Science AI skills, agents & prompts
Lab work, datasets and papers — the jobs a researcher finishes. 104 listings — 101 skills, 1 agent and 2 prompts — each free, credited to its author, with the full source on its page. Filter and sort them →
Genomics & omics
Reads, counts and cells — from raw sequencing to a result you can defend.AnndataData structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or…ArboretoInfer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2…Biopython: Computational Molecular Biology in PythonComprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB)…Bulk rnaseqEnd-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim…COBRApy - Constraint-Based Reconstruction and AnalysisConstraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for…CZ CELLxGENE CensusQuery the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics…DepMap — Cancer Dependency MapQuery the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug…ETE Toolkit 4Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4…FlowioRead, inspect, and write Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for…Folklore variant evidenceRetrieve ClinGen gene-disease validity assertions for a public gene or disease, and review source-linked…Genomic coordinatesConvert genomic intervals between coordinate conventions, normalise and compare variant representations, and…GgetFast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral…GlycoengineeringAnalyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict…Hugging scienceUse when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy…LamindbUse when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models…MAGeCK pooled-screen analysisAnalyzes pooled CRISPR screen FASTQ reads and guide-count matrices with MAGeCK, validates guide libraries…Pathogen variant surveillanceQuery live pathogen genomic surveillance data through the GenSpectrum LAPIS API to find which viral lineages…Pathway enrichmentRun pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results…PhylogeneticsBuild and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and…Polars bioHigh-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap…Pydeseq2Differential gene expression analysis for bulk RNA-seq with PyDESeq2, including formulaic designs, Wald…PysamPython/HTSlib workflows for genomic files. Use when reading, querying, filtering, or writing SAM/BAM/CRAM…Scanpy: Single-Cell AnalysisStandard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction…Scikit bioBiological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta…scVelo — RNA Velocity AnalysisRNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics…Scvi toolsDeep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI)…TiledbvcfEfficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion…Sequencing toolkitComplete outreach sequencing toolkit — Smartlead, Instantly, Salesloft, Outreach, Lemlist setup and…
Molecules & structures
Docking, folding and the shape of the thing you are studying.Datamol Cheminformatics SkillPythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug…DeepchemMolecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity)…DiffDock: Molecular Docking with Diffusion ModelsDiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or…MatchmsProcess, clean, compare, and search tandem mass spectra with matchms. Use for MS/MS file I/O, metadata…MedchemMedicinal chemistry filters for compound triage. Apply drug-likeness rules (Lipinski, Veber, CNS)…Molecular dynamicsRun and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule…Molfeat - Molecular Featurization HubMolecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa)…PymatgenAnalyze, validate, convert, and transform materials structures and computed materials data with current…PyopenmsComplete mass spectrometry analysis platform. Use for proteomics and metabolomics workflows—feature…PyTDC (Therapeutics Data Commons)Use Therapeutics Data Commons through the PyTDC Python package for registry discovery, approved dataset…RDKit Cheminformatics ToolkitCheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP…TorchdrugBuild and troubleshoot TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised…Umap learnUse UMAP-learn for nonlinear dimensionality reduction, 2D/3D embeddings, clustering preprocessing…Research brief generatorUse this agent when you need to transform a user's research query into a structured, actionable research…
Clinical & trials
Protocols, patient data and the reports regulators read.Brain Imaging Data Structure (BIDS)Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and…HistolabLightweight WSI tile extraction and preprocessing. Use for basic slide processing, tissue detection, tile…Neurokit2Use NeuroKit2 to build or audit reproducible research workflows for physiological time-series preprocessing…PathmlUse PathML for local, research-only computational pathology workflows: load and tile slides, build…PydicomUse pydicom to read, inspect, write, transform, and safely preflight local DICOM datasets and pixel data…PyhealthBuild clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets…RELSA severity assessment and humane endpoint forecastingMultivariate severity assessment and humane endpoint prediction for laboratory animal studies using the…Scikit survivalBuild, evaluate, and audit right-censored or competing-risk survival workflows with scikit-survival…
Physics & astronomy
Signals, spectra and sky surveys.AstropyCore Python library for astronomy and astrophysics workflows that need Astropy APIs, including…Cirq - Quantum Computing with PythonGoogle quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware…FluidsimPlan, configure, inspect, restart, and analyze bounded FluidSim computational-fluid-dynamics simulations…OpenpivParticle Image Velocimetry (PIV) analysis with OpenPIV. Use when extracting velocity fields from PIV image…PennylaneHardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits…PufferlibVersion-aware guidance for PufferLib reinforcement-learning environments, vectorization, policies, PuffeRL…QiskitBuild, simulate, transpile, and execute quantum circuits with Qiskit and IBM Quantum Runtime. Use for Qiskit…QuTiP 5Simulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory…SimpyBuild, inspect, test, and analyze bounded process-based discrete-event simulations with SimPy, including…Uncertainty and unitsTrack physical units and propagate measurement uncertainty in scientific calculations using pint and…
Research data
