Resources & downloads

# Everything in one place

The whole data-access package — the `oryza19k` helper and example notebooks, the precomputed tables, and the Supplementary Note — bundled into this site. Grab individual files below, or the complete package as one archive.

⬇ Download everything (.zip) Read Supplementary Note 10 in your browser →

## Python — the `oryza19k` access cookbook

The client-side cookbook that orchestrates every platform (see the API page for what it is and what it needs). `import oryza19k as o19`, then `o19.<function>(...)`.

File | What it is |
--- | --- | ---
`oryza19k.py` | The access-cookbook helper (Ensembl REST, tabix, CLIMtools, models, summaries) | download
`requirements.txt` | Library requirements (core + optional groups) | download
`workflow_A_mads14_heading_date.py` | Workflow A — MADS14 → heading-date hypothesis | download
`workflow_B_tb1_tiller_number.py` | Workflow B — rare TB1/FC1 variant → tiller number | download
`workflow_C_imputation_benchmark.py` | Workflow C — whole-collection imputation & benchmarking | download
`README.md` | How to run the notebooks; full `oryza19k` reference | read in browser · .md

The workflows are jupytext percent-format `.py` files — valid notebook sources. Convert to `.ipynb` with `jupytext --to notebook workflow_*.py`, or run as plain scripts.

## Precomputed summary tables

DOI-citable summaries so common questions need no large query (manifest: read in browser · .md). At publication these are mirrored on Zenodo.

Table | Contents | Size |
--- | --- | --- | ---
`allele_frequency_core_snps.tsv` | 165,640 SNPs × global + per-group allele frequency | ~19 MB | download
`genomic_prediction_benchmark.tsv` | 23 models × 5 traits (Spearman, R², training time) | ~13 KB | download
`accession_passport.tsv` | accession, varietal group, #phenotypes scored | ~0.4 MB | download
`phenotypes_by_accession.tsv` | accession × 24 phenotypes (+ group) | ~1.4 MB | download
`generate_tables.py` | Reproducible generator for the tables above | ~8 KB | download

## Documentation

Document | What it is |
--- | --- | ---
Supplementary Note 10 | Data Access and Visualization (§§10.1–10.6) | read in browser · .md
Package README | Overview of the whole package | read in browser · .md

Using the .zip: it contains the full site with everything bundled under `site/resources/`. Unzip, then `python -m http.server 8000 --directory site` and open `http://localhost:8000/`.