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biosymphony-structure-factory

biosymphony-structure-factory is a skill for Claude Code, Codex from BioSymphony/structure-factory. It costs 47 tokens per session (1,615 once invoked), scanned A, original, MIT.

A planning tool for structural biology work, such as studying the shapes of biological molecules and designing candidate binders. It turns a research idea into a multi-step campaign that other workers can continue and check.

In plain words
What is it for?
Use it to plan target studies, compare models, rank candidates, map structures, define cloud-GPU work, and prepare task packs for systems such as Symphony or Linear.
Why use it?
It organizes long-running biology projects that would be difficult to manage as a single request or answer.

Skill for Claude CodeCodex

Written for Claude Code and Codex: shipped in a Claude Code plugin, but also agents/openai.yaml present. Also seen: mentions AGENTS.md.

Part of the biosymphony-structure-factory plugin — 2 skills shipped together , and of biosymphony-structure-factory

not rated 5repo changed 6d ago A scan 47 tokens original MIT

Good fit Use it to plan target studies, compare models, rank candidates, map structures, define cloud-GPU work, and prepare task packs for systems such as Symphony or Linear.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/biosymphony/structure-factory/biosymphony-structure-factory
View source ↗ BioSymphony/structure-factory
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add BioSymphony/structure-factory --skill biosymphony-structure-factory
Clone the repo
git clone --depth 1 https://github.com/BioSymphony/structure-factory

Made for: Claude Code, Codex.

Or install biosymphony-structure-factory, the plugin that ships this one along with the rest of its 2 skills.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for biosymphony-structure-factory

README.md
[![agentmods](https://agentmods.dev/badge/skills/biosymphony/structure-factory/biosymphony-structure-factory/github.svg)](https://agentmods.dev/skills/biosymphony/structure-factory/biosymphony-structure-factory)
Your own site
<a href="https://agentmods.dev/skills/biosymphony/structure-factory/biosymphony-structure-factory"><img src="https://agentmods.dev/badge/skills/biosymphony/structure-factory/biosymphony-structure-factory/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for biosymphony-structure-factory

Your own site · 80×15
<a href="https://agentmods.dev/skills/biosymphony/structure-factory/biosymphony-structure-factory"><img src="https://agentmods.dev/badge/skills/biosymphony/structure-factory/biosymphony-structure-factory.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 47 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,615 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00047 $0.01615
Opus 5 $0.00023 $0.00807
Sonnet 5 $0.00009 $0.00323
Haiku 4.5 $0.00005 $0.00161

Measured 6d ago against content hash 87a9e95be95d, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

biosymphony-structure-factory scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 6d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/biosymphony-structure-factory/SKILL.md · 113 lines

How it starts

The opening of the file, as written. The whole thing — 113 lines — stays where its author put it; the contents beside it link to each section on GitHub.

BioSymphony Structure Factory

Use this skill to turn a target, accession, or campaign request into a campaign manifest, task plan, provider contract, candidate report, or structure report.

Always Read

  • references/README.md
  • references/AGENTS.md
  • references/NON_CLAIMS.md

Read When Applicable

  • references/docs/intake-interview.md for ambiguous, data-bearing, license-bearing, cost-bearing, or workflow-sized requests.
  • references/docs/agentic-biology-harness.md before multi-agent or provider-coordinated work.
  • references/docs/public-export-shape.md before release, publication, or public handoff work.
  • references/docs/linear-orchestration.md before generating or dispatching Symphony or Linear task packs.
  • references/docs/compute-backends.md when selecting local, FAL, Modal, RunPod, Lambda Cloud, AWS Batch, SSH or HPC, generic cloud, or neocloud execution.
  • references/docs/runpod-stack.md before RunPod prep or launch.
  • references/docs/tooling-and-licensing.md before selecting, installing, baking, or running tool lanes.
  • references/docs/confidence-sidecars.md before editing or launching any fold, cofold, scoring, ranking, or render lane that depends on confidence metrics.
  • references/docs/no-false-success-hardening.md before provider-backed execution or scientific closeout.
  • references/docs/operational-gotchas.md before any paid GPU dispatch: a 45-class catalog of failure modes with pre-flight probes and fixes.
  • references/docs/preflight-checklist.md for the 10-gate pre-dispatch checklist pattern (PDB chain identity, hotspot atom-spec, output-count validation, operator approval, etc.).
  • references/docs/agent-run-learnings.md for execution checks and public record boundaries.
  • references/examples/pd-l1-binder-design-public/README.md for the public binder-design fast path.
  • references/docs/binder-lane-round.md for multi-arm binder comparisons and mixed-backend handoff contracts.
  • references/docs/binder-study-decision-loop.md before choosing the target, study mode, tools, execution routes, budget, rounds, metric, and stopping rule.
  • references/docs/binder-controls.md before deriving or adopting measured-control gates for a round decision.
  • references/docs/quickstart-tour.md, references/docs/cli-reference.md, and references/docs/agent-recipes.md when helping a public user start from scratch.
  • references/docs/faq.md and references/docs/glossary.md when a user or a general-purpose agent is unfamiliar with structural biology terms, agent harness conventions, or how to operate the repo without a tracker.

Read the full file on GitHub · 113 lines

Files

What ships with it

60 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 6d ago Changed · +1 lines 87a9e95be95d
  2. 10d ago First seen · 112 lines · 47 tokens per session scan A 3f6d5b993906

Subscribe to this mod's changes

biosymphony-structure-factory is a skill published in the GitHub repository BioSymphony/structure-factory (5 stars, last pushed 8d ago), licensed MIT. It adds 47 tokens to every session and 1,615 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

PlanningScientificagentic-aiai-agentsbinder-designbioinformaticscloud-computingcomputational-biology
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