K-Dense-AI/scientific-agent-skills▌

### Peer Review - name: "peer-review" - description: "Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compli..." - allowed-tools: "Read Write Edit Bash"

### Paper Lookup - name: "paper-lookup" - description: "Search 10 academic paper databases via REST APIs for research papers, preprints, and scholarly articles. Covers PubMed, PMC (full text), bioRxiv, medRxiv, arXiv, OpenAlex, Crossref, Semantic Scholar, ..."

### Scientific Brainstorming - name: "scientific-brainstorming" - description: "Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-st..."

### Infographics - name: "infographics" - description: "Create professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Integrates research-lookup and web search for accurate data. Supports 1..." - allowed-tools: "Read Write Edit Bash"

### Scientific Writing - name: "scientific-writing" - description: "Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research..." - allowed-tools: "Read Write Edit Bash"

### Optimize For Gpu - name: "optimize-for-gpu" - description: "GPU-accelerate Python code using CuPy, Numba CUDA, Warp, cuDF, cuML, cuGraph, KvikIO, cuCIM, cuxfilter, cuVS, cuSpatial, and RAFT. Use whenever the user mentions GPU/CUDA/NVIDIA acceleration, or wants..."

### Latex Posters - name: "latex-posters" - description: "Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design,..." - allowed-tools: "Read Write Edit Bash"

### Statistical Analysis - name: "statistical-analysis" - description: "Guided statistical analysis with test selection and reporting. Use when you need help choosing appropriate tests for your data, assumption checking, power analysis, and APA-formatted results. Best for..."

### Sympy - name: "sympy" - description: "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 approxi..." - allowed-tools: "Read Write Edit Bash"

### Pytorch Lightning - name: "pytorch-lightning" - description: "Deep learning framework (PyTorch Lightning / lightning package). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, T..." - allowed-tools: "Read Write Edit Bash"

### Transformers - name: "transformers" - description: "Hugging Face Transformers for loading Hub models, running pipeline inference, text generation, and Trainer fine-tuning on NLP, vision, audio, and multimodal tasks. Use when working with AutoModel, pip..."

### Xlsx - name: "xlsx" - description: "Create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm) where the workbook file is the primary deliverable. Use for formulas, formatting, financial models, multi-sheet workbooks, and tabul..." - allowed-tools: "Read Write Edit Bash Grep Glob"

### Zarr Python - name: "zarr-python" - description: "Chunked N-D arrays for cloud storage (Zarr-Python 3). Compressed arrays, parallel I/O, S3/GCS via fsspec, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines." - allowed-tools: "Read Write Edit Bash"

### Scvi Tools - name: "scvi-tools" - description: "Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI,..."

### What If Oracle - name: "what-if-oracle" - description: "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 ..."

### Usfiscaldata - name: "usfiscaldata" - description: "Query the U.S. Treasury Fiscal Data REST API for federal financial data. No API key required. Use for national debt (Debt to the Penny), Daily Treasury Statements, Monthly Treasury Statements, Treasur..." - allowed-tools: "Read Write Edit Bash"

### Vaex - name: "vaex" - description: "Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, ef..." - allowed-tools: "Read Write Edit Bash Grep Glob"

### Venue Templates - name: "venue-templates" - description: "Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML..." - allowed-tools: "Read Write Edit Bash"

### Umap Learn - name: "umap-learn" - description: "UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data."

### Simpy - name: "simpy" - description: "Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems,..."

### Scikit Bio - name: "scikit-bio" - description: "Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis." - allowed-tools: "Read Write Edit Bash"

### Treatment Plans - name: "treatment-plans" - description: "Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic d..." - allowed-tools: "Read Write Edit Bash"

### Statsmodels - name: "statsmodels" - description: "Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and inference. Best for econometrics, time series,..."

### Tiledbvcf - name: "tiledbvcf" - description: "Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel queries, and export capabilities for populat..."

### Scientific Critical Thinking - name: "scientific-critical-thinking" - description: "Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias)..." - allowed-tools: "Read Write Edit"

### Scientific Schematics - name: "scientific-schematics" - description: "Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.1 Pro Preview for quality review. Only regenerates if quality is below threshold fo..." - allowed-tools: "Read Write Edit Bash"

### Seaborn - name: "seaborn" - description: "Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaults. Best for box plots, violin plots, pa..."

