Skill directory · Science

Science and Research agent skills

Skills for scientific and academic work: bioinformatics, chemistry, materials, literature search and research statistics. They give an agent the domain procedures and library knowledge a lab or research team would otherwise explain in every prompt.

210 listed skills
8 repositories
26 with full pages

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All 210 science and research skills

Skill	Repository	What it does
academic-plotting 77/100 · C	Orchestra-Research/AI-Research-SKILLs	Generates publication-quality figures for ML papers, including architecture diagrams via Gemini and data-driven charts via matplotlib or seaborn, from research context.
analytical-method-validation 88/100 · B	K-Dense-AI/claude-scientific-skills	Plans, executes, and documents validation, verification, and transfer of analytical procedures under frameworks such as ICH Q2(R2), USP, and ISO/IEC 17025.
citation-management 89/100 · B	K-Dense-AI/claude-scientific-skills	Manages academic citations by searching OpenAlex, PubMed, and Google Scholar, extracting metadata, validating references, and generating formatted BibTeX entries.
convergence-study 84/100 · B	HeshamFS/materials-simulation-skills	Performs spatial and temporal convergence analysis for numerical solutions, computing observed convergence orders, Richardson extrapolation, and Grid Convergence Index per ASME V&V 20.
differentiation-schemes 82/100 · B	HeshamFS/materials-simulation-skills	Selects and applies numerical differentiation schemes for PDE and ODE discretization, including finite-difference stencils, central, upwind, compact and spectral methods.
firecrawl-research-index 76/100 · C	firecrawl/skills	Finds papers that answer a research query in Firecrawl's paper index, covering biomedical and life-science literature plus arXiv preprints, using semantic search and verification.
firecrawl-research-papers 75/100 · C	firecrawl/skills	Finds and synthesizes research papers using semantic search and related-paper expansion over Firecrawl's index of largely biomedical and life-science literature plus arXiv preprints.
hpc-runtime-doctor 85/100 · B	HeshamFS/materials-simulation-skills	Diagnoses HPC runtime and scheduler problems for already-submitted materials simulation jobs that failed, ran slowly, were killed, or behaved differently on a cluster.
lab-hardware-cad 86/100 · B	K-Dense-AI/claude-scientific-skills	Designs custom laboratory hardware as parametric build123d models and exports STEP, STL, and DXF files for fabrication.
linear-solvers 82/100 · B	HeshamFS/materials-simulation-skills	Selects and configures linear solvers for Ax=b systems, covering direct and iterative methods, preconditioners, sparsity and conditioning analysis, and diagnosing convergence stagnation.
literature-review 89/100 · B	K-Dense-AI/claude-scientific-skills	Conducts systematic, scoping, and narrative literature reviews using sources such as PubMed, arXiv, and bioRxiv, tracking search coverage and evidence limitations.
mesh-generation 82/100 · B	HeshamFS/materials-simulation-skills	Plans and evaluates mesh generation for numerical simulations, covering grid resolution, mesh quality checks, and structured, unstructured, or adaptive refinement choices.
neuropixels-analysis 87/100 · B	K-Dense-AI/claude-scientific-skills	Analyzes Neuropixels extracellular recordings with SpikeInterface, covering data loading, preprocessing, drift correction, Kilosort4 spike sorting, quality metrics, and unit curation.
nonlinear-solvers 82/100 · B	HeshamFS/materials-simulation-skills	Selects and configures nonlinear solvers for root-finding, optimization, and least-squares problems, including Newton variants, quasi-Newton methods, globalization, and convergence rate diagnosis.
numerical-integration 82/100 · B	HeshamFS/materials-simulation-skills	Selects and configures time integration methods for ODE and PDE simulations, including error tolerances, adaptive step-size control, and IMEX operator splitting.
numerical-stability 84/100 · B	HeshamFS/materials-simulation-skills	Analyzes numerical stability for time-dependent PDE simulations, covering CFL and Fourier criteria, von Neumann analysis, stiffness detection, and explicit versus implicit time-stepping recommendations.
onekgpd 87/100 · B	K-Dense-AI/claude-scientific-skills	Queries the 1000 Genomes Project dataset to find which individuals carry specific variants, return variants with allele frequencies, and check relatedness between individuals.
ontology-explorer 82/100 · B	HeshamFS/materials-simulation-skills	Parses, navigates, and queries materials science ontology structures, including class hierarchies, property definitions, term search, and OWL/XML summaries, currently for CMSO and ASMO.
ontology-mapper 82/100 · B	HeshamFS/materials-simulation-skills	Maps materials science terms, crystal structures, and sample descriptions to standardized ontology classes and properties, producing ontology-compliant annotations and sample metadata.
ontology-validator 82/100 · B	HeshamFS/materials-simulation-skills	Validates material sample annotations against ontology constraints, checking that terms exist, relationships are consistent, and required properties are present.
parameter-optimization 82/100 · B	HeshamFS/materials-simulation-skills	Explores and optimizes simulation parameters using design of experiments, sensitivity analysis, optimizer selection, and surrogate models, including parameter sweep planning.
pkpd-modeling 88/100 · B	K-Dense-AI/claude-scientific-skills	Supports pharmacokinetic and pharmacodynamic modelling and simulation, including non-compartmental analysis, population PK, exposure-response, bioequivalence, and dosing regimen evaluation from concentration-time data.
primer-design 87/100 · B	K-Dense-AI/claude-scientific-skills	Designs and audits PCR and RT-qPCR primers with Primer3, including off-target amplification searches, existing primer checks, and in-silico PCR and BLAST screening.
relsa-severity-assessment 88/100 · B	K-Dense-AI/claude-scientific-skills	Combines welfare readouts from laboratory animal studies into a daily severity score per animal and forecasts which animals may reach a humane endpoint.
systems-paper-writing 77/100 · C	Orchestra-Research/AI-Research-SKILLs	Guides writing systems papers for OSDI, SOSP, ASPLOS, NSDI, and EuroSys with structural blueprints, writing patterns, venue checklists, reviewer guidelines, LaTeX templates, and deadlines.
