-- Time may be days, hours, or minutes — just keep it monotonic per animal. The RELSA
-  convention codes the baseline time point as `-1`.
-- **One row per animal per time point.** Average hourly telemetry to one value per interval
-  first (the published models average heart rate, HRV, and temperature, and sum activity).
-- Leave missing measurements empty. They are dropped from the score, never imputed — a
-  missing value treated as "no deviation" biases severity downward.
-
-`assets/example_cohort.csv` is a small synthetic cohort (6 mice, 9 days, temperature, body
-weight, an 0–8 clinical score, and an IL-6-like biomarker) used by every command below, so
-each one is runnable as written.
-
-## The four decisions that determine the result
-
-Make these explicitly and write them into the methods. Nothing else about the procedure
-matters as much.
-
-**1. Directionality — which variables rise under worsening?** Falling is the default (body
-weight, activity, food intake, burrowing, wheel running). Variables that *rise* must be
-declared as `--turned`: clinical scores, inflammatory biomarkers, fever, tachycardia. Get
-this wrong and the variable contributes nothing at all, silently, because deviations in the
-"wrong" direction are floored at zero. Body temperature is model-dependent — it *falls* in
-sepsis and endotoxaemia, *rises* in fever models. Nothing in the data can settle this for you:
-in the published sepsis model activity legitimately swings further above baseline than below,
-so only a variable that *never once* moves the declared way is detectable, and
-`build_reference()` warns about exactly that case.
-
-**2. The reference set — relative to what?** RELSA scores mean nothing without it. Use the
-group assumed to carry the greatest burden in your model (the published studies use the
-highest-dose or endpoint-reaching treatment group). Too mild a reference pushes every score
-above 1; too severe compresses everything toward 0. Save it with `--save-reference` and reuse
-it with `--load-reference` so later cohorts stay on the same scale.
-
-**3. Scores with a zero baseline.** A clinical score of 0 in a healthy animal cannot be
-ratio-normalized — `0/0` is undefined. Use `--score-scale score=8` to map the score's scale
-instead (healthy → 100%, worst possible → 200%), which also marks it as turned. This mapping
-is a modelling choice about how much one score point is worth relative to one percent of body
-weight; state it. The alternative is to keep the score out of RELSA and use it as an
-independent endpoint criterion.
-
-**4. Which variables are measured throughout.** Because the score averages over whichever
-variables are available, a variable that appears or disappears mid-trajectory moves the score
-by itself. In the published sepsis data, adding body weight — recorded only on the day of
-euthanasia — drops that animal's endpoint score from 0.93 to 0.83 for no biological reason.
-`relsa_scores()` warns when composition changes; score the variables present throughout.
-
-## Workflow
-
-### Step 1 — compute RELSA scores
-
-```bash
-python scripts/relsa_score.py assets/example_cohort.csv \
-    --variables weight,temp,score,il6 \
-    --normalize weight,temp,il6 \
-    --turned il6 \
-    --score-scale score=8 \
-    --baseline-time -1 \
-    --reference-group condition=endpoint \
-    --save-reference reference.json \
-    --out relsa_scores.csv
-```
-
-The reference model is echoed so the scale is auditable:
-
-```
-reference model: assets/example_cohort.csv [condition=endpoint]
-  animals=2  rows=18  baseline_time=-1.0
-  variable      turned   max reached   max delta
-  weight            no         82.40       17.60
-  temp              no         92.79        7.21
-  score            yes        187.50       87.50
-  il6              yes        797.72      697.72
-```
-
-`relsa_scores.csv` holds each variable's weight alongside the score, which is what makes a
-score explainable — here M01 deteriorating to its endpoint, M03 peaking on day 3 and
-recovering:
-
-```
- id  time  weight  temp  score  il6  n_vars  relsa
-M01     1    0.46  0.49   0.57 0.52       4   0.51
-M01     3    0.84  0.76   1.00 0.89       4   0.88
-M01     5    1.00  1.00   1.00 1.00       4   1.00
-M03     3    0.56  0.44   0.57 0.54       4   0.53
-M03     5    0.35  0.26   0.43 0.32       4   0.35
-M03     7    0.12  0.06   0.14 0.11       4   0.11
-```
-
-A weight of 1.00 means that variable hit the reference maximum; `n_vars` is how many
-variables entered the score at that time point.
