Agent Skills

---

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 transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

---

name: benchling-integration

description: Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

---

name: bioinformatics

---

name: biomni

description: Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.

---

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, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

---

name: brenda-database

description: Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.

---

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-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.

---

name: clinpgx-database

description: Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.

---

name: cobrapy

description: Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

---

name: context-audit

description: Audit an agent's context layout against the four places: system prompt, tools, history, tail. Use when the user asks to audit, review or fix their agent's context, prompt caching, token spend per turn, or CLAUDE.md / AGENTS.md layout. Read-only: reports findings and a fix list, changes nothing. Do NOT use for writing evals (evals-bootstrap) or for loop design (goal-test).

---

name: cosmic-database

description: Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.

---

name: deeptools

description: NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

---

name: detect_common_wetlab_errors

description: Detects common wet-lab procedural and safety errors from XR or fixed-camera lab video. Identifies pipette volume deviations, forgotten reagent additions, uncapped tubes, contamination risks, sample mix-ups, and other observable hazards. Outputs structured JSON with error type, timestamp, severity, and corrective action suggestions for real-time alerts or post-hoc audit.

---

name: dnanexus-integration

description: DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.

---

name: egocentric_view_to_structured_log

description: Converts first-person XR headset video into a structured experiment timeline log. Extracts timestamped events (action, object, location, result) via VLM or action recognition, outputs Markdown or JSON for downstream analysis, reporting, protocol compliance audit, or ELN attachment.

---

name: ena-database

description: Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.

---

name: ensembl-database

description: Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.

---

name: esm

description: Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

---

name: etetoolkit

description: Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

---

name: evals-bootstrap

description: Scaffold a first eval suite for an agent: mine real failures into cases, write behavioural checks over traces, and generate the runner. Use when the user wants evals, regression tests for an agent, a golden set, or asks how to know a prompt/model change did not break things. Do NOT use for a single task's done-check (goal-test) or for auditing context (context-audit).

---

name: extract_experiment_data_from_video

description: General-purpose experimental data extractor from lab video streams. Ingests footage from XR headsets or fixed cameras and extracts typed, timestamped measurements — liquid volume levels, color/turbidity shifts, cell and colony counts, pipette readouts, instrument display values, gel band intensities — emitting a time-series JSON or CSV table ready for downstream analysis, charting, or ELN attachment.

---

name: flowio

description: Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.

---

name: gate-check

description: Find the decisions in a pipeline that do not need the expensive model and propose the gate for each: a rule, a classic classifier, or a small model, with fail-closed routing. Use when the user asks to cut model costs or latency, says the big model handles everything, or wants a triage / routing / filter layer in front of an agent. Analysis plus an optional baseline scaffold. Do NOT use for auditing context layout (context-audit) or for building eval suites (evals-bootstrap).

---

name: gene-database

description: Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.