science▌

### 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..."

### 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."

### 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"

### 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..."

### Autoskill - name: "autoskill" - description: "Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition recipes that chain existing ones..." - allowed-tools: "Read Write Edit Bash"

### Arboreto - name: "arboreto" - description: "Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify t..."

### Adaptyv - name: "adaptyv" - description: "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, Foundry API, protein binding ..."

### Bids - name: "bids" - description: "Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectros..."

### Clinvar Database - name: "clinvar-database" - description: "Use when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls for human genomic var..."

### Unibind Database - name: "unibind-database" - description: "Queries the UniBind database for experimentally validated transcription factor (TF) binding sites. Use when retrieving direct TF-DNA interaction datasets, downloading binding site coordinates (BED/FAS..."