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/hmdb-databasenpx skills add synthetic-sciences/openscience --skill hmdb-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/hmdb-database)<a href="https://agentmods.dev/skills/synthetic-sciences/openscience/hmdb-database"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/hmdb-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 | $0.00046 | $0.01754 |
| Opus 5 | $0.00023 | $0.00877 |
| Sonnet 5 | $0.00009 | $0.00351 |
| Haiku 4.5 | $0.00005 | $0.00175 |
Grade A, and why
hmdb-database 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 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.
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.
Copies of this mod
6 near-identical copies found in the catalogue:
- hmdb-database — 100% identical, 3 lines differ
- hmdb-database — 100% identical, 3 lines differ
- hmdb-database — 97% identical, 7 lines differ
- hmdb-database — 89% identical, 6 lines differ
- hmdb-database — 89% identical, 6 lines differ
- hmdb-database — 89% identical, 6 lines differ
How it starts
The opening of the file, as written. The whole thing — 196 lines — stays where its author put it; the contents beside it link to each section on GitHub.
HMDB Database
Overview
The Human Metabolome Database (HMDB) is a comprehensive, freely available resource containing detailed information about small molecule metabolites found in the human body.
When to Use This Skill
This skill should be used when performing metabolomics research, clinical chemistry, biomarker discovery, or metabolite identification tasks.
Database Contents
HMDB version 5.0 (current as of 2025) contains:
- 220,945 metabolite entries covering both water-soluble and lipid-soluble compounds
- 8,610 protein sequences for enzymes and transporters involved in metabolism
- 130+ data fields per metabolite including:
- Chemical properties (structure, formula, molecular weight, InChI, SMILES)
- Clinical data (biomarker associations, diseases, normal/abnormal concentrations)
- Biological information (pathways, reactions, locations)
- Spectroscopic data (NMR, MS, MS-MS spectra)
- External database links (KEGG, PubChem, MetaCyc, ChEBI, PDB, UniProt, GenBank)
Core Capabilities
1. Web-Based Metabolite Searches
Access HMDB through the web interface at https://www.hmdb.ca/ for:
Text Searches:
- Search by metabolite name, synonym, or identifier (HMDB ID)
- Example HMDB IDs: HMDB0000001, HMDB0001234
- Search by disease associations or pathway involvement
- Query by biological specimen type (urine, serum, CSF, saliva, feces, sweat)
Structure-Based Searches:
- Use ChemQuery for structure and substructure searches
- Search by molecular weight or molecular weight range
- Use SMILES or InChI strings to find compounds
Spectral Searches:
- LC-MS spectral matching
- GC-MS spectral matching
- NMR spectral searches for metabolite identification
Advanced Searches:
- Combine multiple criteria (name, properties, concentration ranges)
- Filter by biological locations or specimen types
- Search by protein/enzyme associations
2. Accessing Metabolite Information
When retrieving metabolite data, HMDB provides:
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 · 196 lines · 46 tokens per session scan A 70965f832d70
hmdb-database is a skill published in the GitHub repository synthetic-sciences/openscience (3,473 stars, last pushed today), licensed Apache-2.0. It adds 46 tokens to every session and 1,754 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 2026-09-03.
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