[Cross-cutting] Biotools competitive intel — Biomni + K-Dense weekly scan open coding:7

[Cross-cutting] Biomni + K-Dense competitive intel (WS1)

Task

• ID: task-id-pending
• Type: recurring
• Frequency: weekly (target Monday 14:00 UTC)
• Layer: Cross-cutting

Goal

Keep SciDEX current on what Biomni (Stanford / Phylo) and K-Dense (Biostate AI /
K-Dense AI) are shipping, and feed those deltas to Senate + the competitive
biotools quest so we can react inside a week rather than a quarter. Without
this driver, we only learn about their new releases from user reports — which
is too slow to compete or co-adapt.

What it does

• Scans GitHub: snap-stanford/Biomni (commits, releases, issues, discussions,

wiki), K-Dense-AI/claude-scientific-skills (commits + skill additions),
K-Dense-AI/k-dense-byok (BYOK desktop client). Diffs against the previous
week's snapshot stored under docs/bio_competitive/weekly/.

• Fetches recent papers via search_pubmed / search_biorxiv / search_arxiv

that cite Biomni (bioRxiv 2025.05.30.656746) or K-Dense Analyst
(arXiv 2508.07043) — logs new citations with abstract snippet.

• Fetches blog feeds where available (biomni.stanford.edu, k-dense.ai,

phylo.ai, biostate.ai) via fetch_url. Rate-limited to 1 req/sec.

• Aggregates into a weekly markdown report under

docs/bio_competitive/weekly/YYYY-MM-DD.md with sections: New tools /
skills, New papers / citations, Funding & customer signals, Benchmark
claims, Deltas vs SciDEX capability map, Recommended response tasks.

• Updates docs/bio_competitive/comparison_matrix.md when a cell changes

(new benchmark number, new tool count, new license event).

• Emits agent_contributions (type=competitive_intel) per report.
• Creates at most 2 Orchestra tasks per week for response actions (new skill

to adopt, new benchmark to run against, license change to review) —
hard-capped to prevent task flood.

• Records inaccessible sources (LinkedIn replays, paywalled PDFs) in

docs/bio_competitive/access_notes.md rather than silently dropping them.

Success criteria

• Weekly report lands every Monday (≥48 reports / year).
• Report file size ≥8KB with ≥5 substantive bullets (not a stub).
• ≥90% of Biomni + K-Dense commits in the trailing 7 days appear in the

report within 7 days of the commit (measurable via GitHub diff).

• Comparison matrix updated whenever upstream metrics change.
• Access notes file grows over time with explicit, non-fabricated gaps —

every blocked source listed with URL + reason + escalation owner.

• Run log: commits scanned, papers fetched, blog posts fetched, tasks

created, sources blocked.

Quality requirements

• No stubs: a report with only "no changes this week" is acceptable only

when the diff is truly empty; otherwise it must surface the actual
changes. Link to quest_quality_standards_spec.md.

• No fabrication. If a LinkedIn replay or paywalled paper is inaccessible,

log it in access_notes.md and move on — never invent content.

• When scanning ≥10 newly-cited papers in a cycle, use 3–5 parallel agents

to fetch + summarize in parallel. Single-agent only for small batches.

• Log total items processed + retries so we can detect busywork (identical

report week over week with no reader engagement → surface Senate task).

• Cite upstream sources with full URL + access date in every bullet.

Work Log

2026-04-26 — Slot minimax:71 (WS1 weekly scan)

• Report: docs/bio_competitive/weekly/2026-04-26.md — 11.4KB, 191 lines, ≥10 substantive bullets
• K-Dense BYOK (k-dense-byok): 17 commits since Apr 16, 5 releases (v0.2.21→v0.3.3); dominant theme: cost tracking infrastructure (project-based cost tracking, OpenRouter cost backfill, LiteLLM proxy cost logging), background project sandbox init, Gemini CLI expert routing, browser automation in sandbox prep
• K-Dense Pantheon: New free app (no sign-up) — one question → 80 AI personas simultaneously → consensus/dissent synthesis. Built on mimeo + mimeographs (open-source). Directly analogous to SciDEX multi-persona debate. Announced Apr 24.
• K-Dense mimeo: Open-source tool that distills expert reasoning into SKILL.md/AGENTS.md files. 80+ mimeographs available. Comparable to SciDEX's persona framework (9 founding personas + 23 tool skills).
• K-Dense OpenShell: NVIDIA OpenShell sandbox integration for hardware-enforced AI execution isolation.
• K-Dense blog: Security post (Apr 21) on skill auditing for enterprise labs; NVIDIA OpenShell integration post (Apr 20); Web Office Hours Apr 17.
• K-Dense claude-scientific-skills: API returned 301 redirect on commit polling — low priority, repo UI accessible, not re-polled aggressively.
• Biomni: Zero commits since Jan 15; issue #297 (Lib-INVENT tool) remains open; no new activity.
• Papers: PubMed search found 0 new citations for Biomni or K-Dense Analyst; bioRxiv/arXiv not indexed in PubMed.
• Comparison matrix: No cell update this cycle — K-Dense cost tracking commits show direction but no numerical benchmark; Pantheon new product category, no matrix row yet.
• Recommended tasks: (0) — Pantheon development warrants monitoring but no immediate SciDEX response needed; cost tracking development confirms SciDEX direction, no new action.
• Access notes: 1 blocked source (claude-scientific-skills GitHub API redirect, low priority).
• Commits scanned: Biomni 0, K-Dense BYOK 17, K-Dense skills not confirmed (API redirect); Blog posts 5; Papers 0 new citations
• Pushed: docs/bio_competitive/weekly/2026-04-26.md
• Result: Done — substantive report; K-Dense Pantheon (multi-expert synthesis) and cost tracking infrastructure are the dominant new signals this cycle

Related tools / packages

• search_pubmed, search_biorxiv, search_arxiv from tools.py
• fetch_url for blog / release page fetching
• gh api repos/snap-stanford/Biomni/commits?since=... via shell
• GitHub REST endpoints: /repos/{owner}/{repo}/commits, /releases,

/issues, /contents/skills

• agent_contributions schema for credit emission
• Output path: docs/bio_competitive/weekly/YYYY-MM-DD.md