treatment-plans 91/100 · A	K-Dense-AI/claude-scientific-skills	Formats and structurally validates treatment-plan documentation after licensed professionals have supplied and verified clinical decisions, without making clinical decisions itself.
13c-metabolic-flux 87/100 · B	K-Dense-AI/claude-scientific-skills	Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope…
adaptyv 77/100 · C	K-Dense-AI/claude-scientific-skills	Uses the Adaptyv Bio Foundry API and Python SDK to design protein characterization experiments, estimate costs, submit sequences, monitor laboratory…
aeon 87/100 · B	K-Dense-AI/claude-scientific-skills	This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection…
alphagenome 87/100 · B	K-Dense-AI/claude-scientific-skills	Looks up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus…
anndata 79/100 · C	K-Dense-AI/claude-scientific-skills	Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem. This is the data format…
ara-compiler 69/100 · D	Orchestra-Research/AI-Research-SKILLs	Compiles any research input — PDF papers, GitHub repositories, experiment logs, code directories, or raw notes — into a complete Agent-Native…
arbor 81/100 · B	K-Dense-AI/claude-scientific-skills	Applies Arbor Hypothesis Tree Refinement to research artifacts with repeatable evaluators, including model training, agent harnesses, data synthesis…
arboreto 87/100 · B	K-Dense-AI/claude-scientific-skills	Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3. Use for…
astropy 85/100 · B	K-Dense-AI/claude-scientific-skills	Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time…
autoresearch 66/100 · D	Orchestra-Research/AI-Research-SKILLs	Orchestrates end-to-end autonomous AI research projects using a two-loop architecture. The inner loop runs rapid experiment iterations with clear…
benchling-integration 87/100 · B	K-Dense-AI/claude-scientific-skills	Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries…
benchmark-and-mms-planner 81/100 · B	HeshamFS/materials-simulation-skills	Plan verification and validation campaigns for simulation codes using manufactured solutions, canonical benchmark problems, grid/time refinement…
bgpt-paper-search 82/100 · B	K-Dense-AI/claude-scientific-skills	Searches BGPT scientific papers by topic or DOI and retrieves claim-level evidence extracted from full text, including experiments, reported…
bids 79/100 · C	K-Dense-AI/claude-scientific-skills	Organizes, queries, validates, and converts Brain Imaging Data Structure (BIDS) datasets. Supports organizing neuroscience and biomedical data (MRI…
biopython 79/100 · C	K-Dense-AI/claude-scientific-skills	Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access…
bioservices 81/100 · B	K-Dense-AI/claude-scientific-skills	Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem. Used for cross-database…
brainstorming-research-ideas 74/100 · C	Orchestra-Research/AI-Research-SKILLs	Guides researchers through structured ideation frameworks to discover high-impact research directions. Use when exploring new problem spaces…
bulk-rnaseq 87/100 · B	K-Dense-AI/claude-scientific-skills	Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. Covers nf-core/rnaseq and standalone…
cantera 87/100 · B	K-Dense-AI/claude-scientific-skills	Runs Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks, and numerical refinement…
cellprofiler 79/100 · C	K-Dense-AI/claude-scientific-skills	Runs reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements. Supports…
cellxgene-census 87/100 · B	K-Dense-AI/claude-scientific-skills	Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need…
cirq 87/100 · B	K-Dense-AI/claude-scientific-skills	Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum…
clinical-decision-support 79/100 · C	K-Dense-AI/claude-scientific-skills	Prepares and validates research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and…
clinical-reports 79/100 · C	K-Dense-AI/claude-scientific-skills	Creates safety-bounded draft structures and runs local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research…
cobrapy 79/100 · C	K-Dense-AI/claude-scientific-skills	Performs constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling, growth media, production…
creative-thinking-for-research 71/100 · C	Orchestra-Research/AI-Research-SKILLs	Applies cognitive science frameworks for creative thinking to CS and AI research ideation. Use when seeking genuinely novel research directions by…
cudaq-guide 79/100 · C	NVIDIA/skills	Use for CUDA-Q setup, simulation targets, QPU access, and @cudaq.kernel authoring guidance.
cudaq-importing 81/100 · B	NVIDIA/skills	Use when porting circuits from another framework (e.g. Qiskit) into CUDA-Q kernels while preserving the source algorithm and validation fidelity.
cuopt-multi-objective-exploration 70/100 · C	NVIDIA/skills	Trace, complete, and interpret the Pareto frontier across competing objectives using repeated single-objective cuOpt solves (weighted-sum and…
cuopt-numerical-optimization-formulation 68/100 · D	NVIDIA/skills	LP, MILP, QP — concepts, problem-text parsing, and formulation patterns (parameters, constraints, decisions, objective). Concepts only; no API.
datalad 85/100 · B	K-Dense-AI/claude-scientific-skills	Retrieves, versions, and publishes scientific datasets with DataLad and git-annex, and captures computational provenance with datalad run, rerun…
datamol 79/100 · C	K-Dense-AI/claude-scientific-skills	Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing…
deepchem 81/100 · B	K-Dense-AI/claude-scientific-skills	Builds molecular property prediction and MoleculeNet workflows with DeepChem, including SMILES featurization, scaffold or grouped holdouts, masked…
deepspot-m 79/100 · C	K-Dense-AI/claude-scientific-skills	Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Used for predicted log1p-CPM expression from…
deeptools 81/100 · B	K-Dense-AI/claude-scientific-skills	NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq…
depmap 79/100 · C	K-Dense-AI/claude-scientific-skills	Retrieves and analyzes Cancer Dependency Map (DepMap) release data, including CRISPR Chronos gene effects, cancer model annotations, omics…
dicom-metadata-extract 73/100 · C	NVIDIA/skills	Used for extracting selected metadata from one DICOM file and flagging standard-tag PHI presence. Not for anonymization or clinical use.
dicom-series-preflight 73/100 · C	NVIDIA/skills	Used for header-only preflight of one DICOM series folder before conversion or inference. Not for de-identification or clinical clearance.
dicom-series-to-volume 73/100 · C	NVIDIA/skills	Used for converting one CT DICOM series folder to a HU NIfTI volume with affine evidence. Not for multi-frame DICOM or clinical use.