### Scientific Slides - name: "scientific-slides" - description: "Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific..." - allowed-tools: "Read Write Edit Bash"

### Scientific Visualization - name: "scientific-visualization" - description: "Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journ..."

### Scikit Survival - name: "scikit-survival" - description: "Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival data, performing time-to-event analysis, fitt..."

### Timesfm Forecasting - name: "timesfm-forecasting" - description: "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/Dat..." - allowed-tools: "Read Write Edit Bash"

### Torchdrug - name: "torchdrug" - description: "PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model de..."

### Stable Baselines3 - name: "stable-baselines3" - description: "Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick prototyping, and well-documented algorithm impleme..." - allowed-tools: "Read Write Edit Bash"

### Scvelo - name: "scvelo" - description: "RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-..."

### Scikit Learn - name: "scikit-learn" - description: "Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hy..." - allowed-tools: "Read Write Edit Bash"

### Torch Geometric - name: "torch-geometric" - description: "PyTorch Geometric (PyG) for graph neural networks — node/link/graph classification, message passing (GCN, GAT, GraphSAGE, GIN), heterogeneous graphs, neighbor sampling, and custom datasets. Use when w..."

### Shap - name: "shap" - description: "Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP p..."

### Pdf - name: "pdf" - description: "Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multiple PDFs into one, splitting PDFs apart, rota..."

### Pymatgen - name: "pymatgen" - description: "Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science."

### Paperzilla - name: "paperzilla" - description: "Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask for recent project recommendations, canonical paper details, markdown-based summaries, reco..."

### Pymc - name: "pymc" - description: "Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference."

### Protocolsio Integration - name: "protocolsio-integration" - description: "Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and..."

### Phylogenetics - name: "phylogenetics" - description: "Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial g..."

### Pathway Enrichment - name: "pathway-enrichment" - description: "Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use whenever the user has a set of genes (differentially expressed genes from PyDESeq2/Scanp..."

### Pacsomatic - name: "pacsomatic" - description: "Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate pacsomatic-compliant samplesheets, prepare r..."

### Polars Bio - name: "polars-bio" - description: "High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF intervals. Streaming, cloud-n..." - allowed-tools: "Read Write Edit Bash"

### Polars - name: "polars" - description: "Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel execution, Apache Arrow backend. Best for 1-100GB da..."

### Opentrons Integration - name: "opentrons-integration" - description: "Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2 features. Best for production Opentrons pro..."

### Pathml - name: "pathml" - description: "Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model tra..."

### Scholar Evaluation - name: "scholar-evaluation" - description: "Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and wri..."

### Primekg - name: "primekg" - description: "Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more."

### Scanpy - name: "scanpy" - description: "Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA..."

### Qutip - name: "qutip" - description: "Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system d..."

### Qiskit - name: "qiskit" - description: "IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quan..."

### Rowan - name: "rowan" - description: "Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and tautomer ensembles, docking and analogue dock..."

### Research Grants - name: "research-grants" - description: "Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation na..." - allowed-tools: "Read Write Edit Bash"

### Pyzotero - name: "pyzotero" - description: "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..." - allowed-tools: "Read Write Edit Bash"

### Research Lookup - name: "research-lookup" - description: "Look up current research information using parallel-cli search (primary, fast web search), the Parallel Chat API (deep research), or Perplexity sonar-pro-search (academic paper searches). Automaticall..." - allowed-tools: "Read Write Edit Bash"

### Rdkit - name: "rdkit" - description: "Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard w..."

### Pysam - name: "pysam" - description: "Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines."

### Pyhealth - name: "pyhealth" - description: "Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining tasks (mortality, readmission..."

### Nextflow - name: "nextflow" - description: "Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextflow, nf-core, .nf files, nextflow.config, DSL2, processes/channels/operators, sample..."

