RMDB

Contribute an entry

RMDB now accepts new entries via pull request against DasLab/rmdb.github.io. With the rdat_kit ≥ 1.8.0 CLI the whole submission is essentially three commands.

One-time setup

pip install 'rdat_kit>=1.8.0' matplotlib   # matplotlib only needed for thumbnail
gh auth login                              # GitHub CLI; needed for the Release upload
git clone https://github.com/<you>/rmdb.github.io   # your fork
cd rmdb.github.io

Per-entry submission

ID="MY_ENTRY_0000"

# 1. Validate the RDAT file
rdat_kit validate path/to/$ID.rdat
#    path/to/MY_ENTRY_0000.rdat: OK   (16 construct(s), 990 data row(s), RDAT_VERSION=0.34)

# 2. Generate the entry .md from the RDAT (auto-fills everything except citation)
rdat_kit to_md path/to/$ID.rdat > _entries/$ID.md
$EDITOR _entries/$ID.md     # fill in the citation block

# 3. Render the reactivity-heatmap thumbnail
rdat_kit thumbnail path/to/$ID.rdat --out assets/thumbnails/

# 4. Upload the .rdat to the right Release tag (see table below)
gh release upload data-general path/to/$ID.rdat --repo DasLab/rmdb.github.io

# 5. Commit + PR
git add _entries/$ID.md assets/thumbnails/$ID.png
git commit -m "Add entry $ID"
git push origin HEAD
gh pr create --fill

Pick the right Release tag

Tag Holds
data-eterna Eterna / OpenKnot library experiments
data-puzzle RNA Puzzles community blind-prediction challenges
data-riboswitches TPP, SAM, glycine, FMN, fluoride, ZTP, etc. riboswitches
data-rna-structures rRNA, tRNA, viral RNA, large mutate-and-map libraries
data-general Everything else (default if you’re unsure)

Update the rdat: URL in your _entries/<ID>.md if you used a non-general tag — the default the stub emits is data-general.

Using an LLM agent

The workflow is short and well-defined, which makes it ideal for LLM coding agents (e.g. Claude Code, Cursor). A prompt like:

“I have my_entry.rdat and this publication PDF. Read RMDB’s CONTRIBUTING.md, run rdat_kit to_md to produce the .md stub, fill the citation block from the PDF (or fetch by PMID), render the thumbnail with rdat_kit thumbnail, upload the .rdat to data-general via gh release upload, and open a PR.”

is usually enough — the agent reads the contributing guide, runs the three rdat_kit commands, fills the citation, uploads, and opens the PR. Review and merge.

Full reference

Step-by-step instructions plus the YAML front-matter schema are in the repository’s CONTRIBUTING.md.

Preview your entry locally

bundle install
bundle exec jekyll serve --config _config.yml,_config_local.yml
# Open http://localhost:4000/detail/<RMDB_ID>/

What happens after merge