diffdock 89/100 · B	K-Dense-AI/claude-scientific-skills	Predicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or sequence plus SMILES/SDF/MOL2. Covers batch docking, pose…
diffdock-nim 74/100 · C	NVIDIA/skills	Run DiffDock molecular docking via NVIDIA NIM to predict small-molecule binding poses against protein targets. Use for DiffDock, molecular docking…
dnanexus-integration 79/100 · C	K-Dense-AI/claude-scientific-skills	Builds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow…
drug-discovery-pipeline 68/100 · D	NVIDIA/skills	NOTE: molecule and target inputs and your NGC_API_KEY are transmitted to external NVIDIA-hosted API endpoints on every call. Use local NIM…
earth2studio-create-datasource 85/100 · B	NVIDIA/skills	Create and validate Earth2Studio data source wrappers (DataSource, ForecastSource, DataFrameSource, ForecastFrameSource) from remote stores. Do NOT…
earth2studio-create-diagnostic 85/100 · B	NVIDIA/skills	Create Earth2Studio diagnostic model wrappers for single-step data transformations, including simple derived diagnostics, packaged AutoModel…
earth2studio-create-prognostic 83/100 · B	NVIDIA/skills	Create Earth2Studio prognostic (time-stepping forecast) model wrappers. Do NOT use for diagnostic models, data sources, or installation.
earth2studio-data-fetch 82/100 · B	NVIDIA/skills	Fetch weather/climate data via Earth2Studio data sources for specific variables and times. Do NOT use for inference pipelines, model discovery, or…
earth2studio-deterministic-forecast 85/100 · B	NVIDIA/skills	Build deterministic forecast scripts with Earth2Studio (model, data source, IO, inference). Do NOT use for ensemble, diagnostics, data-only fetch…
earth2studio-discover 82/100 · B	NVIDIA/skills	Find Earth2Studio models, data sources, and examples for a weather/climate use case. Do NOT use for writing inference code, downloading data, or…
earth2studio-install 82/100 · B	NVIDIA/skills	Guide installing Earth2Studio via uv or pip, selecting model extras, and configuring the environment. Do NOT use for writing inference code…
esm 79/100 · C	K-Dense-AI/claude-scientific-skills	Uses the Biohub esm Python SDK for ESM3 protein generation, ESMC embeddings, and ESMFold2 all-atom folding. Applies to local model inference and…
etetoolkit 81/100 · B	K-Dense-AI/claude-scientific-skills	Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. Supports Newick/Nexus tree I/O…
evo2-nim 79/100 · C	NVIDIA/skills	Generate and analyze DNA sequences using NVIDIA's Evo 2 BioNeMo NIM microservice. Use for Evo2/Evo 2, DNA generation, genomic sequence generation…
exa-search 79/100 · C	K-Dense-AI/claude-scientific-skills	Searches scientific and technical web content with Exa and extracts page or PDF text from URLs in batches. Supports scholarly discovery with the…
experimental-design 88/100 · B	K-Dense-AI/claude-scientific-skills	Designs experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so…
exploratory-data-analysis 81/100 · B	K-Dense-AI/claude-scientific-skills	Performs bounded, local exploratory analysis of explicitly supported scientific files. Supports redacted CSV/TSV/JSON profiles; optional NumPy…
fair-simulation-packager 73/100 · C	HeshamFS/materials-simulation-skills	Create FAIR-minded reproducibility bundles for materials simulations by collecting input/output file inventories, hashes, units, engine versions…
flowio 89/100 · B	K-Dense-AI/claude-scientific-skills	Reads, inspects, and writes Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for low-level FCS metadata and channel…
flowkit 87/100 · B	K-Dense-AI/claude-scientific-skills	Analyzes flow cytometry data with FlowKit, including spillover compensation, logicle and biexponential transforms, hierarchical gating, GatingML…
fluidsim 89/100 · B	K-Dense-AI/claude-scientific-skills	Plans, configures, inspects, restarts, and analyzes bounded FluidSim computational-fluid-dynamics simulations with explicit numerical-validity and…
folklore-variant-evidence 77/100 · C	K-Dense-AI/claude-scientific-skills	Retrieves ClinGen gene-disease validity assertions for a public gene or disease, and reviews source-linked public evidence and literature for one…
geniml 81/100 · B	K-Dense-AI/claude-scientific-skills	Supports audited local Geniml genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEmbed runs, inspect…
genmol-nim 77/100 · C	NVIDIA/skills	Generate novel drug-like molecules using the GenMol NIM microservice. Use for de novo generation, scaffold decoration, motif extension, lead…
genomic-coordinates 80/100 · B	K-Dense-AI/claude-scientific-skills	Converts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming…
genomic-intelligence 80/100 · B	K-Dense-AI/claude-scientific-skills	Predicts regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA language…
genomics-workflow-acceleration 77/100 · C	NVIDIA/skills	Use when accelerating existing genomics workflows with NVIDIA Parabricks, improving runtime or price/performance, converting pipeline steps to GPUs…
geomaster 87/100 · B	K-Dense-AI/claude-scientific-skills	Supports geospatial research workflows for remote sensing, vector and raster GIS, spatial statistics, terrain and network analysis, and machine…
gget 81/100 · B	K-Dense-AI/claude-scientific-skills	Queries 20+ bioinformatics resources through CLI/Python. Supports quick lookups of gene info, BLAST/BLAT, viral sequence downloads, PDB/mmCIF…
ginkgo-cloud-lab 77/100 · C	K-Dense-AI/claude-scientific-skills	Guides protocol selection, input preparation, pricing checks, and browser ordering on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio). Applies to…
glycoengineering 87/100 · B	K-Dense-AI/claude-scientific-skills	Analyzes and engineers protein glycosylation by scanning canonical N-glycosylation sequons, describing S/T-rich regions, checking curated glycan…
gtars 81/100 · B	K-Dense-AI/claude-scientific-skills	Supports Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing…
histolab 85/100 · B	K-Dense-AI/claude-scientific-skills	Extracts and preprocesses whole-slide histology image tiles with Histolab. Use for WSI inspection, tissue masks, random/grid/score-based tile…
hugging-science 79/100 · C	K-Dense-AI/claude-scientific-skills	Discovers and evaluates scientific datasets, models, methodology posts, and Spaces through the Hugging Science catalog. Used when selecting…
huggingface-papers 80/100 · B	huggingface/skills	Look up and read Hugging Face paper pages in markdown, and use the papers API for structured metadata such as authors, linked…