Getting the dataset clean, documented and reusable.Data visualisation designDesign rules, chart selection and review checklists for charts, graphs, plots and dashboards. Use this skill…Analytical method validationPlan, execute, and document validation, verification, and transfer of analytical procedures under the…AutoskillObserve the user's screen via screenpipe, detect repeated research workflows, match them against existing…BioservicesUnified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt…Database lookupQuery documented public database APIs with explicit endpoints, filters, pagination, and provenance. Use when…Experimental designDesign experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and…Ginkgo cloud labSubmit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for…Lab hardware cadDesign custom laboratory hardware as parametric build123d models and export fabrication-ready STEP, STL, and…LiteParse — Local Document ParsingLocal document and PDF parsing that returns spatial text with bounding boxes. Use for extracting text from…MatplotlibLow-level plotting library for full customization. Use when you need fine-grained control over every plot…NetworkxCreate, analyze, and visualize complex networks and graphs in Python with NetworkX. Use when working with…Omero integrationSecurely inspect and automate microscopy data workflows against OMERO.server with omero-py, BlitzGateway…Ontology term resolutionResolve free-text scientific labels to ontology term IDs and validate existing CURIEs against the EBI…Open notebookSelf-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use…Opentrons integrationAuthor, review, migrate, simulate, and troubleshoot official Opentrons Python Protocol API v2 protocols for…Parallel Web ToolkitUse Parallel CLI for web search, URL extraction, deep research, structured data enrichment, entity…PylabrobotDevelop and review PyLabRobot lab-automation resources, liquid-handling plans, offline simulations, and…Seaborn Statistical VisualizationStatistical visualization with pandas integration. Use for quick exploration of distributions…ShapExplain and audit machine-learning predictions with SHAP. Use for selecting SHAP explainers and maskers…Statistical analysisGuided statistical analysis for research data - test selection, assumption checking, effect sizes, power…Timesfm forecastingZero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series…VaexUse this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available…
Papers & citations
The literature going in, and the manuscript coming out.Research paper writingImprove academic paper writing quality for ML/CV/NLP-style papers with clear section structure, paragraph…Act as a senior research paper evaluatorUse this prompt to critically evaluate academic papers. Ideal for reviewers aiming to assess the quality and…Bibliographic review writing assistantAssist users in drafting and reviewing bibliographic literature reviews, ensuring compliance with APA 7th…Citation managementComprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for…Exa Web ToolkitWeb toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs…
LaTeX Research PostersCreate professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for…Literature reviewConduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv…Paper lookupSearch 18 scholarly APIs for papers, preprints, citations, open-access full text, repository records, and…PaperzillaChat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask…Peer reviewPrepare evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Use for…PyzoteroInteract with Zotero reference management libraries using the pyzotero Python client. Retrieve, create…Research Grant WritingWrite competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting…Research lookupCompile current scholarly evidence for a scientific manuscript or research brief. Use when the user…Scholar evaluationProvide qualitative-first, evidence-traceable developmental review of scholarly works and audit low-stakes…Scientific brainstormingFacilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit…Scientific Hypothesis GenerationFormulate evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or…Scientific writingDraft, revise, and audit scientific manuscripts or reports with explicit evidence provenance…Venue templatesPrepare journal manuscripts, conference papers, research posters, and grant documents using venue-specific…Litreview — Academic Literature OrientationAcademic literature orientation skill that searches papers via free keyless APIs (PubMed E-utilities +…Grant Proposal SkillWrite a structured grant proposal or funding application for any grant type. Use when asked to write a grant…Literature Review SkillStructure and write a literature review for any research topic. Use when asked to write a literature review…Story maintenanceThis skill should be used when the user asks to validate, reindex, repair registries, check links, check…
LaTeX Research PostersCreate professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for…Literature reviewConduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv…Paper lookupSearch 18 scholarly APIs for papers, preprints, citations, open-access full text, repository records, and…PaperzillaChat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask…Peer reviewPrepare evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Use for…PyzoteroInteract with Zotero reference management libraries using the pyzotero Python client. Retrieve, create…Research Grant WritingWrite competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting…Research lookupCompile current scholarly evidence for a scientific manuscript or research brief. Use when the user…Scholar evaluationProvide qualitative-first, evidence-traceable developmental review of scholarly works and audit low-stakes…Scientific brainstormingFacilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit…Scientific Hypothesis GenerationFormulate evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or…Scientific writingDraft, revise, and audit scientific manuscripts or reports with explicit evidence provenance…Venue templatesPrepare journal manuscripts, conference papers, research posters, and grant documents using venue-specific…Litreview — Academic Literature OrientationAcademic literature orientation skill that searches papers via free keyless APIs (PubMed E-utilities +…Grant Proposal SkillWrite a structured grant proposal or funding application for any grant type. Use when asked to write a grant…Literature Review SkillStructure and write a literature review for any research topic. Use when asked to write a literature review…Story maintenanceThis skill should be used when the user asks to validate, reindex, repair registries, check links, check…