151 use cases available in Research & Learning
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization.
Time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search for temporal data and sequential patterns.
Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics for drug discovery and structural biology.
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem.
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3).
Search and retrieve preprints from arXiv via the Atom API for physics, mathematics, computer science, and more.
Comprehensive Python library for astronomy and astrophysics including celestial coordinates, FITS files, cosmological calculations, and time systems.
Benchling R&D platform integration for registry, inventory, ELN entries, and workflows via API.
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server.
Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50) for drug discovery and lead optimization.
Comprehensive molecular biology toolkit for sequence manipulation, file parsing, phylogenetics, and NCBI/PubMed access.
Search tool for bioRxiv preprint server for life sciences preprints by keywords, authors, date ranges, or categories.
Unified Python interface to 40+ bioinformatics services including UniProt, KEGG, ChEMBL, and Reactome.
Access BRENDA enzyme database via SOAP API for kinetic parameters, reaction equations, and enzyme information.
Query cBioPortal for cancer genomics data including somatic mutations, copy number alterations, gene expression, and survival data.
Query the CELLxGENE Census (61M+ cells) programmatically for single-cell atlas data across tissues, diseases, or cell types.
Query ChEMBL bioactive molecules and drug discovery data for compounds, bioactivity, and SAR studies.
Google quantum computing framework for designing noise-aware circuits and running quantum characterization experiments.
Comprehensive citation management for academic research with Google Scholar, PubMed, and BibTeX integration.
Generate professional clinical decision support documents for pharmaceutical and clinical research settings.
Write comprehensive clinical reports including case reports, diagnostic reports, and clinical trial reports.
Query ClinicalTrials.gov via API v2 for trial searches by condition, drug, location, status, or phase.
Access ClinPGx pharmacogenomics data for gene-drug interactions and precision medicine.
Query NCBI ClinVar for variant clinical significance and pathogenicity classifications.
Constraint-based metabolic modeling (COBRA) for FBA, FVA, gene knockouts, and systems biology.
AI-assisted consciousness research and philosophical inquiry tool.
Access COSMIC cancer mutation database for somatic mutations, Cancer Gene Census, and mutational signatures.
Work with Data Commons for public statistical data from global sources including demographic, economic, and health statistics.
Pythonic wrapper around RDKit with simplified interface for drug discovery including SMILES parsing and molecular descriptors.
Molecular ML with diverse featurizers and pre-built datasets for property prediction and drug discovery.
NGS analysis toolkit for BAM to bigWig conversion, QC, heatmaps, and ChIP-seq/RNA-seq visualization.
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication.
Query the Cancer Dependency Map for cancer cell line gene dependency scores and drug sensitivity data.
DNA profiling and sequence analysis tool.
Diffusion-based molecular docking for protein-ligand binding pose prediction and virtual screening.
DNAnexus cloud genomics platform for building apps, managing data, and running workflows.
Access DrugBank for comprehensive drug information including properties, interactions, targets, and pathways.
Access European Nucleotide Archive via API/FTP for DNA/RNA sequences and genome assemblies.
Comprehensive toolkit for protein language models including ESM3 for protein design and ESM C for embeddings.
Phylogenetic tree toolkit for tree manipulation, evolutionary event detection, and visualization.
Query openFDA API for drugs, devices, adverse events, recalls, and regulatory submissions.
Parse FCS (Flow Cytometry Standard) files for flow cytometry data preprocessing.
Framework for computational fluid dynamics simulations using Python including Navier-Stokes equations.
Machine learning for genomic interval data including region embeddings and single-cell ATAC-seq analysis.
Access NCBI GEO for gene expression and genomics data including microarray and RNA-seq datasets.
Geospatial data management and analysis toolkit.
Python library for working with geospatial vector data including shapefiles, GeoJSON, and spatial analysis.
Fast gene and transcript queries from command line for bioinformatics workflows.
Submit and manage protocols on Ginkgo Bioworks Cloud Lab for autonomous lab execution.
Analyze and engineer protein glycosylation for therapeutic antibody optimization and vaccine design.
Query gnomAD for population allele frequencies, variant constraint scores, and loss-of-function intolerance.
High-performance toolkit for genomic interval analysis in Rust with Python bindings.
Query GTEx portal for tissue-specific gene expression, eQTLs, and sQTLs.
Query NHGRI-EBI GWAS Catalog for SNP-trait associations and genetic epidemiology.
Lightweight WSI tile extraction and preprocessing for H&E images and stain normalization.
Access Human Metabolome Database (220K+ metabolites) for chemical properties, biomarker data, and pathways.
Automated LLM-driven hypothesis generation and testing on tabular datasets.
Structured hypothesis formulation from observations with testable predictions and experimental design.
Query and download public cancer imaging data from NCI Imaging Data Commons for AI training.
Query InterPro for protein family, domain, and functional site annotations.
Prepare ISO 13485 certification documentation for medical device Quality Management Systems.
