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BioSymphony GeneCluster Agent Guide

This repo is the public BioSymphony GeneCluster skill kit for agents and agent harnesses.

Operating Rules

  • Keep durable public docs in docs/.
  • Keep reusable skill material under skills/.
  • Use templates/linear-issue.md for tracker-neutral issue drafts.
  • Do not store API keys, tokens, provider IDs, private run logs, raw/heavy biological data, or unpublished biological sequences in this repo.
  • Prefer placeholders such as <AUTONOMY_HOME>, <RUNPOD_ENV_FILE>, and <PUBLIC_REPO_URL> over local workstation paths.

Dev Commands

  • Inspect repo status: git status --short --branch
  • List public files: find docs skills templates pipeline images data -maxdepth 2 -type f | sort
  • Run the full public release check: make public-release-check
  • Scan for accidental local raw/heavy artifacts: make artifact-scan
  • Run the local GeneCluster demo harness: make demo-campaign-dry-run
  • Run smaller/larger demo scopes: make demo-campaign-smoke or make demo-campaign-public-mining
  • Probe local capabilities: python3 skills/biosymphony/scripts/capability_probe.py --json
  • Check the public skill: python3 skills/biosymphony/scripts/biosymphony_public_skill_audit.py --skill-root skills/biosymphony
  • Check a drafted issue: python3 skills/biosymphony/scripts/preflight_check.py templates/linear-issue.md
  • Check GeneCluster example ledgers: use the command in README.md.

Product Direction

BioSymphony GeneCluster should help agents run comparative-genomics campaigns that are easier to plan, inspect, and resume:

  • Linear or another tracker stores task contracts, dependencies, acceptance criteria, check commands, and artifact handoffs.
  • Symphony-style workers execute bounded source scouting, candidate search, comparative analysis, visualization, QA, and review-limit checks.
  • Provider lanes handle heavy search and model work behind finite launch contracts.
  • Review surfaces should keep conclusions tied to ledgers, versions, hashes, and stated limits.
  • A capable Codex/Claude-style agent remains the orchestrator: use the repo's contracts and checks, but make ordinary campaign decisions without waiting for every detail to be encoded as a script.
  • For /goal or solo-agent setups, use templates/goal-prompt.md and the same artifact contracts instead of forcing a tracker when one is unnecessary.

Public Safety

  • Do not copy private structures, raw reads, unpublished sequences, API keys, tokens, provider response JSON, or private tracker text into this repo.
  • Public examples must use public, synthetic, or placeholder data.
  • Provider examples must use environment variable names or placeholder paths only, with no secret values.
  • Runtime outputs belong under ignored .runtime/ and should not be committed.