synthetic-sciences/openscience is an AI workbench that carries out scientific research by reading papers, forming hypotheses, writing and running code, conducting experiments, analyzing results, and preparing reports. Researchers use it for work in machine learning, biology, physics, and chemistry with remote or local models. Catalogue add-ons extend its scientific workflows through skills and instructions.
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.
npx agentmods add skills/synthetic-sciences/openscience/metabolomics-workbench-databasenpx skills add synthetic-sciences/openscience --skill metabolomics-workbench-databasegit clone --depth 1 https://github.com/synthetic-sciences/openscienceWrote 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/synthetic-sciences/openscience/metabolomics-workbench-database)<a href="https://agentmods.dev/skills/synthetic-sciences/openscience/metabolomics-workbench-database"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/metabolomics-workbench-database.svg" alt="Measured on agentmods" height="20"></a>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 | $0.00053 | $0.02345 |
| Opus 5 | $0.00026 | $0.01172 |
| Sonnet 5 | $0.00011 | $0.00469 |
| Haiku 4.5 | $0.00005 | $0.00234 |
Grade A, and why
metabolomics-workbench-database scanned grade A with 1 finding 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 2d 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5281365/all/json') Copies of this mod
7 near-identical copies found in the catalogue:
- metabolomics-workbench-database — 97% identical, 3 lines differ
- metabolomics-workbench-database — 97% identical, 7 lines differ
- metabolomics-workbench-database — 97% identical, 7 lines differ
- alterlab-metabolomics-wb — 86% identical, 42 lines differ
- metabolomics-workbench-database — 84% identical, 6 lines differ
- metabolomics-workbench-database — 84% identical, 6 lines differ
- metabolomics-workbench-database — 84% identical, 6 lines differ
How it starts
The opening of the file, as written. The whole thing — 259 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Metabolomics Workbench Database
Overview
The Metabolomics Workbench is a comprehensive NIH Common Fund-sponsored platform hosted at UCSD that serves as the primary repository for metabolomics research data. It provides programmatic access to over 4,200 processed studies (3,790+ publicly available), standardized metabolite nomenclature through RefMet, and powerful search capabilities across multiple analytical platforms (GC-MS, LC-MS, NMR).
When to Use This Skill
This skill should be used when querying metabolite structures, accessing study data, standardizing nomenclature, performing mass spectrometry searches, or retrieving gene/protein-metabolite associations through the Metabolomics Workbench REST API.
Core Capabilities
1. Querying Metabolite Structures and Data
Access comprehensive metabolite information including structures, identifiers, and cross-references to external databases.
Key operations:
- Retrieve compound data by various identifiers (PubChem CID, InChI Key, KEGG ID, HMDB ID, etc.)
- Download molecular structures as MOL files or PNG images
- Access standardized compound classifications
- Cross-reference between different metabolite databases
Example queries:
import requests
# Get compound information by PubChem CID
response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5281365/all/json')
# Download molecular structure as PNG
response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/11/png')
# Get compound name by registry number
response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/11/name/json')
2. Accessing Study Metadata and Experimental Results
Query metabolomics studies by various criteria and retrieve complete experimental datasets.
Key operations:
- Search studies by metabolite, institute, investigator, or title
- Access study summaries, experimental factors, and analysis details
- Retrieve complete experimental data in various formats
- Download mwTab format files for complete study information
- Query untargeted metabolomics data
What ships with it
1 file 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.
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.
- 2d ago First seen · 259 lines · 53 tokens per session scan A 0c03da928dd3
metabolomics-workbench-database is a skill published in the GitHub repository synthetic-sciences/openscience (3,473 stars, last pushed today), licensed Apache-2.0. It adds 53 tokens to every session and 2,345 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
Other skills, from other repositories
meta-paper-write
Use this meta-skill instead of answering directly when the current user asks to draft or produce a new academic/research paper or LaTeX manuscript. It uses multi-skill orchestration for manuscript workflows that need source search, citation planning, experiment or figure/table placeholders, drafting, length checks…
paper-revision-author
Revise independently drafted paper sections into one coherent LaTeX body before the abstract is written.
paper-section-author
Write one publication-style research-paper section as a bounded, citation-grounded LaTeX fragment from a writing plan, outline, citation plan, and optional figure/table context.
meta-arxiv-daily-digest-deck
Fetch the day's top arXiv submissions in a chosen category, write a structured per-paper digest, render the digest as a PPTX deck (one slide per paper), and persist the digest to long-term memory. Use for a daily 'arxiv morning briefing' — manual fire or cron-scheduled.
paper-quality-gate
Deterministic pre-compile gate for meta-paper-write. Enforces length/citation verdicts and rejects unsupported empirical-result claims when no user evidence was supplied.
paper-latex-sanitizer
Deterministically normalize safe LaTeX punctuation and replace unsupported forecast magnitudes with explicit placeholders before meta-paper-write publication gates run.