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mims-harvard

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1. ▌
   Setup Scvi Remote Tool · mims-harvard bundle

   Set up, launch, validate, and troubleshoot the scVI ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
   11 installs
2. ▌
   Devtu Benchmark Harness · mims-harvard bundle

   Continuous improvement system for ToolUniverse tools, skills, and plugin. Run benchmarks, diagnose failures, route fixes to devtu skills, retest. Use after skill optimization, tool additions, or as regression check.
   13 installs
3. ▌
   Setup Boltz Remote Tool · mims-harvard bundle

   Set up, launch, validate, and troubleshoot the Boltz-2 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
   14 installs
4. ▌
   Setup Liana Remote Tool · mims-harvard bundle

   Set up, launch, validate, and troubleshoot the LIANA ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
   12 installs
5. ▌
   Setup Macs3 Remote Tool · mims-harvard bundle

   Set up, launch, validate, and troubleshoot the MACS3 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
   12 installs
6. ▌
   Tooluniverse Immunology · mims-harvard

   Immunology research workflows: antibody-antigen interactions, T/B cell repertoire, MHC/HLA binding prediction, autoimmune disease genetics, vaccine epitope mapping. Uses IEDB, IMGT, SAbDab, UniProt. Use for adaptive immunity questions, immune response analysis, antibody/TCR/BCR characterization, immunogenicity prediction, and immune-pathway-to-disease mapping.
   11 installs
7. ▌
   Tooluniverse Lipidomics · mims-harvard

   Lipid analysis and lipid-disease associations using LIPID MAPS classification, HMDB metabolite data, KEGG/Reactome lipid pathways (sphingolipid, eicosanoid, steroid, fatty acid), and PubChem chemical info. Use for lipid identification, lipid metabolism pathway mapping, and lipid-associated disease analysis (cardiovascular, diabetes, NAFLD).
   13 installs
8. ▌
   Tooluniverse Toxicology · mims-harvard

   Drug and chemical toxicity assessment via adverse outcome pathways (AOPs), real-world FAERS adverse event signals, FDA labels, and toxicogenomic associations. Triangulates molecular initiating event to cellular outcome to organ-level toxicity to clinical adverse event. Use for hepatotoxicity/cardiotoxicity/nephrotoxicity prediction and toxicology reports.
   14 installs
9. ▌
   Setup Borzoi Remote Tool · mims-harvard bundle

   Set up, launch, validate, and troubleshoot the Borzoi ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
   15 installs
10. ▌
    Setup Scanvi Remote Tool · mims-harvard bundle

    Set up, launch, validate, and troubleshoot the scANVI ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
    17 installs
11. ▌
    Setup Scvelo Remote Tool · mims-harvard bundle

    Set up, launch, validate, and troubleshoot the scVelo ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
    14 installs
12. ▌
    Tooluniverse Custom Tool · mims-harvard bundle

    Add custom local tools to ToolUniverse alongside the 1000+ built-in tools. Covers JSON-config tools (simplest, no code), Python class tools (REST/SOAP/GraphQL APIs, computational logic), and best-practices for return schemas. Use for wrapping new APIs, adding domain-specific computations, or contributing tools to the registry.
    11 installs
13. ▌
    Tooluniverse Epigenomics · mims-harvard bundle

    Genomics and epigenomics analysis: DNA methylation (CpG, 5mC, 5hmC, bisulfite, RRBS), m6A RNA modification (MeRIP-seq), ChIP-seq peaks, ATAC-seq accessibility, histone modifications, chromatin state, multi-omics integration. Combines pandas/scipy/pysam computation with ToolUniverse annotation tools. Use for genome-wide epigenomic statistics, methylation analysis, and chromatin-genome integration.
    11 installs
14. ▌
    Tooluniverse Self Review · mims-harvard bundle

    Review existing work against the user's actual goal and surface evidence-backed strengths, gaps, risks, and next fixes. Use when asked to eval, evaluate, review, assess, or check current/this/my/our work; decide whether a task is complete; build a definition-of-done checklist or rubric; or perform grading, LLM-as-judge, Qworld, or RET evaluation. Treat plain eval/review requests as qualitative: resolve "current work" from the conversation, artifacts, files, or diff, and never assign numeric scores unless the user explicitly requests scores, grades, points, ratings, weighted criteria, Qworld, or RET. Do not use for implementing automated eval suites, tests, graders, or benchmarks.
    11 installs
15. ▌
    Tooluniverse Single Cell · mims-harvard bundle

    Single-cell RNA-seq analysis with scanpy/anndata — h5ad data loading, scRNA-seq quality control and QC gating (n_genes_by_counts, total_counts, mitochondrial percent / pct_counts_mt, pct_counts_ribo, doublet detection with Scrublet/scDblFinder, ambient RNA / SoupX awareness, empty-droplet filtering, MAD-based thresholds), normalization, dimensionality reduction (PCA, UMAP, t-SNE), clustering (Leiden, Louvain), marker gene identification, cell-type annotation, pseudotime/trajectory analysis. Use for any scRNA-seq workflow, including deciding which cells to filter, flag, or investigate before downstream analysis.
    12 installs
16. ▌
    Create Tooluniverse Skill · mims-harvard bundle

    Create high-quality ToolUniverse skills following test-driven, implementation-agnostic methodology.
    12 installs
17. ▌
    Setup Harmony Remote Tool · mims-harvard bundle

