k-dense-ai/scientific-agent-skills

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uspto-database Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, …

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zinc-database Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for doc…

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bindingdb-database Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), comp…

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gtex-database Query GTEx (Genotype-Tissue Expression) portal for tissue-specific gene expression, eQTLs (expression quantitative tr…

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interpro-database Query InterPro for protein family, domain, and functional site annotations. Integrates Pfam, PANTHER, PRINTS, SMART, …

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cbioportal-database Query cBioPortal for cancer genomics data including somatic mutations, copy number alterations, gene expression, and …

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gnomad-database Query gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF),…

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jaspar-database Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs). Search by TF name, species, or class;…

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monarch-database Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species. Integrates OMIM,…

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13c-metabolic-flux Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated ato…

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alphagenome Looks up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 …

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cantera Runs Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation check…

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cellprofiler Runs reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescenc…

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datalad Retrieves, versions, and publishes scientific datasets with DataLad and git-annex, and captures computational provena…

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fictiv Operates Fictiv (app.fictiv.com), the on-demand manufacturing platform, end to end in the user's browser. Covers uplo…

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flowkit Analyzes flow cytometry data with FlowKit, including spillover compensation, logicle and biexponential transforms, hi…

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folklore-variant-evidence Retrieves ClinGen gene-disease validity assertions for a public gene or disease, and reviews source-linked public evi…

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mageck Analyzes pooled CRISPR screen FASTQ reads and guide-count matrices with MAGeCK, validates guide libraries and contras…

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marine-carbonate-chemistry Solves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-c…

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nmrglue Processes calibrated one-dimensional complex NMR free-induction decays with nmrglue into phased spectra, peak candida…

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nwb-conversion Converts neuroscience acquisition data to Neurodata Without Borders files with NeuroConv and PyNWB, preserves metadat…

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primer-design Designs and audits PCR and RT-qPCR primers with Primer3, explicit thermodynamic conditions, reference-based off-targe…

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pybamm Simulates lithium-ion battery charge, discharge and rest experiments with PyBaMM, records parameter-set provenance, c…

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pycalphad Computes finite-temperature CALPHAD equilibria, phase fractions, and phase compositions from thermodynamic TDB databa…

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qiime2-amplicon Processes paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy with retained artifact provenance. Checks pair…

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relion Validates and executes RELION single-particle cryo-EM refinement and half-map postprocessing. Supports STAR optics/ac…

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tellurium Simulates biochemical kinetic models from SBML or Antimony with Tellurium and libRoadRunner, checks model units, comp…

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arxiv-database Search and retrieve preprints from arXiv via the Atom API. Use this skill when searching for papers in physics, mathe…

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writing Use this skill to create high-quality academic papers, literature reviews, grant proposals, clinical reports, and oth…

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pymc-bayesian-modeling Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, post…

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planning-with-files Implements Manus-style file-based planning to organize and track progress on complex tasks. Creates task_plan.md, fin…

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biomni biomni — an installable skill for AI agents, published by k-dense-ai/scientific-agent-skills.

k-dense-ai/scientific-agent-skills

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