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scholaraio: Skill for Claude Code

.claude/skills/scientific-runtime/SKILL.md

scientific-runtime is a skill for Claude Code from ZimoLiao/scholaraio. It costs 41 tokens per session (914 once invoked), scanned A, original, MIT.

A shared operating guide for using scientific command-line software through ScholarAIO. It tells an agent how to find commands and options, handle incomplete documentation, and work with tool-specific guides.

In plain words
What is it for?
Use it when asking about scientific command-line tools, their parameters, program pages, or workflows. It is intended to be combined with a guide for the specific tool, such as a molecular-dynamics or computational-fluid-dynamics program.
Why use it?
Scientific software often has many commands and settings, while its available documentation may be incomplete. This guide helps the agent give useful help without making the user repair internal documentation.

Skill for Claude Code

Written for Claude Code: installed under .claude/.

This is ZimoLiao/scholaraio's own configuration. It tells Claude Code how to work on scholaraio itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything scholaraio configures →

Part of the scholaraio plugin — 44 skills, 1 hook shipped together

not rated 584repo +1 10d ago A scan SkillSpector: warn 41 tokens original MIT
View source ↗ ZimoLiao/scholaraio zimoliao.github.io
Reuse

Borrowing it

Nothing to install: this file belongs to ZimoLiao/scholaraio. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/ZimoLiao/scholaraio/main/.claude/skills/scientific-runtime/SKILL.md
Clone the repo
git clone --depth 1 https://github.com/ZimoLiao/scholaraio

Made for: Claude Code.

Or install scholaraio, the plugin that ships this one along with the rest of its 44 skills, 1 hook.

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 scientific-runtime

README.md
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Your own site
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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.

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Your own site · 80×15
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Per session 41 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 914 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. Third-party audits
  • NVIDIA SkillSpector warn 7 Sept 2026
SkillSpector: 1 finding, up to medium

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

  • medium Excessive Agency · line 84
    Skill enables autonomous high-impact decisions without human-in-the-loop verification. Critical operations (destructive commands, financial transactions, data deletion) should require explicit user confirmation.
    Fix: Add human-in-the-loop confirmation for destructive, irreversible, or high-impact operations. Never auto-execute commands that modify files, send data, or alter system state.
How audits are shown
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 $0.00041 $0.00914
Opus 5.5 $0.00016 $0.00366
Sonnet 5.5 $0.00008 $0.00183
Haiku 4.5 $0.00004 $0.00091

Measured 2mo ago against content hash 58510d510b4f, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

scientific-runtime 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 2mo 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.

.claude/skills/scientific-runtime/SKILL.md · 131 lines

How it starts

The opening of the file, as written. The whole thing — 131 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Scientific Runtime Protocol

This is a shared runtime skill for scientific CLI work.

It is not a tool manual. It tells the agent how to behave when serving real users on scientific tool tasks.

Use it alongside a tool-specific scientific skill such as:

  • quantum-espresso
  • lammps
  • gromacs
  • openfoam
  • bioinformatics

Core Principle

ScholarAIO is for users, not for people who want to co-maintain the internal documentation layer.

So the agent should absorb complexity whenever possible.

The user should experience:

  • natural language help
  • reliable parameter lookup
  • graceful fallback when coverage is partial

The user should not experience:

  • being asked to manually patch toolref
  • being forced to learn internal parser gaps
  • being blocked because a documentation layer is imperfect

Runtime Protocol

For any scientific CLI task:

  1. Identify the scientific tool or sub-tool that matches the problem.
  2. Use the tool-specific skill for workflow and scientific norms.
  3. Use toolref first for commands, parameters, program pages, and option meanings.
  4. If toolref is sufficient, continue normally.
  5. If toolref is partial, fall back to official docs and continue the task.
  6. Mention the coverage gap briefly only when it affects confidence or maintainability.
  7. Do not turn the current user task into documentation maintenance work.

Toolref-First Behavior

The agent should prefer:

  • scholaraio toolref show <tool> ... for precise lookups
  • scholaraio toolref search <tool> "..." for natural-language entry

The stable public surfaces are:

  • the scholaraio toolref ... CLI
  • the top-level scholaraio.stores.toolref package facade

The agent should not route users through internal implementation modules such as:

  • scholaraio.stores.toolref.fetch
  • scholaraio.stores.toolref.manifest
  • scholaraio.stores.toolref.storage
  • scholaraio.stores.toolref.search

Those internal module boundaries may change during refactors. User-facing guidance should stay anchored to the CLI and the top-level package behavior.

Read the full file on GitHub · 131 lines

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. 2mo ago First seen · 131 lines · 41 tokens per session scan A 58510d510b4f

Subscribe to this mod's changes

scientific-runtime is a skill published in the GitHub repository ZimoLiao/scholaraio (584 stars, last pushed 10d ago), licensed MIT. It adds 41 tokens to every session and 914 once invoked, about $0.0002 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.

Scientificagentic-scienceagentic-searchai-agentcomputational-researchresearch-workflowscientific-computing
Related

scientific-runtime compared with skills from other repositories

scientific-runtime next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
scientific-runtimeZimoLiao/scholaraioSkill58410d agoMITA41Claude Code
infrastructure-validationdocxology/templateSkill23yesterdayApache-2.0A54Claude Code, Codex
provenance-dagdocxology/templateSkill23yesterdayApache-2.0A103Claude Code, Codex
scientific-connectorsdocxology/templateSkill23yesterdayApache-2.0A87Claude Code, Codex
infrastructure-search-literaturedocxology/templateSkill23yesterdayApache-2.0A123Claude Code, Codex
template-academic-paper-reviewerdocxology/templateSkill23yesterdayApache-2.0A52Claude Code, Codex
template-reproducibility-auditdocxology/templateSkill23yesterdayApache-2.0A70Claude Code, Codex