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-molecular-cloninggit 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-molecular-cloning)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-molecular-cloning"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-molecular-cloning/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-molecular-cloning"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-molecular-cloning.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 | $0.00000 | $0.01942 |
| Opus 5.5 | $0.00000 | $0.00777 |
| Sonnet 5.5 | $0.00000 | $0.00388 |
| Haiku 4.5 | $0.00000 | $0.00194 |
Grade A, and why
tooluniverse-molecular-cloning 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 1mo 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 — 112 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Molecular Cloning Assembly Design (Gibson & Golden Gate)
Plan how to join DNA fragments into a construct: design the overlaps (Gibson) or Type IIS overhangs (Golden Gate) and avoid the failures that come from internal sites and non-unique junctions.
Step 0 — Pick the method
| Use Gibson Assembly when | Use Golden Gate when |
|---|---|
| A few fragments, scarless/seamless junctions anywhere you choose | Many parts, standardized reusable parts (MoClo/modular), one-pot |
| You can add ~20–40 bp homology by PCR | You can remove internal BsaI/BbsI sites (domestication) |
| One-off constructs | Combinatorial libraries / repeated assemblies |
Both are sequence-independent (no scar at the junction for Gibson; a 4-bp fusion scar for Golden Gate). For 2–4 unique fragments, Gibson is usually simplest; for libraries or a parts toolkit, Golden Gate.
Step 1 — Gibson Assembly
tu run DNA_gibson_design '{"operation":"gibson_design",
"fragments":["ATGGCG...GAGGAC","GAGGAC...GGCAAG","GGGCAAG...ATCCT"],
"overlap_length":20}'
For each fragment it returns left_overlap, right_overlap, and with_overlaps (the fragment extended with the homology arms you'd add to your PCR primers — hand these to tooluniverse-primer-design).
Gibson design rules
- Overlap length 15–40 bp (20–25 typical); longer for GC-poor junctions.
- Overlap Tm ≈ 48–65 °C and balanced between junctions.
- Fragment order matters — list fragments in assembly order; the last fragment's 3′ overlaps the first only if you're making a circle (vector).
- Avoid repeats/secondary structure at the junctions (hairpins, direct repeats) → misassembly.
- Unique junctions — if two junctions share homology, fragments can swap; redesign so each overlap is unique.
Step 2 — Golden Gate Assembly
tu run DNA_golden_gate_design '{"operation":"golden_gate_design",
"parts":["ATGGCG...AAGAAC","CTGAGC...CTGATC","GAGGAG...GTGGTG"],
"enzyme":"BsaI"}'
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.
- 1mo ago Changed · +38 lines · -121 tokens per session 12b33f10d99d
- 1mo ago First seen · 74 lines · 121 tokens per session scan A 2266f5ecdd2e
tooluniverse-molecular-cloning is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,744 stars, last pushed yesterday), licensed Apache-2.0. It costs nothing until one of its globs matches a file; then it loads 1,942 tokens. 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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