-
-Same thing from Python, when you need the objects:
-
-```python
-import sys; sys.path.insert(0, "scripts")
-from _common import read_relsa_table, score_to_percent
-from relsa_score import prepare, build_reference, relsa_scores
-
-frame = read_relsa_table("assets/example_cohort.csv")
-frame["score"] = score_to_percent(frame["score"], max_score=8)   # 0-8 clinical score
-VARS, TURNED = ["weight", "temp", "score", "il6"], ["score", "il6"]
-
-prepared  = prepare(frame, normalize=["weight", "temp", "il6"], baseline_time=-1)
-reference = build_reference(prepared[prepared.condition == "endpoint"],
-                           variables=VARS, turned=TURNED, baseline_time=-1,
-                           label="endpoint-reaching animals")
-scores    = relsa_scores(prepared, reference)
-```
-
-### Step 2 — forecast the endpoint
-
-Train on everything up to the time point *before* the endpoint, predict the score at the
-endpoint, and score the prediction:
-
-```bash
-python scripts/forecast_relsa.py relsa_scores.csv \
-    --animals M01,M02 --endpoints M01=5 --endpoints M02=6 \
-    --group-col condition --plot-dir figs --endpoint-line 1.0
-```
-
-```
- id  time  predicted    lower    upper        model  actual
-M01   5.0   0.932585 0.670443 1.194728 ARIMA(1,1,0)    1.00
-M02   6.0   0.955696 0.748309 1.163084 ARIMA(1,1,0)    0.94
-
-   group             id        model  n   rmse  picp  mpiw
-endpoint            M01 ARIMA(1,1,0)  1 0.0674 100.0 0.524
-endpoint            M02 ARIMA(1,1,0)  1 0.0157 100.0 0.415
-endpoint -- endpoint --               2 0.0489 100.0 0.470
-                OVERALL               2 0.0489 100.0 0.470
-```
-
-Report all three metrics together. **RMSE** is point accuracy, **PICP** the percentage of
-actual values inside the interval, and **MPIW** the mean interval width in RELSA units — a
-model can reach PICP = 100% by making the interval so wide it says nothing, which is exactly
-what the paper's pancreatic cancer row (PICP 100%, MPIW 7.35, i.e. 735% of the RELSA range)
-shows.
-
-For live monitoring, forecast one step ahead at every time point instead:
-
-```bash
-python scripts/forecast_relsa.py relsa_scores.csv --mode rolling --animals M03
-```
-
-Two things to know before trusting a forecast:
-
-- **Interpolation is on by default** (`--interpolate-step 0.1`), because one measurement per
-  day is far too sparse for ARIMA. It buys usable model selection and narrower intervals at
-  the cost of honest uncertainty. Set `--interpolate-step 0` when measurement frequency
-  allows.
-- **ARIMA cannot predict a cliff.** It assumes stationarity and linearity, so an abrupt
-  collapse in the last hours before an endpoint will not be forecast from a smooth prior
-  trajectory — the paper's own failure case. Act on the *upper* bound of the interval, and
-  never let a low forecast override an animal that looks unwell.
-
-### Step 3 — put the score in context with severity zones
-
-```bash
-python scripts/kde_thresholds.py relsa_scores.csv \
-    --group treatment=treated --n-thresholds 2 --plot zones.png --json zones.json
-```
-
-```
-KDE on 33 RELSA scores  (bandwidth = 0.1502)
-  candidate thresholds (density minima): 0.703
-  density modes: 0.264, 0.866
-  normal    [0.000, 0.703)  n=25 (75.8%)
-  danger    >= 0.703  n=8 (24.2%)
-```
-
-Thresholds are the *minima* of the score density — the sparse valleys between clusters of
-scores. Include endpoint animals, survivors, and shams: the zones are meant to separate
-those states, so all of them must be represented.
