BioWatch

BioWatch: a lifeguard for busy bioinformaticians — staying afloat on the bioinformatics methods tide, so you never drown and only swim toward what's worth your time.

What this is

A small group of bioinformaticians (different specialities, limited reading time) keeping up with new methods and tools together instead of each person scanning the literature alone. Every 2 weeks (configurable), an AI agent scouts bioRxiv, GitHub, GitLab and PubMed for new/updated bioinformatics methods and writes a short, structured report. The reports build into a searchable Obsidian vault (this repo), and the group reviews/discusses them in a recurring meeting.

Structure

• automated_findings/ — the regular biweekly reports, one file per cycle.
• specialized_findings/ — one-off, narrower runs anyone can request on their own topic (see howto/agent-query-types.md).
• AGENT_INSTRUCTIONS.md — the prompt behind every report. Self-contained; point your own agent at it to run a query.
• TAG_VOCABULARY.md — the fixed tag list each report entry is tagged from (2-3, max 5 per entry), so tags stay mergeable instead of drifting into near-duplicates.
• in_vault_queries/ — Dataview queries for browsing/searching reports.
• REVIEW_CHECKLIST.md — track what's been read/discussed.
• bin/run_biowatch.sh — the scheduled-run script (currently Eve's machine; see the issue tracker for moving this to GitHub Actions).

Using this as an Obsidian vault

Built and tested with Obsidian 1.15.0. If you're on an older version and a plugin fails to load, update Obsidian first before troubleshooting further.

1. Clone this repo.

2. Open the cloned folder as a vault in Obsidian (not inside another vault — keep it standalone).

3. Install these community plugins (Settings → Community plugins → Browse), matching .obsidian/community-plugins.json. Several plugins share similar names, so check the author shown in the browser to get the right one:

   Plugin	Plugin ID	Author
   Dataview	dataview	Michael Brenan (blacksmithgu)
   Tag Folder	obsidian-tagfolder	check author shown in-app — do not confuse with a similarly-named plugin
   Colored Tags	colored-tags	check author shown in-app — do not confuse with a similarly-named plugin
   Advanced Tables	table-editor-obsidian	Tony Grosinger (tgrosinger) — plugin ID still says "table-editor-obsidian" from an earlier name; not the separate "Markdown Table Editor" plugin

   Plugin binaries aren't committed to this repo — install them fresh, works the same on any OS.

4. Browse in_vault_queries/ for ready-made searches, or write your own Dataview query against automated_findings//specialized_findings/. New to Dataview or how we use tags? See howto/in-vault-queries-dataview-basics.md.

Contributing a specialized query

See howto/agent-query-types.md. Short version: take AGENT_INSTRUCTIONS.md, narrow it to your question, run it with your own agent, save the result into specialized_findings/ with the same frontmatter fields so it's still searchable.

Issues

All issues live on the canonical repo, NorwegianVeterinaryInstitute/BioWatch — that's the single backlog for everyone, Eve included. Issues are disabled on Eve's fork (evezeyl/BioWatch) to keep it that way: GitHub doesn't sync issues between a fork and its upstream, so having two trackers open would just split the backlog.

License

Apache 2.0 (see LICENSE).