Borrowing it
Nothing to install: this file belongs to softnanolab/bagel. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/softnanolab/bagel/main/.claude/skills/bagel-script-builder/SKILL.mdgit clone --depth 1 https://github.com/softnanolab/bagelWrote 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.
[](https://agentmods.dev/skills/softnanolab/bagel/bagel-script-builder)<a href="https://agentmods.dev/skills/softnanolab/bagel/bagel-script-builder"><img src="https://agentmods.dev/badge/skills/softnanolab/bagel/bagel-script-builder/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.
<a href="https://agentmods.dev/skills/softnanolab/bagel/bagel-script-builder"><img src="https://agentmods.dev/badge/skills/softnanolab/bagel/bagel-script-builder.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
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.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00235 | $0.04376 |
| Opus 5.5 | $0.00094 | $0.01750 |
| Sonnet 5.5 | $0.00047 | $0.00875 |
| Haiku 4.5 | $0.00023 | $0.00438 |
Grade A, and why
bagel-script-builder 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 17d 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.
How it starts
The opening of the file, as written. The whole thing — 283 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Building BAGEL protein-design scripts, interactively
BAGEL (pip name biobagel, imported as import bagel as bg) frames protein design as
minimizing an energy landscape: you describe what a good design looks like as a sum of
weighted energy terms, then a Monte-Carlo minimizer mutates the mutable residues to lower that
energy. The scripts are the documentation — there is no config/YAML layer.
This skill is not a one-shot code generator. It runs an interactive workflow so the user ends up with correct, fully-specified, well-explained, reviewable scripts. Work through the phases below in order. Do not skip the interview: silently guessing the parts of a design the user left unspecified is the main failure mode this skill exists to prevent.
The workflow at a glance
- Understand & draft — read the natural-language goal, write a first-pass draft script.
- Interview to close gaps — walk the user through the draft and ask about everything the description left unclear, until every State, Chain, and EnergyTerm (and each term's inputs) is explicitly pinned down.
- Write the design script — verbose, heavily commented, saved to disk for review.
- Document the script — always write the two companion files,
Instructions_for_script.mdandExtended_description_and_goals.md, next to it. - Smoke test — generate a minimal test script; run it on Modal if credentials are available, and report exactly what worked or failed.
- Single run or sweep? — ask whether this is one run or a repeat over some "difference".
- Execution harness — if a sweep, generate the launcher (SLURM / PBS / Modal-parallel / serial-background), one output folder per run, runnable via a single command.
Always save every script to disk (never only paste into chat) so the user can review, edit,
and re-run them. Default to a bagel_designs/<short-project-name>/ directory in the working
directory unless the user names a location; put the design script, its two documentation files,
the smoke test, and any sweep harness there together.
What ships with it
10 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.
- assets/pbs_job.sh 1.4 KB runs code
- assets/slurm_job.sh 1.5 KB runs code
- assets/submit_cluster.py 4.2 KB runs code
- assets/sweep_config.py 5.1 KB runs code
- assets/sweep_runner.py 7.7 KB runs code
- references/api-reference.md 14 KB
- references/clarification-checklist.md 5.7 KB
- references/documentation-outputs.md 8.8 KB
- references/execution-harness.md 6.4 KB
- references/patterns.md 11 KB
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.
- 17d ago Changed · +45 lines · -87 tokens per session 9015cb8ce4b7
- 2mo ago First seen · 238 lines · 322 tokens per session scan A a4d158ad54b3
bagel-script-builder is a skill published in the GitHub repository softnanolab/bagel (147 stars, last pushed 10d ago), licensed MIT. It adds 235 tokens to every session and 4,376 once invoked, about $0.0009 per session on Opus 5.5. 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 2026-08-30.
bagel-script-builder compared with skills from other repositories
| Mod | Type | Stars | Last push | Licence | Scan | Tokens | Works with |
|---|---|---|---|---|---|---|---|
| bagel-script-buildersoftnanolab/bagel | Skill | 147 | 10d ago | MIT | A | 235 | Claude Code |
| instrument-data-to-allotropeanthropics/knowledge-work-plugins | Skill | 35k | yesterday | Apache-2.0 | A | 123 | Claude Code |
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| phylogeneticsK-Dense-AI/scientific-agent-skills | Skill | 56k | 6d ago | MIT | A | 71 | Claude Code, Codex |
| research-engineerdavila7/claude-code-templates | Skill | 33k | today | MIT | A | 43 | Claude Code, Codex |
| mapping-to-snomedmaziyarpanahi/openmed | Skill | 5.8k | today | Apache-2.0 | A | 205 | Claude Code |