-
-**Check the bandwidth before believing a threshold.** On the published sepsis data this
-implementation finds minima at 0.355 and 0.655 (published: 0.337 and 0.643) — but a 10%
-larger bandwidth removes both minima entirely. Run the sweep in
-`references/thresholds-and-zones.md` and report the sweep, not a bare pair of numbers. An
-empty threshold list is a legitimate answer: the scores form one cluster and there is no
-data-driven place to cut.
-
-## Boundaries: state these when you report
-
-- **RELSA is an aid to severity assessment, not a decisive parameter.** An animal with a low
-  RELSA score that shows other signs of distress must still be handled accordingly. Neither
-  procedure is a validated predictor of death.
-- **KDE zones are not regulatory severity gradings.** EU Directive 2010/63/EU's categories
-  (non-recovery, mild, moderate, severe) are assigned prospectively by a different process.
-  The paper is explicit that its thresholds "should not be confused with regulatory severity
-  gradings" and are not directly translatable to them.
-- **Scores are not comparable across reference sets or models.** RELSA is relative by
-  construction, and clinical scoring is not harmonized between laboratories. Always report
-  the reference set with the score.
-- **The published evidence is a proof of concept**: 13 animals across seven models, five of
-  those rows resting on one or two animals. The overall RMSE of 0.069 and PICP of 96% come
-  from 13 endpoint predictions.
-- **An underestimated score is the dangerous error**, because it discourages attention and can
-  delay a euthanasia decision, whereas an overestimate merely prompts extra care.
-
-## Reporting checklist
-
-A severity analysis is reproducible only if all of this is stated:
-
-1. Outcome measures, their units, and their **directionality** (which were turned, and why).
-2. The **baseline** time point or window, and which variables were normalized.
-3. Any **score mapping** applied to ordinal variables, with its scale.
-4. The **reference set**: which animals, which group, how many, and why they are assumed to
-   carry the greatest burden.
-5. Humane endpoint criteria actually applied in the study, separately from the RELSA score.
-6. For forecasts: interpolation step, the selected ARIMA order per animal, and RMSE, PICP,
-   *and* MPIW.
-7. For thresholds: the bandwidth, the number of scores, and a bandwidth sensitivity sweep.
-8. Software versions, and the statement that thresholds are model-specific and not regulatory
-   gradings.
-
-## Common pitfalls
-
-1. **Wrong directionality** — a rising variable not listed in `--turned` contributes exactly
-   zero, silently, and no warning is possible unless it never once falls. Check the reference
-   model table yourself: `max reached` should be below 100 for a falling variable and above 100
-   for a turned one, and `max delta` should be a plausible size for that measure.
-2. **Normalizing a percentage twice** — `bwc [%]` and mapped scores are already on the percent
-   scale; passing them to `--normalize` flattens them.
-3. **A zero baseline** — a clinical score of 0 makes the ratio undefined; the variable becomes
-   all-NaN with a warning. Use `--score-scale`.
-4. **A reference set that does not express the burden** — a variable that never deviates in it
-   raises an error rather than dividing by zero, and one that barely deviates inflates every
-   score.
-5. **Changing variable composition along a trajectory** — see decision 4 above.
-6. **Reading MPIW as a good thing** — a wide interval raises PICP while destroying the
-   forecast's usefulness.
-7. **Reporting a KDE threshold without its bandwidth** — thresholds can vanish under a 10%
-   bandwidth change.
-8. **Treating the forecast as permission to wait** — the model cannot see abrupt
-   deterioration, and the humane endpoint criteria of the protocol always take precedence.