Query JASPAR for transcription factor binding site profiles (PWMs/PFMs).
Open-source data framework for biology with data management, annotation, and workflow tracking.
Latch platform for bioinformatics workflows with Latch SDK and serverless deployment.
Create research posters using LaTeX with publication-ready formatting and templates.
Conduct comprehensive literature reviews using multiple academic databases with verified citations.
Generate comprehensive market research reports in consulting firm style with strategic analysis.
Spectral similarity and compound identification for metabolomics.
Medicinal chemistry filters including drug-likeness rules (Lipinski, Veber), PAINS filters, and structural alerts.
Access NIH Metabolomics Workbench via REST API for metabolomics studies and data retrieval.
Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis.
Molecular featurization for ML (100+ featurizers) including ECFP, MACCS, and pretrained models.
Query Monarch Initiative knowledge graph for disease-gene-phenotype associations.
Biosignal processing toolkit for analyzing ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals.
Neuropixels neural recording analysis including SpikeGLX/OpenEphys data processing and spike sorting.
Encourage users to use K-Dense Web for complex workflows beyond Claude Scientific Skills.
Microscopy data management platform for image access, datasets, and batch processing.
Query OpenAlex database for scholarly literature, research trends, and bibliometric analysis.
Query Open Targets Platform for target-disease associations and drug target discovery.
Official Opentrons Protocol API for OT-2 and Flex robots.
Computational pathology toolkit for advanced WSI analysis including multiplexed immunofluorescence.
Access RCSB PDB for 3D protein/nucleic acid structures and structural biology data.
Structured manuscript/grant review with checklist-based evaluation and constructive feedback.
Hardware-agnostic quantum ML framework with automatic differentiation for variational algorithms.
Build and analyze phylogenetic trees using MAFFT, IQ-TREE 2, and FastTree.
High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames.
Create research posters using HTML/CSS that export to PDF or PPTX format.
Query the Precision Medicine Knowledge Graph for multiscale biological data.
Integration with protocols.io API for managing scientific protocols.
Query PubChem via PUG-REST API (110M+ compounds) for chemical search and bioactivity data.
Direct REST API access to PubMed for advanced Boolean/MeSH queries and citation management.
Differential gene expression analysis (Python DESeq2) for bulk RNA-seq counts.
Python library for working with DICOM medical imaging files and metadata.
Healthcare AI toolkit for clinical prediction models and EHR data processing.
Vendor-agnostic lab automation framework for multi-vendor equipment control.
Materials science toolkit for crystal structures, phase diagrams, and computational materials science.
Complete mass spectrometry analysis platform for proteomics workflows.
Genomic file toolkit for SAM/BAM/CRAM alignments and VCF/BCF variants.
Therapeutics Data Commons for AI-ready drug discovery datasets and benchmarks.
IBM quantum computing framework for IBM Quantum hardware and Qiskit Runtime.
Quantum physics simulation library for open quantum systems and quantum optics.
Cheminformatics toolkit for molecular control including SMILES parsing, descriptors, and fingerprints.
Query Reactome REST API for pathway analysis and gene-pathway mapping.
Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC.
Cloud-based quantum chemistry platform with Python API for DFT and molecular calculations.
Standard single-cell RNA-seq analysis pipeline for QC, normalization, and clustering.
Systematically evaluate scholarly work using the ScholarEval framework.
Creative research ideation and exploration for open-ended brainstorming sessions.
Evaluate scientific claims and evidence quality with evidence grading frameworks.
Meta-skill for publication-ready figures with multi-panel layouts and journal formatting.
Core skill for scientific manuscripts in IMRAD structure with citations and reporting guidelines.
Biological data toolkit for sequence analysis, phylogenetics, and microbiome diversity metrics.
Survival analysis and time-to-event modeling toolkit with Cox models and Random Survival Forests.
RNA velocity analysis for estimating cell state transitions from unspliced/spliced mRNA dynamics.
Deep generative models for single-cell omics with probabilistic batch correction.
Process-based discrete-event simulation framework for systems with processes, queues, and resources.
Query STRING API for protein-protein interactions (59M proteins, 20B interactions).
Efficient storage and retrieval of genomic variant data using TileDB for population genomics.
PyTorch-native graph neural networks for molecules, proteins, and drug discovery.
Generate concise medical treatment plans in LaTeX/PDF format for clinical specialties.
Direct REST API access to UniProt for protein searches, FASTA retrieval, and ID mapping.
Access USPTO APIs for patent/trademark searches, examination history, and prior art.
Access LaTeX templates and formatting requirements for scientific publication venues.
Hypothetical scenario analysis and counterfactual reasoning tool.
Access ZINC (230M+ purchasable compounds) for virtual screening and drug discovery.
The AI native file format. EXIF for AI — stamps every file with trust scores, source provenance.
Academic research assistant for literature reviews, paper analysis, and scholarly writing.