Show the other 110 science and research skills

Skill	Repository	What it does
hyperlocal-weather-precip 69/100 · D	gooseworks-ai/goose-skills	Hyperlocal weather data - precipitation, temperature, wind, soil moisture and more
hypogenic 93/100 · A	K-Dense-AI/claude-scientific-skills	Plans and audits use of ChicagoHAI HypoGeniC/HypoRefine for LLM-assisted hypothesis generation from labeled text datasets. Use for the `hypogenic`…
hypothesis-generation 79/100 · C	K-Dense-AI/claude-scientific-skills	Formulates evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational claims, discriminating…
imaging-data-commons 76/100 · C	K-Dense-AI/claude-scientific-skills	Queries and downloads public cancer imaging data from NCI Imaging Data Commons. Supports IDC collection discovery, DICOM access, radiology (CT, MR…
labarchive-integration 79/100 · C	K-Dense-AI/claude-scientific-skills	Integrates with the official LabArchives ELN REST-like API and Inventory API v1. Supports regional endpoint selection, signed-request construction…
lamindb 85/100 · B	K-Dense-AI/claude-scientific-skills	Manages biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema validation, Bionty ontology…
latchbio-integration 89/100 · B	K-Dense-AI/claude-scientific-skills	Builds, registers, debugs, and operates bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake…
latex-posters 89/100 · B	K-Dense-AI/claude-scientific-skills	Creates research posters in LaTeX using beamerposter, tikzposter, or baposter. Use for conference posters, academic presentations, multi-column…
mageck 87/100 · B	K-Dense-AI/claude-scientific-skills	Analyzes pooled CRISPR screen FASTQ reads and guide-count matrices with MAGeCK, validates guide libraries and contrasts, measures replicate and…
marine-carbonate-chemistry 87/100 · B	K-Dense-AI/claude-scientific-skills	Solves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research. Use for paired…
matchms 93/100 · A	K-Dense-AI/claude-scientific-skills	Processes, cleans, compares, and searches tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral…
md-analysis-planner 73/100 · C	HeshamFS/materials-simulation-skills	Plan molecular dynamics post-processing for materials simulations, including RDF, MSD and diffusion, VACF/VDOS, coordination numbers, bond-angle…
medchem 81/100 · B	K-Dense-AI/claude-scientific-skills	Applies medicinal chemistry filters for compound triage, using drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR…
ml-paper-writing 67/100 · D	Orchestra-Research/AI-Research-SKILLs	Write publication-ready ML/AI papers for NeurIPS, ICML, ICLR, ACL, AAAI, COLM. Use when drafting papers from research repos, structuring arguments…
molecular-dynamics 77/100 · C	K-Dense-AI/claude-scientific-skills	Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs…
molfeat 79/100 · C	K-Dense-AI/claude-scientific-skills	Featurizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML. Covers ECFP/MACCS fingerprints…
molmim-nim 77/100 · C	NVIDIA/skills	Use this skill for MolMIM, NVIDIA's BioNeMo NIM microservice for small-molecule latent-space generation and optimization. Invoke for MolMIM…
msa-search-nim 79/100 · C	NVIDIA/skills	Generate multiple sequence alignments (MSAs) for protein sequences using the ColabFold MSA-Search NIM. Use for homolog search, UniRef30/ColabFold…
msa-structure-prediction-pipeline 68/100 · D	NVIDIA/skills	NOTE: your protein sequence and the retrieved MSA alignment are transmitted to external NVIDIA-hosted APIs (health.api.nvidia.com) on every call…
ncats-arax 93/100 · A	K-Dense-AI/claude-scientific-skills	Queries the NCATS Translator ARAX production API for bounded, typed, provenance-rich one-hop and endpoint-pinned two-hop biomedical knowledge-graph…
neurokit2 93/100 · A	K-Dense-AI/claude-scientific-skills	Builds and audits reproducible NeuroKit2 research workflows for physiological time-series preprocessing, event/interval analysis, multimodal…
nextflow 85/100 · B	K-Dense-AI/claude-scientific-skills	Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows. Use for Nextflow, nf-core, .nf files, nextflow.config…
nmrglue 87/100 · B	K-Dense-AI/claude-scientific-skills	Processes calibrated one-dimensional complex NMR free-induction decays with nmrglue into phased spectra, peak candidates, and signed integration…
nv-generate-ct-rflow 87/100 · B	NVIDIA/skills	Used for generating synthetic CT volumes and masks with NV-Generate-CTMR rflow-ct. Not for production training data without review.
nv-generate-mr 87/100 · B	NVIDIA/skills	Used for generating synthetic body MRI volumes with NV-Generate-CTMR rflow-mr. Not for paired masks or production training data.
nv-generate-mr-brain 87/100 · B	NVIDIA/skills	Used for generating synthetic T1, T2, FLAIR, SWI, or MRA brain MRI volumes with NV-Generate-CTMR MR-Brain v1. Not for production training data.
nv-generate-mr-brain-finetune 78/100 · C	NVIDIA/skills	Used for finetuning NV-Generate-CTMR MR-Brain v1 for T1, T2, FLAIR, SWI, or MRA data from a NIfTI datalist. Not for clinical or production data…
nv-generate-vae-finetune 76/100 · C	NVIDIA/skills	Used for finetuning the NV-Generate-CTMR MAISI VAE from CT/MRI NIfTI datalists. Not for clinical or production data approval.
