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-primer-designgit 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-primer-design)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-primer-design"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-primer-design/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-primer-design"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-primer-design.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 1 finding, up to medium
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- medium analysis-evasion · line 1 Suspicious Unicode normalization or mixed-script contentFix: Review the flagged content for security risks. Ensure no credentials, secrets, or sensitive data are exposed.
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 | $0.00120 | $0.01483 |
| Opus 5.5 | $0.00048 | $0.00593 |
| Sonnet 5.5 | $0.00024 | $0.00297 |
| Haiku 4.5 | $0.00012 | $0.00148 |
Grade A, and why
tooluniverse-primer-design 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 — 80 lines — stays where its author put it; the contents beside it link to each section on GitHub.
PCR / qPCR Primer & Oligo Design
Design primers for a target DNA region, get their Tm/Ta, and QC them for the secondary-structure problems that make a PCR fail.
When to use this
- Design a forward/reverse primer pair to amplify a region of a sequence.
- Compute the Tm / annealing temperature of a primer.
- QC an existing primer pair (GC clamp, 3'-end, hairpins, self/cross dimers, Tm match).
Step 1 — Design a primer pair
tu run DNA_primer_design '{"operation":"primer_design",
"sequence":"ATGGCG...AACGTG", # full template; must be >= target_end + flanking primer room
"target_start":40, "target_end":125,
"tm_target":60, "product_size_min":80, "product_size_max":140}'
Returns forward_primer / reverse_primer (sequence, tm, gc_content, length, position) and product_size. (target_end is clamped to the sequence length, so a too-short template silently shrinks the target — see the constraint quirk below.)
Constraint quirk — read this or it will error.
target_start..target_endis the region the amplicon must cover, and the design only succeeds when that span fits inside the product-size window AND good-Tm primers can be placed flanking it. So you need roughly:product_size_min ≤ (target span) ≤ product ≤ product_size_max, with enough flanking sequence on both sides. Common errors and the fix:
- "Target region (N bp) is smaller than product_size_min" → your target is narrower than
product_size_min; lowerproduct_size_minor widen the target.- "product does not cover the target / does not span" → the target is too wide for
product_size_max, or runs too close to a sequence end; widenproduct_size_maxor give more flanking sequence.
Step 2 — Get Tm / annealing temperature for specific primers
tu run NEB_Tm_calculate '{"primer_sequence":"CTACCTGAAGAACCTGAG",
"primer_sequence_2":"CTTGATGTCCTCCAGCAT",
"polymerase":"Q5", "primer_concentration":500, "monovalent_salt_mm":50}'
NEB returns Tm for each primer and a recommended annealing temperature (Ta) for the chosen polymerase. IDT_analyze_oligo (sequence, salt/Mg/dNTP/oligo concentrations) adds GC%, molecular weight, and hairpin / self-dimer screening. DNA_calculate_gc_content is a quick GC check.
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 First seen · 80 lines · 120 tokens per session scan A 75d22ce2b027
tooluniverse-primer-design is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,744 stars, last pushed yesterday), licensed Apache-2.0. It adds 120 tokens to every session and 1,483 once invoked, about $0.0005 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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Draft a LaTeX research paper from all previous stage outputs.
construct-toy-examples
Generate and analyze simpler examples that satisfy both the assumptions and the conclusion of a theorem statement or subgoal. Use when you are stuck in reasoning and need simpler examples to regain traction, or when you want to see where the assumptions take effect and gain intuition.
obtain-immediate-conclusions
Derive immediate mathematical consequences from a theorem statement or subgoal. Use when starting a new problem, branch, or subgoal, or when cheap progress or a cleaner reformulation is needed before deeper proof search.
clinical-research-analysis-framework
Guided workflow for statistical and ML analysis of clinical data. Use when planning or executing research analyses on MIMIC, eICU, or similar EHR data. Ensures methodological rigor through structured consultation, assumption checking, and stepwise execution with audit trails.
apache-iv-score
Calculate APACHE IV (Acute Physiology and Chronic Health Evaluation IV) score for ICU mortality prediction. Use for severity assessment, hospital mortality prediction, ICU benchmarking, or case-mix adjustment. eICU has pre-computed scores; MIMIC-IV requires custom implementation with diagnosis mapping challenges.