-9. **Comparing RELSA scores between models** — only valid within one reference frame.
-
-## Resources
-
-### Scripts
-
-- `scripts/relsa_score.py` — the RELSA procedure: `prepare()`, `build_reference()`,
-  `relsa_scores()`, `relsa_weights()`, and a `ReferenceModel` that serialises to JSON.
-  Reproduces the R package's published worked example to two decimals.
-- `scripts/forecast_relsa.py` — the foRcast tool: `auto_arima()` (Hyndman–Khandakar stepwise
-  AICc selection), `forecast_animal()`, `predict_endpoint()`, `rolling_forecast()`,
-  `forecast_indirect()`, `summarize()`, and Figure-1-style plots.
-- `scripts/kde_thresholds.py` — severity zones: `bw_nrd0()` (R's bandwidth), `density_curve()`,
-  `find_thresholds()`, zone assignment, and Figure-3-style density plots.
-- `scripts/_common.py` — RELSA-format I/O, validation, `score_to_percent()`,
-  `percent_of_baseline()`, and `forecast_metrics()` (RMSE/PICP/MPIW).
-
-### References
-
-- `references/relsa-method.md` — the four steps in full, the score/zero-baseline problem, the
-  variable-composition trap, parity notes against the R package, and the outcome measures and
-  endpoint criteria of all seven published models.
-- `references/forecasting.md` — ARIMA selection, why interpolation is a distortion, direct vs
-  indirect prediction, the metrics, the published Table 1, and what this port reproduces.
-- `references/thresholds-and-zones.md` — KDE method, published thresholds, the bandwidth
-  sensitivity sweep, the regulatory boundary, and alternatives when KDE gives nothing.
-
-### Assets
-
-- `assets/example_cohort.csv` — synthetic 6-mouse cohort with temperature, body weight, a
-  clinical score, and a biomarker; illustrative only, not real data.
-
-### Related skills
-
-- **experimental-design**, **statistical-power** — designing the study and sizing the groups.
-- **statsmodels**, **timesfm-forecasting** — general time-series modelling.
-- **statistical-analysis**, **scientific-visualization** — group comparisons and figures.
-
-### Key references
-
-- Talbot, S. R. et al. (2022). RELSA — a multidimensional procedure for the comparative
-  assessment of well-being and the quantitative determination of severity in experimental
-  procedures. *Front. Vet. Sci.* 9:937711. R package: <https://github.com/mytalbot/RELSA>
-- Lutscher, S. et al. (2026). Refining humane endpoint detection by time-series forecasting
-  and threshold definition using a multivariate severity score. *Front. Physiol.* 17:1869563.
-- Hyndman, R. J. & Khandakar, Y. (2008). Automatic time series forecasting: the forecast
-  package for R. *J. Stat. Softw.* 27, 1–22.
-- EU Commission (2010). Directive 2010/63/EU on the protection of animals used for scientific
-  purposes.

package/skills/research-grants/SKILL.md

@@ -1,296 +0,0 @@
----
-name: research-grants
-description: Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.
-allowed-tools: Read Write Edit Bash
-license: MIT license
-compatibility: Works in Agent Skills-compatible hosts. Grant-writing guidance needs no network; optional figures via the scientific-schematics skill require OPENROUTER_API_KEY and outbound API access.
-metadata:
-  version: "1.2"
-  skill-author: K-Dense Inc.
----
-
-# Research Grant Writing
-
-## Overview
-
-Research grant writing is the process of developing competitive funding proposals for federal agencies and foundations. Master agency-specific requirements, review criteria, narrative structure, budget preparation, and compliance for NSF (National Science Foundation), NIH (National Institutes of Health), DOE (Department of Energy), DARPA (Defense Advanced Research Projects Agency), and Taiwan's NSTC (National Science and Technology Council) submissions.