nv-reason-ct 78/100 · C	NVIDIA/skills	Run NV-Reason-CT inference on user-provided 3D NIfTI chest or abdominal CT volumes for engineering and research workflows. Not for diagnosis…
nv-reason-cxr 76/100 · C	NVIDIA/skills	Used for command-shape or live NV-Reason-CXR chest X-ray reasoning smoke tests. Not for diagnosis or clinical reporting.
nv-segment-ct 70/100 · C	NVIDIA/skills	Used for running NV-Segment-CT VISTA3D on CT NIfTI volumes and recording label-map evidence.
nv-segment-ct-finetune 81/100 · B	NVIDIA/skills	Runs standard or fixed-channel softmax finetuning of NV-Segment-CT VISTA3D on CT NIfTI image/label datasets, with optional MONAI-native MLflow…
nv-segment-ctmr 76/100 · C	NVIDIA/skills	Used for running NV-Segment-CTMR on CT or MRI NIfTI volumes and recording label-map evidence. Not for clinical interpretation.
nvmolkit-usage 73/100 · C	NVIDIA/skills	Use when writing or debugging nvMolKit Python code for GPU-accelerated RDKit fingerprints, similarity, conformers, clustering, and molecular searches.
nwb-conversion 87/100 · B	K-Dense-AI/claude-scientific-skills	Converts neuroscience acquisition data to Neurodata Without Borders files with NeuroConv and PyNWB, preserves metadata and timebases, checks…
omero-integration 87/100 · B	K-Dense-AI/claude-scientific-skills	Inspects and automates microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering…
ontology-term-resolution 88/100 · B	K-Dense-AI/claude-scientific-skills	Resolves free-text scientific labels to ontology term IDs and validates existing CURIEs against the EBI Ontology Lookup Service (OLS4). Also looks…
openfold2-nim 77/100 · C	NVIDIA/skills	Use this skill for OpenFold2, NVIDIA's BioNeMo NIM microservice for monomer protein structure prediction. Invoke whenever the user mentions…
openfold3-nim 77/100 · C	NVIDIA/skills	Use this skill for OpenFold3, NVIDIA's BioNeMo NIM microservice for biomolecular structure prediction. Invoke whenever the user mentions OpenFold3…
openpiv 89/100 · B	K-Dense-AI/claude-scientific-skills	Performs Particle Image Velocimetry (PIV) analysis with OpenPIV. Use when extracting velocity fields from PIV image pairs, analyzing fluid dynamics…
opentrons-integration 93/100 · A	K-Dense-AI/claude-scientific-skills	Authors, reviews, migrates, simulates, and troubleshoots official Opentrons Python Protocol API v2 protocols for Flex and OT-2 robots. Use for…
pacsomatic 87/100 · B	K-Dense-AI/claude-scientific-skills	Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs. Supports samplesheet…
paper-lookup 87/100 · B	K-Dense-AI/claude-scientific-skills	Searches 18 scholarly APIs for papers, preprints, citations, open-access full text, repository records, and journal OA status, and returns results…
paperclip 87/100 · B	K-Dense-AI/claude-scientific-skills	Searches and reads biomedical papers, FDA/PMDA/EMA documents, clinical trials, and protein records with the GXL Paperclip CLI and Python SDK…
paperzilla 77/100 · C	K-Dense-AI/claude-scientific-skills	Reads projects, searches project feeds, and retrieves recommendations and canonical papers in Paperzilla through the pz CLI. Supports recent…
parabricks 75/100 · C	NVIDIA/skills	Plan NVIDIA Parabricks pbrun commands, translate CPU options and check runtime readiness. Use for individual tools, including planning-only questions.
pathml 89/100 · B	K-Dense-AI/claude-scientific-skills	Supports local computational pathology research with PathML: slide loading and tiling, preprocessing and QC, h5path storage, multiplex…
pathogen-variant-surveillance 89/100 · B	K-Dense-AI/claude-scientific-skills	Queries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence proportions, reporting…
pathway-enrichment 86/100 · B	K-Dense-AI/claude-scientific-skills	Performs 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…
peer-review 79/100 · C	K-Dense-AI/claude-scientific-skills	Prepares evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Supports authorized review of scientific…
pennylane 87/100 · B	K-Dense-AI/claude-scientific-skills	Builds and differentiates PennyLane quantum circuits, hybrid PyTorch or JAX models, molecular VQE and QAOA workflows. Use for variational quantum…
performance-profiling 82/100 · B	HeshamFS/materials-simulation-skills	Identify computational bottlenecks, analyze parallel scaling, estimate memory requirements, and generate optimization recommendations for materials…
phylogenetics 79/100 · C	K-Dense-AI/claude-scientific-skills	Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and…
physicsnemo-discover 85/100 · B	NVIDIA/skills	Official NVIDIA-authored guidance for navigating PhysicsNeMo — pick the model, datapipe, or example for a SciML/AI4Science task (surrogates…
polars-bio 87/100 · B	K-Dense-AI/claude-scientific-skills	Performs genomic interval overlap, nearest, merge, coverage, complement and subtraction on Polars DataFrames, and reads or writes BED, VCF, BCF…
post-processing 82/100 · B	HeshamFS/materials-simulation-skills	Extract, analyze, and summarize simulation output data — pull spatial fields at specific timesteps, compute time-series trends and detect steady…
