Research & Knowledge
Research, retrieval, summarization, and knowledge work
Skills List
histolab
Lightweight WSI tile extraction and preprocessing. Use for basic slide processing, tissue detection, tile extraction, and stain normalization for H&E images. Best for simple pipelines, dataset preparation, and quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.
k-dense-aiprotocolsio-integration
Read, validate, and safely export protocols.io data with current official REST/MCP contracts, or create non-executing mutation plans. The bundled client makes bounded official-host GET requests only with explicit --execute. Use only for tasks explicitly targeting protocols.io or an exact protocols.io protocol version.
k-dense-aipennylane
Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms (VQE, QAOA), quantum neural networks, and integration with PyTorch or JAX. For hardware-specific optimizations use qiskit (IBM) or cirq (Google); for open quantum systems use qutip.
k-dense-ailabarchive-integration
Securely integrate with the official LabArchives ELN REST-like API and Inventory API v1. Use for regional endpoint selection, signed-request construction, user authorization and UID flows, local LA container validation, and verified LabArchives integration workflows.
k-dense-aietetoolkit
Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4. Use for Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploration, and publication rendering. Do not use it to infer trees from raw sequences; align sequences and infer a tree first.
k-dense-aicirq
Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.
k-dense-aiumap-learn
Use UMAP-learn for nonlinear dimensionality reduction, 2D/3D embeddings, clustering preprocessing, supervised or semi-supervised UMAP, DensMAP, AlignedUMAP, and Parametric UMAP workflows.
k-dense-aivenue-templates
Prepare journal manuscripts, conference papers, research posters, and grant documents using venue-specific formatting guidance and bundled LaTeX scaffolds. Use when selecting an official template, checking current page or anonymity rules, adapting academic writing to a venue, or inspecting a submission PDF.
k-dense-aibiopython
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
k-dense-aiscikit-bio
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
k-dense-aitimesfm-forecasting
Zero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, sensors, energy, vitals, weather) without training a custom model. Supports CSV/DataFrame/array inputs with point forecasts and prediction intervals. Includes a preflight system checker script to verify RAM/GPU before first use.
k-dense-aiwhat-if-oracle
Run structured What-If scenario analysis with 4–6 branch possibility exploration (best, likely, worst, wild card, contrarian, second-order). Use when the user asks speculative what-if questions about uncertain futures, strategic forks, contingency planning, or stress-testing a decision before committing.
k-dense-aisimpy
Build, inspect, test, and analyze bounded process-based discrete-event simulations with SimPy, including events, resources, interrupts, monitoring, replications, warm-up, and reproducible output analysis.
k-dense-aigeomaster
Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), vector and raster data operations, spatial statistics, point cloud processing, network analysis, cloud-native workflows (STAC, COG, Planetary Computer), and 8 programming languages (Python, R, Julia, JavaScript, C++, Java, Go, Rust) with 500+ code examples. Use for remote sensing workflows, GIS analysis, spatial ML, Earth observation data processing, terrain analysis, hydrological modeling, marine spatial analysis, atmospheric science, and any geospatial computation task.
k-dense-aianndata
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
k-dense-aibioservices
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.
k-dense-aiclinical-reports
Create safety-bounded draft structures and run local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research reports. Use only with synthetic, de-identified, or aggregate inputs and verified source-fact manifests; every output requires qualified review.
k-dense-aigget
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.
k-dense-aipyzotero
Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use this skill when working with Zotero libraries programmatically, managing bibliographic references, exporting citations, searching library contents, uploading PDF attachments, or building research automation workflows that integrate with Zotero.
k-dense-aiaeon
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.
k-dense-aisympy
Use when you need exact symbolic math in Python — algebra, calculus, equation solving, symbolic linear algebra, or code generation via lambdify/LaTeX. Prefer NumPy or SciPy when floating-point approximations are sufficient.
k-dense-aimarket-research-reports
Build evidence-traceable market research reports and assumption-driven market sizing or forecast scenarios. Use for market definition, industry and customer evidence, competitive landscapes, TAM/SAM/SOM reconciliation, forecast sensitivity, and auditable report scaffolds.
k-dense-aiinfographics
Create professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3.6 Flash for quality review. Integrates research-lookup and web search for accurate data. Supports 10 infographic types, 8 industry styles, and colorblind-safe palettes.
k-dense-aiopen-notebook
Self-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use when organizing research materials into notebooks, ingesting diverse content sources (PDFs, videos, audio, web pages, Office documents), generating AI-powered notes and summaries, creating multi-speaker podcasts from research, chatting with documents using context-aware AI, searching across materials with full-text and vector search, or running custom content transformations. Supports 16+ AI providers including OpenAI, Anthropic, Google, Ollama, Groq, and Mistral with complete data privacy through self-hosting.
k-dense-ai