### Pytdc - name: "pytdc" - description: "Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction."

### Pydicom - name: "pydicom" - description: "Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel ..."

### Pyopenms - name: "pyopenms" - description: "Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file fo..."

### Networkx - name: "networkx" - description: "Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, com..."

### Pptx Posters - name: "pptx-posters" - description: "Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. For standard research posters, use late..." - allowed-tools: "Read Write Edit Bash"

### Pylabrobot - name: "pylabrobot" - description: "Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best..."

### Molfeat - name: "molfeat" - description: "Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML." - allowed-tools: "Read Write Edit Bash"

### Open Notebook - name: "open-notebook" - description: "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,..."

### Neurokit2 - name: "neurokit2" - description: "Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activi..."

### Pymoo - name: "pymoo" - description: "Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems." - allowed-tools: "Read Write Edit Bash"

### Medchem - name: "medchem" - description: "Medicinal chemistry filters for compound triage. Apply drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and the medchem query language f..." - allowed-tools: "Read Write Edit Bash"

### Pptx - name: "pptx" - description: "Use this skill any time a .pptx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or presentations; reading, parsing, or extracting text from a..."

### Pufferlib - name: "pufferlib" - description: "High-performance reinforcement learning framework optimized for speed and scale. Use when you need fast parallel training, vectorized environments, multi-agent systems, or integration with game enviro..."

### Parallel Web - name: "parallel-web" - description: "All-in-one web toolkit powered by parallel-cli, with a strong emphasis on academic and scientific sources. Use this skill whenever the user needs to search the web, fetch/extract URL content, enrich d..."

### Modal - name: "modal" - description: "Modal is a serverless cloud platform for running Python on demand, including on-demand GPUs. Use when deploying or serving AI/ML models, running GPU-accelerated workloads (training, fine-tuning, infer..."

### Molecular Dynamics - name: "molecular-dynamics" - description: "Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (..."

### Pennylane - name: "pennylane" - description: "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 ..."

### Omero Integration - name: "omero-integration" - description: "Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows."

### Neuropixels Analysis - name: "neuropixels-analysis" - description: "Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuro..."

### Pydeseq2 - name: "pydeseq2" - description: "Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis."

### Lamindb - name: "lamindb" - description: "This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRN..."

### Deepchem - name: "deepchem" - description: "Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet be..." - allowed-tools: "Read Write Edit Bash"

### Flowio - name: "flowio" - description: "Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing."

### Clinical Decision Support - name: "clinical-decision-support" - description: "Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment ..." - allowed-tools: "Read Write Edit Bash"

### Cobrapy - name: "cobrapy" - description: "Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis." - allowed-tools: "Read Write Edit Bash"

### Get Available Resources - name: "get-available-resources" - description: "This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file wi..."

### Clinical Reports - name: "clinical-reports" - description: "Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP,..." - allowed-tools: "Read Write Edit Bash"

### Exploratory Data Analysis - name: "exploratory-data-analysis" - description: "Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, conten..."

### Matchms - name: "matchms" - description: "Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral..."

### Exa Search - name: "exa-search" - description: "Web toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search the web or fetch/extract URL content. Covers: web search (semantic lookups, researc..."

### Docx - name: "docx" - description: "Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', or requests to produce ..."

### Geopandas - name: "geopandas" - description: "Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate..."

### Matlab - name: "matlab" - description: "MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Use when writing MATLAB/Octave scripts for linear algebra, signal processing, i..."

### Datamol - name: "datamol" - description: "Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3..." - allowed-tools: "Read Write Edit Bash"

### Liteparse - name: "liteparse" - description: "Local document and PDF parsing with spatial text and bounding boxes. Use for extracting text from PDFs, DOCX, Office files, and images; OCR on scans; layout-preserved JSON for RAG; batch-ingesting pap..." - allowed-tools: "Read Write Edit Bash"

### Matplotlib - name: "matplotlib" - description: "Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export ..."

### Markitdown - name: "markitdown" - description: "Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more." - allowed-tools: "Read Write Edit Bash"

### Dnanexus Integration - name: "dnanexus-integration" - description: "DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution."

### Diffdock - name: "diffdock" - description: "Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction."

### Literature Review - name: "literature-review" - description: "Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature..." - allowed-tools: "Read Write Edit Bash"

### Market Research Reports - name: "market-research-reports" - description: "Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation with scien..." - allowed-tools: "Read Write Edit Bash"

### Markdown Mermaid Writing - name: "markdown-mermaid-writing" - description: "Comprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Establishes text-based diagrams as the default documentation st..." - allowed-tools: "Read Write Edit Bash"

### Labarchive Integration - name: "labarchive-integration" - description: "Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows."