primekg 87/100 · B	K-Dense-AI/claude-scientific-skills	Queries a pinned Precision Medicine Knowledge Graph (PrimeKG) CSV for typed gene, drug, disease, and phenotype nodes, direct associations, disease…
proteinmpnn-nim 79/100 · C	NVIDIA/skills	Run ProteinMPNN inverse folding via NVIDIA NIM to design protein sequences for a target backbone. Sends user-provided PDB files and design…
protocolsio-integration 81/100 · B	K-Dense-AI/claude-scientific-skills	Reads, validates, and safely exports protocols.io data with current official REST/MCP contracts, or creates non-executing mutation plans. The…
pybamm 87/100 · B	K-Dense-AI/claude-scientific-skills	Simulates lithium-ion battery charge, discharge and rest experiments with PyBaMM, records parameter-set provenance, checks mesh and solver…
pycalphad 87/100 · B	K-Dense-AI/claude-scientific-skills	Computes finite-temperature CALPHAD equilibria, phase fractions, and phase compositions from thermodynamic TDB databases using pycalphad. Use for…
pydeseq2 89/100 · B	K-Dense-AI/claude-scientific-skills	Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests…
pydicom 79/100 · C	K-Dense-AI/claude-scientific-skills	Reads, inspects, writes, transforms, and preflights local DICOM datasets and pixel data. Applies to DICOM metadata, transfer syntaxes, compression…
pyhealth 85/100 · B	K-Dense-AI/claude-scientific-skills	Builds and validates PyHealth clinical machine-learning pipelines for EHR, signals, imaging, and medical codes. Use for PyHealth dataset loading…
pylabrobot 81/100 · B	K-Dense-AI/claude-scientific-skills	Develops and reviews PyLabRobot lab-automation resources, liquid-handling plans, offline simulations, and supported-device integrations. Supports…
pymatgen 89/100 · B	K-Dense-AI/claude-scientific-skills	Analyzes, validates, converts, and transforms materials structures and computed materials data with pymatgen. Use for local phase diagrams, symmetry…
pymc 89/100 · B	K-Dense-AI/claude-scientific-skills	Builds and checks Bayesian models with PyMC, including hierarchical models, NUTS MCMC, variational inference, mutable-data predictions, posterior…
pymoo 81/100 · B	K-Dense-AI/claude-scientific-skills	Solves and validates single-, multi-, and many-objective optimization with pymoo, including NSGA-II, NSGA-III, MOEA/D, constraints, Pareto…
pyopenms 81/100 · B	K-Dense-AI/claude-scientific-skills	Processes mass spectrometry data with pyOpenMS. Supports proteomics and metabolomics workflows—feature detection, peptide/protein identification…
pysam 81/100 · B	K-Dense-AI/claude-scientific-skills	Provides Python/HTSlib workflows for genomic files. Used when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix…
pytdc 89/100 · B	K-Dense-AI/claude-scientific-skills	Provides Therapeutics Data Commons workflows through PyTDC for registry discovery, dataset access, task-aware splits, evaluator metrics, benchmark…
pyzotero 87/100 · B	K-Dense-AI/claude-scientific-skills	Manages Zotero reference libraries using the pyzotero Python client: retrieves, creates, updates, and deletes items, collections, tags, and…
qiime2-amplicon 79/100 · C	K-Dense-AI/claude-scientific-skills	Processes paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy with retained artifact provenance. Checks paired FASTQ manifests, primer…
qiskit 87/100 · B	K-Dense-AI/claude-scientific-skills	Builds, simulates, transpiles, and executes quantum circuits with Qiskit and IBM Quantum Runtime. Use for Qiskit 2.x circuits and operators, V2…
qutip 87/100 · B	K-Dense-AI/claude-scientific-skills	Simulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory, steady-state, spectral, and phase-space…
rdkit 81/100 · B	K-Dense-AI/claude-scientific-skills	Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search…
relion 79/100 · C	K-Dense-AI/claude-scientific-skills	Validates and executes RELION single-particle cryo-EM refinement and half-map postprocessing. Supports STAR optics/acquisition checks…
research-grants 87/100 · B	K-Dense-AI/claude-scientific-skills	Supports research proposal preparation and review for NSF, NIH, DOE, DARPA, and Taiwan NSTC, including opportunity-specific requirements, aims…
research-lookup 87/100 · B	K-Dense-AI/claude-scientific-skills	Compiles current scholarly evidence for a scientific manuscript or research brief when the user explicitly asks to gather literature, references…
rfdiffusion-nim 77/100 · C	NVIDIA/skills	Run RFDiffusion protein backbone design via NVIDIA NIM. Use for de novo protein backbones, motif scaffolding, binder design, hotspot residues…
rowan 85/100 · B	K-Dense-AI/claude-scientific-skills	Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction…
scanpy 79/100 · C	K-Dense-AI/claude-scientific-skills	Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk…
scholar-evaluation 89/100 · B	K-Dense-AI/claude-scientific-skills	Provides qualitative-first, evidence-traceable developmental review of scholarly works and audit low-stakes research-assessment rubrics with…
scientific-brainstorming 87/100 · B	K-Dense-AI/claude-scientific-skills	Facilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit assumptions, transparent evaluation…