-
-**Critical Principle: Grants are persuasive documents that must simultaneously demonstrate scientific rigor, innovation, feasibility, and broader impact.** Each agency has distinct priorities, review criteria, formatting requirements, and strategic goals that must be addressed.
-
-## When to Use This Skill
-
-This skill should be used when:
-- Writing research proposals for NSF, NIH, DOE, DARPA, or NSTC programs
-- Preparing project descriptions, specific aims, or technical narratives
-- Developing broader impacts or significance statements
-- Creating research timelines and milestone plans
-- Preparing budget justifications and personnel allocation plans
-- Responding to program solicitations or funding announcements
-- Addressing reviewer comments in resubmissions
-- Planning multi-institutional collaborative proposals
-- Writing preliminary data or feasibility sections
-- Preparing biosketches, CVs, or facilities descriptions
-
-## Visual Enhancement (Optional)
-
-Strong proposals often include 1–3 figures (timelines, workflow diagrams, preliminary data). Figures support review but are not a substitute for clear aims and methods.
-
-**When figures help:**
-- Research methodology and workflow diagrams
-- Project timeline or Gantt charts
-- Conceptual framework or system architecture (technical proposals)
-- Experimental design flowcharts
-- Broader impacts activity diagrams
-- NSTC CM03 research architecture diagrams (often expected)
-
-**How to create figures:**
-- **Preferred:** Use the **scientific-schematics** skill (`--doc-type grant`) for AI-generated diagrams from a natural-language description
-- **Alternative:** Build figures in your usual tools (matplotlib, Illustrator, PowerPoint, etc.)
-
-From the `scientific-schematics` skill directory, with `OPENROUTER_API_KEY` set:
-
-```bash
-python scripts/generate_schematic.py "project timeline with Year 1-3 milestones" -o figures/timeline.png --doc-type grant
-```
-
-**Disclosure:** AI schematic generation sends your prompt to [OpenRouter](https://openrouter.ai/) (a third-party API). Do not include unpublished sensitive details unless that transmission is appropriate for your project.
-
----
-
-## Agency-Specific Overview
-
-### NSF (National Science Foundation)
-**Mission**: Promote the progress of science and advance national health, prosperity, and welfare
-
-**Key Features**:
-- Follow [PAPPG 24-1](https://www.nsf.gov/policies/pappg) (effective May 20, 2024) unless a solicitation overrides it
-- Intellectual Merit + Broader Impacts (equally weighted)
-- 15-page project description limit (most programs; includes Results from Prior NSF Support, max 5 pages)
-- Emphasis on education, diversity, and societal benefit
-- Collaborative research encouraged
-- Open data and open science emphasis
-- Merit review process with panel + ad hoc reviewers
-
-### NIH (National Institutes of Health)
-**Mission**: Enhance health, lengthen life, and reduce illness and disability
-
-**Key Features**:
-- Specific Aims (1 page) + Research Strategy (12 pages for R01)
-- Significance, Innovation, Approach as core review criteria
-- Preliminary data typically required for R01s
-- Emphasis on rigor, reproducibility, and clinical relevance
-- Modular budgets ($250K increments) for most R01s
-- Multiple resubmission opportunities
-
-### DOE (Department of Energy)
-**Mission**: Ensure America's security and prosperity through energy, environmental, and nuclear challenges
-
-**Key Features**:
-- Focus on energy, climate, computational science, basic energy sciences
-- Often requires cost sharing or industry partnerships
-- Emphasis on national laboratory collaboration
-- Strong computational and experimental integration
-- Energy innovation and commercialization pathways
-- Varies by office (ARPA-E, Office of Science, EERE, etc.)
-
-### DARPA (Defense Advanced Research Projects Agency)
-**Mission**: Make pivotal investments in breakthrough technologies for national security
-
-**Key Features**:
-- High-risk, high-reward transformative research
-- Focus on "DARPA-hard" problems (what if true, who cares)
-- Emphasis on prototypes, demonstrations, and transition paths
-- Often requires multiple phases (feasibility, development, demonstration)
-- Strong project management and milestone tracking
-- Teaming and collaboration often required
-- Varies dramatically by program manager and BAA (Broad Agency Announcement)
-
-### NSTC (National Science and Technology Council - Taiwan)
-**Mission**: Advance scientific breakthrough, industrial application, and societal impact in Taiwan.
