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-immune-repertoire-analysisgit 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-immune-repertoire-analysis)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-immune-repertoire-analysis"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-immune-repertoire-analysis/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-immune-repertoire-analysis"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-immune-repertoire-analysis.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- Socket pass
- Snyk warn
- 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 | $0.00076 | $0.02952 |
| Opus 5.5 | $0.00030 | $0.01181 |
| Sonnet 5.5 | $0.00015 | $0.00590 |
| Haiku 4.5 | $0.00008 | $0.00295 |
Grade A, and why
tooluniverse-immune-repertoire-analysis 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 — 200 lines — stays where its author put it; the contents beside it link to each section on GitHub.
ToolUniverse Immune Repertoire Analysis
Comprehensive skill for analyzing T-cell receptor (TCR) and B-cell receptor (BCR) repertoire sequencing data to characterize adaptive immune responses, clonal expansion, and antigen specificity.
Domain Reasoning
Repertoire diversity reflects immune history. High clonality — a few clones dominating — indicates antigen-driven expansion, as seen in active infection, tumor-infiltrating lymphocytes, or chronic stimulation. Low diversity points to immunodeficiency or treatment-induced lymphopenia. Always compare observed metrics against healthy donor reference distributions before drawing conclusions; a Shannon entropy of 7 is unremarkable in a healthy adult but alarming post-chemotherapy.
LOOK UP DON'T GUESS
- Clonotype frequency thresholds, CDR3 length ranges, and convergence ratios: query IEDB or VDJdb; do not assume values from memory.
- Epitope specificities for expanded clones: search
iedb_search_tcell_assaysandBVBRC_search_epitopes; never infer antigen identity from CDR3 alone. - V gene family usage biases in healthy donors: retrieve published reference data or query ImmPort; do not assume baseline distributions are uniform.
- Sequencing depth adequacy: compute rarefaction curves from the actual data; do not guess whether depth is sufficient.
Overview
Adaptive immune receptor repertoire sequencing (AIRR-seq) enables comprehensive profiling of T-cell and B-cell populations through high-throughput sequencing of TCR and BCR variable regions. This skill provides an 8-phase workflow for:
- Clonotype identification and tracking
- Diversity and clonality assessment
- V(D)J gene usage analysis
- CDR3 sequence characterization
- Clonal expansion and convergence detection
- Epitope specificity prediction
- Integration with single-cell phenotyping
- Longitudinal repertoire tracking
Core Workflow
Phase 1: Data Import & Clonotype Definition
Load AIRR-seq data from common formats (MiXCR, ImmunoSEQ, AIRR standard, 10x Genomics VDJ). Standardize columns to: cloneId, count, frequency, cdr3aa, cdr3nt, v_gene, j_gene, chain. Define clonotypes using one of three methods:
- cdr3aa: Amino acid CDR3 sequence only
- cdr3nt: Nucleotide CDR3 sequence
- vj_cdr3: V gene + J gene + CDR3aa (most common, recommended)
What ships with it
2 files 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.
- 10d ago Changed · +5 lines 5e21328a9069
- 1mo ago First seen · 195 lines · 76 tokens per session scan A ea1c648f8343
tooluniverse-immune-repertoire-analysis is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,744 stars, last pushed yesterday), licensed Apache-2.0. It adds 76 tokens to every session and 2,952 once invoked, about $0.0003 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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