research▌

### Jaspar Database - name: "jaspar-database" - description: "Query the JASPAR database for Transcription Factor (TF) binding profiles. Use when retrieving Position Frequency Matrices (PFMs) or Position Weight Matrices (PWMs) for specific TFs, resolving gene sym..."

### 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"

### 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..."

### 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"

### Literature Search Europepmc - name: "literature-search-europepmc" - description: "Search Europe PMC for scientific literature and download open-access full texts and PDFs. Retrieve full-text XML/plain text by PMCID, get citation lists and bibliography."

### 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"