ToolUniverse is a collection of tools, interfaces, and supporting components for building AI systems that perform scientific work. It is for developers creating AI scientist agents that use APIs, databases, machine-learning tools, and domain-specific utilities. The catalogue includes skills, commands, an MCP server, an agent, and a hook for working with the ecosystem.
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 skills add mims-harvard/ToolUniverse --skill tooluniverse-natural-product-dereplicationgit clone --depth 1 https://github.com/mims-harvard/ToolUniverseWrote 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/mims-harvard/tooluniverse/tooluniverse-natural-product-dereplication)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-natural-product-dereplication"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-natural-product-dereplication/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/mims-harvard/tooluniverse/tooluniverse-natural-product-dereplication"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-natural-product-dereplication.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 | $0.00194 | $0.03956 |
| Opus 5.5 | $0.00078 | $0.01582 |
| Sonnet 5.5 | $0.00039 | $0.00791 |
| Haiku 4.5 | $0.00019 | $0.00396 |
Grade A, and why
tooluniverse-natural-product-dereplication 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 10d 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 — 180 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Natural Product Dereplication & Chemotaxonomy
Decide whether a putative natural product is already known, identify the microbe that produces it, attach the literature reference, and assign its ChemOnt chemical class. This is the dereplication question every NP chemist and metabolomics analyst asks of a new feature: "have we seen this before, and what makes it?"
LOOK UP DON'T GUESS: Never assume an NPAID, producing organism, exact mass, or chemical class. Every identity, provenance, and taxonomy claim must come from a live tool call.
Scope (microbial NPs only): NPAtlas covers natural products from bacteria and fungi. It does NOT cover plant, animal, or marine-invertebrate metabolites unless a microbial producer was reported. A "no NPAtlas hit" therefore means not a known microbial NP — it does not prove the molecule is novel in an absolute sense.
Backing Tools (all keyless; verify before quoting)
| Tool | Input | Returns |
|---|---|---|
NPAtlas_search_compounds |
name / inchikey / formula / smiles, limit |
list of {npaid, name, molecular_formula, molecular_weight, exact_mass, inchikey, smiles}. (origin_organism is null here — fetch the full record for provenance) |
NPAtlas_get_compound |
npaid (e.g. NPA014588) |
full record incl. origin_organism (producing microbe + taxonomic lineage) and origin_reference (title/doi/journal/year) |
ClassyFire_classify_by_inchikey |
inchikey (full 27-char) |
ChemOnt kingdom→superclass→class→subclass→direct_parent, molecular_framework, substituents. classified:false if not in cache |
OPSIN_name_to_structure |
name (systematic IUPAC) |
smiles / inchi / inchikey. parsed:false for trade/trivial names |
PubChem_get_CID_by_compound_name |
name |
{IdentifierList:{CID:[...]}} |
PubChem_get_compound_properties_by_CID |
cid, properties (e.g. ["MolecularFormula","MolecularWeight","InChIKey","IUPACName"]) |
property table — use to obtain an InChIKey for arbitrary compounds |
LOTUS_search_natural_products |
query (name / SMILES / InChIKey) |
list of natural-product occurrence records (lotus_id, smiles, inchikey, contains_sugar, heavy_atom_number) |
LOTUS_search_by_inchikey |
inchikey |
same shape as above, InChIKey-scoped |
LOTUS_get_compound |
compound_id (internal LOTUS id) |
full occurrence record incl. reported source organism(s) |
MIBiG_list_clusters |
search_term (compound/organism name) |
biosynthetic gene clusters (BGC accession, quality, completeness, product name(s)) |
MIBiG_get_stats |
none | repository-wide counts by status and biosynthetic class (PKS/NRPS/terpene/...) |
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.
- 10d ago Changed · +10 lines 4f2def972362
- 1mo ago First seen · 170 lines · 194 tokens per session scan A 74ad51625812
tooluniverse-natural-product-dereplication is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,744 stars, last pushed yesterday), licensed Apache-2.0. It adds 194 tokens to every session and 3,956 once invoked, about $0.0008 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 2026-09-03.
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