Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition r…
Workflow MiningSkill DraftingScreen Observation
26.7K 2.8K 0 0
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Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, m…
BIDS Dataset OrganizationMetadata Sidecar WritingBIDS Validation
26.7K 2.8K 0 0
End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCoun…
Bulk RNA-seq PipelineDifferential ExpressionPathway Enrichment
26.7K 2.8K 1 0
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 se…
Web SearchURL Content ExtractionScientific Web Retrieval
26.7K 2.8K 0 0
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, eng…
Scientific Model DiscoveryDataset DiscoveryInteractive Space Discovery
26.7K 2.8K 0 0
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 JS…
Document ParsingOCRLayout-preserved Extraction
26.7K 2.8K 0 0
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, proce…
Nextflow Pipeline Developmentnf-core Workflow ExecutionContainerized Workflow Scaling
26.7K 2.8K 0 0
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-co…
Matched Tumor-normal WorkflowNextflow Launch PreparationSamplesheet Validation
26.7K 2.8K 0 0
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 expr…
Pathway EnrichmentGene Set EnrichmentORA GSEA Interpretation
26.7K 2.8K 0 0
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…
Protein Experimental ValidationCloud Lab Submission
26.2K 2.7K 0 0
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and simi…
Aeon
26.2K 2.7K 0 0
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…
AnnData Matrix Handlingh5ad Zarr Data Exchange
26.2K 2.7K 0 0
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, sin…
Gene Regulatory Mechanism Analysis
26.2K 2.7K 0 0
Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical unit…
Astronomical Data AnalysisFITS Coordinate Processing
26.2K 2.7K 0 0
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data…
Benchling Registry ELN IntegrationLab Data Workflow Automation
26.2K 2.7K 0 0
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including metho…
Structured Paper Data Search
26.2K 2.7K 0 0
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez)…
Sequence ParsingStructure ParsingNCBI Entrez BLAST Query
26.2K 2.7K 0 0
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API.…
Bioinformatics Web Service QueryCross-database Identifier MappingMulti-database Pathway Analysis
26.2K 2.7K 0 0
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…
CELLxGENE Census QuerySingle-cell Reference Atlas Retrieval
26.2K 2.7K 0 0
Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best…
Quantum Circuit SimulationGoogle Quantum Hardware Programming
26.2K 2.7K 0 0
Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properl…
Citation Metadata VerificationBibTeX Generation
26.2K 2.7K 0 0
Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratifie…
Clinical Decision Support Report Generation
26.2K 2.7K 0 0
Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), a…
Clinical Reports
26.2K 2.7K 0 0
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
Constraint-based Metabolic ModelingFlux Balance Analysis
26.2K 2.7K 0 0
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