3,608 skills found · Page 8 of 121
sickn33 / apple-notes-searchSemantic + keyword search and connection-discovery across the user's own Apple Notes via the apple-notes MCP server
sickn33 / agent-memoryA hybrid memory system that provides persistent, searchable knowledge management for AI agents.
sickn33 / agent-tool-builderTools are how AI agents interact with the world. A well-designed
sickn33 / animejs-animationAdvanced JavaScript animation library skill for creating complex, high-performance web animations.
sickn33 / architecture-reviewReview repository architecture using Ontoly Software Graph and MCP capabilities.
sickn33 / api-testing-observability-api-mockYou are an API mocking expert specializing in realistic mock services for development, testing, and demos. Design mocks that simulate real API behavior and enable parallel development.
K-Dense-AI / alphagenomeAlphaGenome API key, free for non-commercial use from deepmind.google.com/science/alphagenome. ALPHA_GENOME_API_KEY is accepted as an alternative spelling.
K-Dense-AI / bulk-rnaseqPrepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. Covers nf-core/rnaseq and standalone quantification, biological replication, strandedness, reference provenance, validated count assembly and a PyDESeq2 handoff.
K-Dense-AI / experimental-designDesigns experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so results are interpretable
K-Dense-AI / fluidsimPlans, configures, inspects, restarts, and analyzes bounded FluidSim computational-fluid-dynamics simulations with explicit numerical-validity and HPC safety checks. Use for FluidSim solver selection, parameter review, FFT/MPI setup, output diagnostics, or restart compatibility.
K-Dense-AI / molecular-dynamicsRuns and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs energy minimization and production MD, and analyzes trajectories (RMSD, RMSF, contact maps, free energy surfaces).
K-Dense-AI / onekgpdQueries the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants
K-Dense-AI / pathogen-variant-surveillanceQueries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence proportions, reporting delays, and descriptive mutation frequencies.
K-Dense-AI / pathway-enrichmentPerforms pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results. Used when the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pa…
K-Dense-AI / primer-designDesigns and audits PCR and RT-qPCR primers with Primer3, explicit thermodynamic conditions, reference-based off-target amplification searches, and traceable sequence coordinates.
K-Dense-AI / pymatgenAnalyzes, validates, converts, and transforms materials structures and computed materials data with pymatgen. Use for local phase diagrams, symmetry sensitivity, electronic-structure I/O, and bounded Materials Project queries.
K-Dense-AI / scientific-visualizationCreates and audits truthful, accessible, publication-ready scientific figures with Matplotlib, Seaborn, or Plotly. Use it for figure design, multi-panel layouts, uncertainty and missing-data displays, color/contrast review, image metadata validation, and journal export planning.
K-Dense-AI / scikit-bioBiological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
K-Dense-AI / statistical-powerCalculates sample sizes and statistical power for study planning. Applies when someone asks "how many subjects/samples/replicates do I need", wants an a priori power analysis, a minimum detectable effect (MDE), a power curve, or needs to justify a sample size for a grant, IRB protocol, or pre-regist…
K-Dense-AI / tiledbvcfStores and retrieves genomic variant calls with TileDB-VCF. Use for indexed single-sample VCF/BCF ingestion, incremental cohorts, region and sample queries, streaming results, allele statistics, QC, and VCF/BCF export locally or through TileDB Cloud.
K-Dense-AI / 13c-metabolic-fluxEstimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope simulation, constrained multistart fitting, and flux-profile diagnostics.
K-Dense-AI / arboretoInfers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3. Use for transcription factor-target association ranking, compatible Dask execution, sparse expression inputs, and network stability checks.
K-Dense-AI / genomic-coordinatesConverts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming mismatches before they corrupt an analysis.
K-Dense-AI / get-available-resourcesDetects host inventory and effective CPU, memory, disk, scheduler, container, and accelerator limits when a user asks for resource-aware planning or before a clearly resource-sensitive local workload.
K-Dense-AI / medchemApplies medicinal chemistry filters for compound triage, using drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and the medchem query language for library filtering.
K-Dense-AI / ontology-term-resolutionResolves free-text scientific labels to ontology term IDs and validates existing CURIEs against the EBI Ontology Lookup Service (OLS4). Also looks up prefixes in Bioregistry, resolves compact identifiers via Identifiers.org, maps lab shorthand with ZOOMA, and builds Ontobee term pages
K-Dense-AI / pymcBuilds and checks Bayesian models with PyMC, including hierarchical models, NUTS MCMC, variational inference, mutable-data predictions, posterior predictive checks, diagnostics, and PSIS-LOO model comparison. Use for probabilistic modeling and uncertainty inference in PyMC.
K-Dense-AI / openpivPerforms Particle Image Velocimetry (PIV) analysis with OpenPIV
K-Dense-AI / telluriumSimulates biochemical kinetic models from SBML or Antimony with Tellurium and libRoadRunner, checks model units, compares deterministic parameter perturbations, and exports and replays SBML plus SED-ML COMBINE archives.
K-Dense-AI / nmrglueProcesses calibrated one-dimensional complex NMR free-induction decays with nmrglue into phased spectra, peak candidates, and signed integration regions.
