STRC Research Monitor Pipeline

STRC Research Monitor — Nightly PubMed Agent Pipeline

The STRC site at strc.egor.lol includes a live Research Monitor (journal.astro) that runs a nightly Claude agent against PubMed. Papers appear on the site automatically. This note documents the architecture so future agents can maintain or extend it.

What it does

Every night at 02:00 UTC, a Claude agent:

1. Queries PubMed for new papers on STRC, stereocilin, DFNB16, cochlear gene therapy, and related terms (PMIDs since yesterday).
2. Reads each abstract and full text where available.
3. Scores relevance 1-10 against the current S/A-tier hypotheses from STRC Hypothesis Ranking.
4. Extracts what the paper means for mini-STRC, delivery, and regulatory path.
5. Commits paper summaries to GitHub as Markdown in research/strc/papers/.
6. GitHub Actions builds and deploys the site. The Brain vault syncs via symlink — papers appear in Obsidian the same morning.

Priority filter

The agent scores papers against current S/A-tier hypotheses. Anything advancing an S-tier hypothesis is high-value. Papers on killed (D-tier) mechanisms get skipped unless they credibly reverse the kill decision.

This means the monitor is hypothesis-aware, not just a topic feed. As STRC Hypothesis Ranking changes, the relevance scoring shifts automatically.

Data flow

PubMed API → Claude agent → paper notes (research/strc/papers/)
                                 ↓
                          GitHub commit → GitHub Actions build
                                 ↓
                          strc.egor.lol/journal (public)
                                 ↓
                          Brain vault symlink (Obsidian)

Site rendering

journal.astro fetches the papers content collection, sorts by date_added (agent run date), not publication date — so ahead-of-print papers stay in the batch they arrived with rather than floating to the top.

The page also renders the current S/A-tier priority list from hypothesis-ranking.md, so visitors see what the agent is looking for.

Connection to Brain vault

Paper notes land in ~/Brain/research/strc/papers/ via the symlink from ~/Sites/site-strc-egor-lol/src/content/papers/. This means every paper the agent processes becomes part of the Brain — no manual ingestion step. The paper notes in research/strc/papers/ follow the standard paper note template (AGENTS.md § Operations) and link back to atomic hypothesis notes.

Connections

• [part-of] STRC Gene Therapy — the research program this monitor serves
• [see-also] STRC Hypothesis Ranking — the priority register the monitor scores papers against
• [see-also] STRC Research Methodology — broader research process context
• STRC Website and Communication — the public-facing site that hosts the monitor