Start with information tasks: collecting literature, extracting study methods, comparing findings or building research notes with sources. Distinguish patient records, public papers and research data, and check required services and runtimes. Verify summaries against original documents. Search results and generated content should not directly determine diagnosis, prescriptions or treatment.
Using only the five attached public papers, create a comparison table covering study population, sample size, design, main findings and author-reported limitations. Cite the original source for each row. Mark absent fields as “not reported” and do not add clinical recommendations.
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstrea
Imported source metadata; verify setup at the official source.
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, vari
Imported source metadata; verify setup at the official source.
This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask to pitch a new research idea, work throu
Imported source metadata; verify setup at the official source.
Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI
Imported source metadata; verify setup at the official source.
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing dat
Imported source metadata; verify setup at the official source.
Set up your bio-research environment and explore available tools. Use when first getting oriented with the plugin, checking which literature, drug-discovery, or visualization MCP servers are connected, or surveying available analysis skills
Imported source metadata; verify setup at the official source.
Boltz job status and result recovery. Use when listing jobs, checking progress, resuming downloads, recovering results, or downloading an existing job ID. Not for starting new jobs.
Imported source metadata; verify setup at the official source.
Submit compact AlphaFold Protein Structure Database API requests for prediction, UniProt summary, sequence summary, and annotation lookups. Use when a user wants AlphaFold metadata or concise structure summaries
Imported source metadata; verify setup at the official source.
Kick off public 16S, 18S, ITS, COI, or other marker-gene amplicon microbiome workflows using nf-core/ampliseq, QIIME2, DADA2, and Cutadapt.
Imported source metadata; verify setup at the official source.
Boltz CLI setup and auth. Use when installing, updating, verifying, or authenticating `boltz-api`, or fixing missing CLI, PATH, sandbox, browser login, or auth errors.
Imported source metadata; verify setup at the official source.
Submit compact Bgee SPARQL requests for healthy wild-type expression metadata and ontology-aware lookup patterns. Use when a user wants concise Bgee summaries; save raw results only on request.
Imported source metadata; verify setup at the official source.
Route BCL, FASTQ, BAM/CRAM, count-matrix, or VCF sequencing requests to the right public NGS analysis skill and ask only the missing assay-specific setup questions.
Imported source metadata; verify setup at the official source.