-
-**Key Features**:
-- **CM03 Form**: The core technical proposal format.
-- **Bilingual**: Abstract required in both Chinese and English.
-- **Innovation & Feasibility**: Primary review focus.
-- **Preliminary Data**: Highly critical for credibility.
-- **Research Architecture Diagram**: A mandatory visual element for clarity.
-
-## Core Components of Research Proposals
-
-Section-by-section guidance for every standard proposal component — specific aims,
-significance, innovation, approach, preliminary data, timeline, budget and justification,
-biosketch, facilities, data management and sharing, and broader impacts — with structure,
-length targets, and worked language, is in
-[references/core_components.md](references/core_components.md).
-
-## Review Criteria, Writing Principles, and Proposal Types
-
-- [references/review_criteria.md](references/review_criteria.md): how NIH, NSF, DOE, and
-  DARPA score proposals, and what each criterion actually rewards.
-- [references/writing_principles.md](references/writing_principles.md): what separates
-  funded proposals from competent ones — framing, specificity, reviewer psychology, and
-  readability.
-- [references/proposal_types_and_resubmission.md](references/proposal_types_and_resubmission.md):
-  the common proposal types and how to handle a resubmission, including responding to
-  a summary statement.
-
-## Common Mistakes to Avoid
-
-### Conceptual Mistakes
-
-1. **Failing to Address Review Criteria**: Not explicitly discussing significance, innovation, approach, etc.
-2. **Mismatch with Agency Mission**: Proposing research that doesn't align with agency goals
-3. **Unclear Significance**: Failing to articulate why the research matters
-4. **Insufficient Innovation**: Incremental work presented as transformative
-5. **Vague Objectives**: Goals that are not specific or measurable
-
-### Writing Mistakes
-
-1. **Poor Organization**: Lack of clear structure and flow
-2. **Excessive Jargon**: Inaccessible to broader review panel
-3. **Verbosity**: Unnecessarily complex or wordy writing
-4. **Missing Context**: Assuming reviewers know your field deeply
-5. **Inconsistent Terminology**: Using different terms for same concept
-
-### Technical Mistakes
-
-1. **Inadequate Methods**: Insufficient detail to judge feasibility
-2. **Overly Ambitious**: Too much proposed for timeline/budget
-3. **No Preliminary Data**: For mechanisms requiring demonstrated feasibility
-4. **Poor Timeline**: Unrealistic or poorly justified schedule
-5. **Misaligned Budget**: Budget doesn't support proposed activities
-
-### Formatting Mistakes
-
-1. **Exceeding Page Limits**: Automatic rejection
-2. **Wrong Font or Margins**: Non-compliant formatting
-3. **Missing Required Sections**: Incomplete application
-4. **Poor Figure Quality**: Illegible or unprofessional figures
-5. **Inconsistent Citations**: Formatting errors in references
-
-### Strategic Mistakes
-
-1. **Wrong Program or Mechanism**: Proposing to inappropriate opportunity
-2. **Weak Team**: Insufficient expertise or missing key collaborators
-3. **No Broader Impacts**: For NSF, failing to adequately address
-4. **Ignoring Program Priorities**: Not aligning with current emphasis areas
-5. **Late Submission**: Technical issues or rushed preparation
-
-## Workflow for Grant Development
-
-### Phase 1: Planning and Preparation (2-6 months before deadline)
-
-**Activities**:
-- Identify appropriate funding opportunities
-- Review program announcements and requirements
-- Consult with program officers (if appropriate)
-- Assemble team and confirm collaborations
-- Develop preliminary data (if needed)
-- Outline research plan and specific aims
-- Review successful proposals (if available)
-
-**Outputs**:
-- Selected funding opportunity
-- Assembled team with defined roles
-- Preliminary outline of specific aims
-- Gap analysis of needed preliminary data
-
-### Phase 2: Drafting (2-3 months before deadline)
-
-**Activities**:
-- Write specific aims or objectives (start here!)