scientific-critical-thinking 79/100 · C	K-Dense-AI/claude-scientific-skills	Evaluates scientific claims and evidence quality. Applies to experimental design validity, biases and confounders, statistical interpretation…
scientific-visualization 89/100 · B	K-Dense-AI/claude-scientific-skills	Creates and audits truthful, accessible, publication-ready scientific figures with Matplotlib, Seaborn, or Plotly. Use it for figure design…
scikit-bio 79/100 · C	K-Dense-AI/claude-scientific-skills	Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA…
scikit-survival 81/100 · B	K-Dense-AI/claude-scientific-skills	Builds, evaluates, and audits right-censored or competing-risk survival workflows with scikit-survival, including leakage-safe preprocessing, model…
scvelo 87/100 · B	K-Dense-AI/claude-scientific-skills	Performs RNA velocity analysis with scVelo from spliced and unspliced single-cell RNA counts. Fits deterministic or dynamical models, examines gene…
scvi-tools 85/100 · B	K-Dense-AI/claude-scientific-skills	Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC…
simpy 89/100 · B	K-Dense-AI/claude-scientific-skills	Builds, inspects, tests, and analyzes bounded process-based discrete-event simulations with SimPy. Use for event scheduling, resource queues…
simulation-failure-triage 74/100 · C	HeshamFS/materials-simulation-skills	First-response triage for cross-code (LAMMPS/VASP/QE/MOOSE) simulation failures: classifies the failure signature (nonconvergence, NaN/Inf…
simulation-orchestrator 82/100 · B	HeshamFS/materials-simulation-skills	Orchestrate multi-simulation campaigns — generate parameter sweep configurations (grid, linspace, or Latin Hypercube sampling), initialize and track…
simulation-validator 82/100 · B	HeshamFS/materials-simulation-skills	Validate simulations across three stages — run pre-flight checks on configuration files (parameter ranges, required fields, disk space), monitor…
slurm-job-script-generator 82/100 · B	HeshamFS/materials-simulation-skills	Generate correct, copy-pasteable SLURM sbatch job scripts and sanity-check HPC resource requests — configure nodes, MPI tasks, OpenMP threads…
statistical-analysis 87/100 · B	K-Dense-AI/claude-scientific-skills	Guided statistical analysis for research data - test selection, assumption checking, effect sizes, power analysis, Bayesian alternatives, and…
statistical-power 90/100 · A	K-Dense-AI/claude-scientific-skills	Calculates sample sizes and statistical power for study planning. Applies when someone asks "how many subjects/samples/replicates do I need", wants…
statsmodels 79/100 · C	K-Dense-AI/claude-scientific-skills	Fits and diagnoses Python statistical models including OLS, GLM, discrete and mixed models, ARIMA and SARIMAX. Supports coefficient inference…
sympy 87/100 · B	K-Dense-AI/claude-scientific-skills	Performs exact symbolic mathematics with SymPy for algebra, calculus, equation solving, symbolic linear algebra, physics, and lambdify or LaTeX code…
tamarind 83/100 · B	K-Dense-AI/claude-scientific-skills	Provides access to a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP…
tellurium 87/100 · B	K-Dense-AI/claude-scientific-skills	Simulates biochemical kinetic models from SBML or Antimony with Tellurium and libRoadRunner, checks model units, compares deterministic parameter…
tiledbvcf 85/100 · B	K-Dense-AI/claude-scientific-skills	Stores and retrieves genomic variant calls with TileDB-VCF. Use for indexed single-sample VCF/BCF ingestion, incremental cohorts, region and sample…
time-stepping 84/100 · B	HeshamFS/materials-simulation-skills	Plan and control time-step policies for transient simulations — couple CFL and physics-based stability limits with adaptive stepping, ramp initial…
torchdrug 87/100 · B	K-Dense-AI/claude-scientific-skills	Builds and troubleshoots TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation…
uncertainty-and-units 90/100 · A	K-Dense-AI/claude-scientific-skills	Tracks physical units and propagates measurement uncertainty in scientific calculations using pint and uncertainties. Use for unit conversion and…
venue-templates 79/100 · C	K-Dense-AI/claude-scientific-skills	Prepares journal manuscripts, conference papers, research posters, and grant documents using venue-specific formatting guidance and bundled LaTeX…
waypoint-bio 79/100 · C	K-Dense-AI/claude-scientific-skills	Supports work with Outpost Bio's open microbiome foundation models - the Waypoint checkpoints (Waypoint-6m, Waypoint-45m, Waypoint-170m), the Atlas…
what-if-oracle 83/100 · B	K-Dense-AI/claude-scientific-skills	Supports structured what-if scenario analysis for research planning, experimental contingencies, and scientific project decisions. Explores…
workflow-engine-mapper 81/100 · B	HeshamFS/materials-simulation-skills	Map computational materials tasks onto workflow engines such as atomate2, jobflow, AiiDA, pyiron, or a simple one-off script. Use when deciding how…
writing-lean-proofs 87/100 · B	trailofbits/skills	Writes and reviews structured Lean 4 proofs and designs Lean libraries following Mathlib conventions. Use when proving theorems in Lean, formalizing…

