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-enzyme-kineticsgit 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-enzyme-kinetics)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-enzyme-kinetics"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-enzyme-kinetics/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-enzyme-kinetics"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-enzyme-kinetics.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 | $0.00123 | $0.01518 |
| Opus 5 | $0.00062 | $0.00759 |
| Sonnet 5 | $0.00025 | $0.00304 |
| Haiku 4.5 | $0.00012 | $0.00152 |
Grade A, and why
tooluniverse-enzyme-kinetics 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 12d 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 — 91 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Enzyme Kinetics (Michaelis-Menten)
Turn substrate concentration vs initial velocity data into Km, Vmax, kcat, and catalytic efficiency — and classify an inhibitor's mechanism.
The Michaelis-Menten model: v = Vmax·[S] / (Km + [S]).
When to use this
- You measured initial reaction rates at several substrate concentrations.
- You need Km (substrate affinity), Vmax, kcat (turnover number), or kcat/Km.
- You have ±inhibitor velocity data and want to classify the inhibition mode + Ki.
For published kinetic constants (someone else's Km/kcat), use the BRENDA tools instead — this skill is for analyzing your own measured data.
Step 1 — Prepare the data
| Issue | What to do |
|---|---|
| Initial velocities, not endpoints | v must be the initial rate (linear phase, <10% substrate consumed). Endpoint or plateaued rates give a wrong Km/Vmax. |
| Substrate range must span Km | Include [S] both well below and well above Km (ideally ~0.2×Km to ~5×Km). Points only above Km can't define Km; only below can't define Vmax. |
| Units — be consistent | One [S] unit (mM, µM) → Km comes back in that unit. One velocity unit. Keep them fixed. |
| For kcat you need [E] | kcat = Vmax / [E]total. The tool's "catalytic_efficiency" is Vmax/Km on the velocity scale; to get true kcat (per-second turnover) and kcat/Km, divide Vmax by the molar enzyme concentration yourself. |
| ≥5–7 points | Few points → unstable fit. Spread them across the range, not clustered. |
Step 2 — Fit Michaelis-Menten
tu run EnzymeKinetics_calculate '{"operation":"michaelis_menten",
"substrate_concs":[0.1,0.25,0.5,1,2,5,10],
"velocities":[8.5,18,32,52,72,90,98]}'
Returns a nonlinear_fit block (Vmax, Km, R2, SSE) — use these as the answer, a lineweaver_burk block (for reference only), catalytic_efficiency (Vmax/Km), and predicted_velocities + residuals.
Prefer the nonlinear fit, not Lineweaver-Burk. The double-reciprocal (Lineweaver-Burk) linearization distorts error (it over-weights low-
[S]points) and is only for visualization/sanity — never report its Km/Vmax as the final values. The tool gives both; citenonlinear_fit.
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.
- 12d ago First seen · 91 lines · 123 tokens per session scan A 5647a3e911fa
tooluniverse-enzyme-kinetics is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,680 stars, last pushed 2d ago), licensed Apache-2.0. It adds 123 tokens to every session and 1,518 once invoked, about $0.0006 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 2026-08-30.
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