### Dhdna Profiler - name: "dhdna-profiler" - description: "Extract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyze how someone thinks, understand cognitive style, profile writing or speech patterns, co..." - allowed-tools: "Read Write"

### Latchbio Integration - name: "latchbio-integration" - description: "Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration."

### Iso 13485 Certification - name: "iso-13485-certification" - description: "Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need help with ISO 13485 QMS documentation, including (1) conduc..."

### Histolab - name: "histolab" - description: "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 prepara..."

### Citation Management - name: "citation-management" - description: "Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. Thi..." - allowed-tools: "Read Write Edit Bash"

### Imaging Data Commons - name: "imaging-data-commons" - description: "Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. N..."

### Database Lookup - name: "database-lookup" - description: "Search 78 public scientific, biomedical, materials science, and economic databases via REST APIs. Covers physics/astronomy (NASA, NIST, SDSS, SIMBAD), earth/environment (USGS, NOAA, EPA), chemistry/dr..."

### Hypothesis Generation - name: "hypothesis-generation" - description: "Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design expe..." - allowed-tools: "Read Write Edit Bash"

### Deeptools - name: "deeptools" - description: "NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization."

### Cirq - name: "cirq" - description: "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 mode..." - allowed-tools: "Read Write Edit Bash"

### Esm - name: "esm" - description: "Comprehensive toolkit for EvolutionaryScale protein language models including ESM3 (generative multimodal design across sequence, structure, and function) and ESM C (efficient embeddings). Use for pro..."

### Hypogenic - name: "hypogenic" - description: "Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content ..."

### Hugging Science - name: "hugging-science" - description: "Use when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate, genomics, materials, medicine, ecology, energy, engineering, math, drug discovery,..."

### Ginkgo Cloud Lab - name: "ginkgo-cloud-lab" - description: "Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs). Use when the user wants to ru..."

### Dask - name: "dask" - description: "Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed..." - allowed-tools: "Read Write Edit Bash"

### Depmap - name: "depmap" - description: "Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilit..."

### Gget - name: "gget" - description: "Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. ..."

### Gtars - name: "gtars" - description: "High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, o..."

### Geomaster - name: "geomaster" - description: "Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satellite imagery processing (Sentin..."

### Glycoengineering - name: "glycoengineering" - description: "Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering tools (NetOGlyc, GlycoShield, Gl..."

### Geniml - name: "geniml" - description: "This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEm..."

### Generate Image - name: "generate-image" - description: "Generate or edit images using AI models (FLUX, Nano Banana 2). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that is not ..."

### Etetoolkit - name: "etetoolkit" - description: "Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics."

### Consciousness Council - name: "consciousness-council" - description: "Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use this skill whenever the user wants diverse viewpoints, needs help making a tough decision, asks ..." - allowed-tools: "Read Write"

### Fluidsim - name: "fluidsim" - description: "Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, o..."

### Biopython - name: "biopython" - description: "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, cu..."

### Cellxgene Census - name: "cellxgene-census" - description: "Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scal..."

### Bioservices - name: "bioservices" - description: "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 analys..." - allowed-tools: "Read Write Edit Bash"

### Aeon - name: "aeon" - description: "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..." - allowed-tools: "Read Write Edit Bash"

### Astropy - name: "astropy" - description: "Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology. Use when implementing ..."

### Bulk Rnaseq - name: "bulk-rnaseq" - description: "End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level cou..."

### Bgpt Paper Search - name: "bgpt-paper-search" - description: "Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, qual..."

### Benchling Integration - name: "benchling-integration" - description: "Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when automating lab data with benchling-sdk or t..." - allowed-tools: "Read Write Edit Bash"

### Adaptyv - name: "adaptyv" - description: "How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding ..."

### Autoskill - name: "autoskill" - description: "Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition recipes that chain existing ones..." - allowed-tools: "Read Write Edit Bash"

### Arboreto - name: "arboreto" - description: "Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify t..."

### Bids - name: "bids" - description: "Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectros..."

### Anndata - name: "anndata" - description: "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 sca..."