    Set up, launch, validate, and troubleshoot the Harmony ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
    12 installs
18. ▌
    Setup Singler Remote Tool · mims-harvard bundle

    Set up, launch, validate, and troubleshoot the SingleR ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
    18 installs
19. ▌
    Setup Squidpy Remote Tool · mims-harvard bundle

    Set up, launch, validate, and troubleshoot the Squidpy ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
    10 installs
20. ▌
    Setup Tangram Remote Tool · mims-harvard bundle

    Set up, launch, validate, and troubleshoot the Tangram ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
    13 installs
21. ▌
    Tooluniverse Codex Plugin · mims-harvard

    Install, set up, verify, update, pin, uninstall, or troubleshoot the ToolUniverse plugin on OpenAI Codex. ALWAYS consult this skill for any of those — don't answer from memory, because the exact marketplace name (mims-harvard/ToolUniverse), the "codex plugin marketplace add" then "codex plugin add -m tooluniverse" flow, Codex's startup auto-upgrade behavior, the uvx tooluniverse MCP server, and the API-key env vars are easy to get wrong. Use it whenever someone wants to get ToolUniverse (or "the 1000+ scientific tools" / "the harvard tools") working on Codex, says the Codex plugin or its tools/skills won't load, hits a uvx or MCP-server startup error, asks how Codex updates it, wants to pin or remove it, or finds it running an old tool version — even if they never say the word "plugin". Not for the Claude Code plugin (use tooluniverse-claude-code-plugin), for running research with the tools, or for authoring new tools or skills.
    14 installs
22. ▌
    Tooluniverse Drug Synergy · mims-harvard bundle

    Drug-combination synergy analysis — quantify whether two drugs together are synergistic, additive, or antagonistic using the standard reference models (Bliss independence, HSA / highest single agent, Loewe additivity, ZIP, and the Chou-Talalay Combination Index). Use when you have measured single-drug and combination effects (inhibition/viability) and need a synergy score. Explains which model to use, what data each one needs, and how to read the score. NOT for looking up pre-computed synergy in a database (use the SYNERGxDB tool / cell-line-profiling skill).
    13 installs
23. ▌
    Tooluniverse Metabolomics · mims-harvard bundle

    Metabolomics research — metabolite identification, study analysis, and database searches across HMDB, MetaboLights, Metabolomics Workbench, KEGG. Use for annotating mass-spec features to known metabolites, finding metabolomics studies of a disease, and structured metabolomics research reports with metabolite-pathway mapping.
    14 installs
24. ▌
    Tooluniverse Neuroscience · mims-harvard

    Neuroscience research workflows: neuroanatomy, neural circuits, neurotransmitter biology, neurological/psychiatric disease genetics, neural-protein function. Uses Allen Brain Atlas, WormBase (C. elegans connectome), UniProt for neural proteins, PubMed for primary literature. Use for brain-region biology, neural development, neurodegeneration mechanisms (Alzheimer's, Parkinson's, ALS), and synaptic-protein characterization.
    14 installs
25. ▌
    Host And Share Remote Tool · mims-harvard bundle

    Host, validate, and privately share a user's own model, Python function, workflow, or existing Streamable HTTP MCP endpoint through ToolUniverse Platform. Use when turning a local CPU/GPU workload or lab endpoint into a stable TU remote tool, diagnosing its setup, or preparing it for controlled sharing.
    12 installs
26. ▌
    Setup Cellrank Remote Tool · mims-harvard bundle

    Set up, launch, validate, and troubleshoot the CellRank ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
    14 installs
27. ▌
    Setup Enformer Remote Tool · mims-harvard bundle

    Set up, launch, validate, and troubleshoot the Enformer ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
    12 installs
28. ▌
    Setup Monocle3 Remote Tool · mims-harvard bundle

    Set up, launch, validate, and troubleshoot the Monocle 3 ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
    13 installs
29. ▌
    Setup Pinnacle Remote Tool · mims-harvard bundle

    Set up, launch, validate, and troubleshoot the PINNACLE ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
    13 installs
30. ▌
    Setup Scrublet Remote Tool · mims-harvard bundle

    Set up, launch, validate, and troubleshoot the Scrublet ToolUniverse remote tool and optionally relay it through ToolUniverse Connect. Use when deploying or auditing this implementation.
    14 installs
31. ▌
    Tooluniverse Dose Response · mims-harvard bundle

    Dose-response / concentration-response curve fitting — IC50, EC50, Hill slope, Emax/Emin efficacy, and relative potency from paired concentration vs response data (enzyme/cell assays, drug screening, agonist/antagonist pharmacology). Fits the 4-parameter logistic (Hill sigmoidal) model. Use when you have concentrations + responses and need a potency value, to compare two compounds' potency, or to judge curve quality. NOT for image-derived dose-response (use tooluniverse-image-analysis) and NOT for survival/regression (use tooluniverse-statistical-modeling).
    13 installs
32. ▌
    Tooluniverse Drug Research · mims-harvard bundle

    Comprehensive drug profiling — mechanism, primary/secondary targets, drug interactions, clinical-trial status, adverse events (FAERS), pharmacogenomics, and approval history. Use for full drug investigation reports, 'tell me about drug X' queries, and assembling drug profiles for clinicians, researchers, or regulatory work.
    9 installs