How to choose science and research skills

Most science skills wrap a specific library or database. Choose by the tool your lab already uses, and check the bundled scripts list on each page, since these skills often run Python against your data.

Database and literature skills may need an API key for the service they query. The Before you install panel shows the environment variables each skill's code reads.

Treat outputs as a starting analysis. The skills encode procedure; your data, controls and domain judgment decide whether a result holds.

Where to start

firecrawl-research-indexFinds papers that answer a research query in Firecrawl's paper index, covering biomedical and life-science literature… Published by Firecrawl. convergence-studyPerforms spatial and temporal convergence analysis for numerical solutions, computing observed convergence orders… From HeshamFS/materials-simulation-skills, cited by 2 curated lists. analytical-method-validationPlans, executes, and documents validation, verification, and transfer of analytical procedures under frameworks such… From K-Dense-AI/claude-scientific-skills, cited by 2 curated lists. academic-plottingGenerates publication-quality figures for ML papers, including architecture diagrams via Gemini and data-driven charts… From Orchestra-Research/AI-Research-SKILLs, cited by 2 curated lists.

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K-Dense-AI/claude-scientific-skills136 science and research skills NVIDIA/skills39 science and research skills HeshamFS/materials-simulation-skills23 science and research skills Orchestra-Research/AI-Research-SKILLs7 science and research skills firecrawl/skills2 science and research skills gooseworks-ai/goose-skills1 science and research skill huggingface/skills1 science and research skill trailofbits/skills1 science and research skill

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