-- Develop project description/research strategy
-- Create figures and data visualizations
-- Draft timeline and milestones
-- Prepare preliminary budget
-- Write broader impacts or significance sections
-- Request letters of support/collaboration
-
-**Outputs**:
-- Complete first draft of narrative sections
-- Preliminary budget with justification
-- Timeline and management plan
-- Requested letters from collaborators
-
-### Phase 3: Internal Review (1-2 months before deadline)
-
-**Activities**:
-- Circulate draft to co-investigators
-- Seek feedback from colleagues and mentors
-- Request institutional review (if required)
-- Mock review session (if possible)
-- Revise based on feedback
-- Refine budget and budget justification
-
-**Outputs**:
-- Revised draft incorporating feedback
-- Refined budget aligned with revised plan
-- Identified weaknesses and mitigation strategies
-
-### Phase 4: Finalization (2-4 weeks before deadline)
-
-**Activities**:
-- Final revisions to narrative
-- Prepare all required forms and documents
-- Finalize budget and budget justification
-- Compile biosketches, CVs, and current & pending
-- Collect letters of support
-- Prepare data management plan (if required)
-- Write project summary/abstract
-- Proofread all materials
-
-**Outputs**:
-- Complete, polished proposal
-- All required supplementary documents
-- Formatted according to agency requirements
-
-### Phase 5: Submission (1 week before deadline)
-
-**Activities**:
-- Institutional review and approval
-- Upload to submission portal
-- Verify all documents and formatting
-- Submit 24-48 hours before deadline
-- Confirm successful submission
-- Receive confirmation and proposal number
-
-**Outputs**:
-- Submitted proposal
-- Submission confirmation
-- Archived copy of all materials
-
-**Critical Tip**: Never wait until the deadline. Portals crash, files corrupt, and emergencies happen. Aim for 48 hours early.
-
-## Integration with Other Skills
-
-This skill works effectively with:
-- **Scientific Schematics**: Optional AI-generated grant figures (`--doc-type grant`)
-- **Scientific Writing**: For clear, compelling prose
-- **Literature Review**: For comprehensive background sections
-- **Peer Review**: For self-assessment before submission
-- **Research Lookup**: For finding relevant citations and prior work
-- **Data Visualization**: For creating effective figures
-
-## Resources
-
-This skill includes comprehensive reference files covering specific aspects of grant writing:
-
-- `references/nsf_guidelines.md`: NSF-specific requirements, formatting, and strategies
-- `references/nih_guidelines.md`: NIH mechanisms, review criteria, and submission requirements
-- `references/doe_guidelines.md`: DOE programs, emphasis areas, and application procedures
-- `references/darpa_guidelines.md`: DARPA BAAs, program offices, and proposal strategies
-- `references/broader_impacts.md`: Strategies for compelling broader impacts statements
-- `references/specific_aims_guide.md`: Writing effective specific aims pages
-- `references/nstc_guidelines.md`: NSTC-specific guidelines and review criteria
-
-Load these references as needed when working on specific aspects of grant writing.
-
-## Templates and Assets
-
-- `assets/nsf_project_summary_template.md`: NSF project summary structure
-- `assets/nih_specific_aims_template.md`: NIH specific aims page template
-- `assets/budget_justification_template.md`: Budget justification structure
-
----
-
-**Final Note**: Grant writing is both an art and a science. Success requires not only excellent research ideas but also clear communication, strategic positioning, and meticulous attention to detail. Start early, seek feedback, and remember that even the best researchers face rejection—persistence and revision are key to funding success.