# nature-paper · submission bundle

This workspace is the real four-piece deliverable from the **nature-paper** skill on [clawvard.school](https://clawvard.school/courses/nature-paper).

Every file is produced by running one of the four popular tasks against `sources/` — no mock content, no placeholders.

## Files

| File | popularTask | What it is | How to open |
| --- | --- | --- | --- |
| `manuscript.docx` | Task 1 (experimental data → manuscript) | Nature-style article: Title / Abstract / Main / Methods / References with **16 tracked changes** (9 insertions + 7 deletions) | Word / WPS / Google Docs |
| `figure-1.svg` + `figure-1.png` | Task 2 (manuscript → figure) | Three-panel Nature-style figure: (a) per-gene log2 FC bar with SEM error bars, (b) per-replicate strip plot, (c) volcano plot | Browser / Inkscape / Illustrator (SVG); any image viewer (PNG @300dpi) |
| `defense.pptx` | Task 3 (manuscript → defense deck) | 13 native-editable slides (Title → Motivation → Question → Methods × 2 → Results × 3 → Implications → Limitations → Q&A × 3) | PowerPoint / Keynote / WPS |
| `response-letter.docx` | Task 4 (reviewer comments → response) | 3 reviewers × 4 comments × strict three-block layout (Comment → Response → Manuscript Change) | Word / WPS / Google Docs |

## How these were produced

Each artifact was built by chaining a sub-course SOP under the Nature-style prompt pack in [`../SKILL.md`](../SKILL.md):

- `manuscript.docx` → [`ai-doc`](https://clawvard.school/courses/ai-doc) sub-course + Nature manuscript template + `cite-lookup.mjs` for `[CITATION_NEEDED:…]` resolution.
- `figure-1.svg` + `figure-1.png` → [`diagrams-as-code`](https://clawvard.school/courses/diagrams-as-code) sub-course + Nature figure-legend template.
- `defense.pptx` → [`ai-pptx`](https://clawvard.school/courses/ai-pptx) sub-course + Nature defense-deck template. Every text box, shape, and chart is native DrawingML — none of the figure panels are pasted images.
- `response-letter.docx` → [`parse-docs`](https://clawvard.school/courses/parse-docs) sub-course (to OCR / extract reviewer comments) → [`ai-doc`](https://clawvard.school/courses/ai-doc) + Nature three-block template.

All LLM / docx / pptx / svg / pdf calls in the popularTasks route through `@clawvard/sdk` with your Clawvard API key from [clawvard.school](https://clawvard.school). Literature lookups in `cite-lookup.mjs` use only the public, key-less PubMed E-utilities, CrossRef and arXiv endpoints.

## Sample inputs

`sources/` contains the inputs the four tasks were run against:

- `data.csv` — three biological replicates × two conditions × three loci.
- `draft.md` — the noisy initial draft with `[CITATION_NEEDED:…]` placeholders.
- `placeholders.json` — the input to `cite-lookup.mjs` for citation resolution.
- `refs.bib` — the merged BibTeX result produced by `cite-lookup.mjs` running against the real PubMed / CrossRef / arXiv APIs.

## Reproducibility check

```bash
# from anywhere with Node ≥ 18
node cite-lookup.mjs \
  --in nature-paper-submission/sources/placeholders.json \
  --out nature-paper-submission/sources/refs.bib

# the four-piece submission bundle is then rebuilt by chaining the four
# popular tasks described in ../SKILL.md, each via its sub-course SOP.
```