Production-ready RNA-seq differential expression analysis using PyDESeq2. Performs DESeq2 normalization, dispersion estimation, Wald testing, LFC shrinkage, and result filtering.
Retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence profiles.
Production-ready single-cell and expression matrix analysis using scanpy, anndata, and scipy. Performs scRNA-seq QC, normalization, PCA, UMAP, Leiden/Louvain clustering,…
Gather comprehensive biological target intelligence from 9 parallel research paths covering protein info, structure, interactions, pathways, expression, variants, drug…
Production-ready VCF processing, variant annotation, mutation analysis, and structural variant (SV/CNV) interpretation for bioinformatics questions.
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep lear — from…
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep lear — from…
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep lear — from…
PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reaso — from…
PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reaso — from…
PyTorch-native Graph Neural Network framework for molecules and proteins. Suitable for building custom GNN architectures for drug discovery, protein modeling, or knowledge graph…
Query UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies.
Generate R/Python code for volcano plots from DEG (Differentially Expressed Genes) analysis results. Triggered when user needs visualization of gene expression data, p-value vs…
Decompose goals into MEOWs (Molecular Expressions of Work) - trackable atomic units following Gas Town's bead-based work model.
Research and plan a knowledge work task thoroughly before execution. Optimized for pharma/biotech clinical development and consulting.
Execute a knowledge work plan efficiently using specialized agents. Use after the research phase to systematically work through a plan.
Navigate organizational redesign for AI with a structured 13-skill toolkit that produces persistent artifacts in $HOME/.ai-first-kit/.
Critically review, score, compare, and rank one or more AI scientist outputs for biology, bioinformatics, computational life science, or adjacent research tasks.
Clinical-grade deep analysis of Apple Health export data. Parses the XML from iPhone's Health app export and produces a comprehensive clinical-quality health assessment report…
End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder…
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis.
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis.
Structure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor. Use this skill when: (1) Predicting protein complex structures, (2) Validating designed…
All-atom protein design using BoltzGen diffusion model. Use this skill when: (1) Need side-chain aware design from the start, (2) Designing around small molecules or ligands, (3)…
Structure prediction using Chai-1, a foundation model for molecular structure. Use this skill when: (1) Predicting protein-protein complex structures, (2) Validating designed…
Query ChEMBL database for bioactivity data on drug-like compounds. Use this skill when: (1) Finding compounds active against a protein target (target-based search), (2) Getting…
Clarifies a vague clinical or biomedical research idea into a structured, bounded, searchable, researchable, and testable question.
Generate clinical trial protocols for medical devices or drugs. This skill should be used when users say "Create a clinical trial protocol", "Generate protocol for [device/drug]",…
Generates complete cross-disease shared-biomarker bioinformatics research designs from a user-provided disease pair and validation direction.
Systematically maps mechanism evidence for a disease from molecules to pathways, cell types, tissues, biological consequences, and clinical phenotypes.
Analyze drug candidate molecules for drug-likeness, ADMET properties, and safety profiles. Use this skill when: (1) Evaluating a molecule's potential as a drug candidate, (2)…
Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology…
Run a structured organizational design health check — operationalizing the governance learning loop and decision ledger by collecting operational evidence, measuring gate…
Use this skill whenever the user wants reproducible CS/AI experiments, model evaluation, regression/classification/clustering analyses, bioinformatics workflows, QC, differential…
Generates complete FAERS-style pharmacovigilance disproportionality research designs from a user-provided drug class, comparator strategy, adverse-event domain, and patie — from…
Design and save a complete governance ecosystem for agentic operations — 6 structured documents (authority matrix, hard boundaries, escalation protocols, policy generation loop,…
Evidence-based medical knowledge and research mentor. Trigger this skill when users ask any question related to medicine, clinical science, pharmacology, pathology, epidemiology,…
Binder design ranking using ipSAE (interprotein Score from Aligned Errors). Use this skill when: (1) Ranking binder designs for experimental testing, (2) Filtering BindCraft or…
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR.
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR.
Ligand-aware protein sequence design using LigandMPNN. Use this skill when: (1) Designing sequences around small molecules, (2) Enzyme active site design, (3) Ligand binding…
Converts an audited medical research gap into a complete, structured, gap-traceable study design. Always use this skill whenever a user already has one or more candidate research…
A medical-research-native literature reading skill for users with clinical, bioinformatics, translational, and basic experimental backgrounds.
Maps whether a biomedical research topic, subtopic, or study angle is truly saturated, superficially crowded, strategically occupied, or still open for differentiated entry.
Generates complete Mendelian Randomization + single-cell transcriptomics (scRNA-seq) research designs from a user-provided direction.
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,…
Generates complete NHANES-style cross-sectional epidemiology + retrospective clinical validation research designs from a user-provided disease and biomarker direction.
Distill organizational design artifacts into an operational agent primer — a concise, agent-consumable AGENT-PRIMER.md encoding identity, values, boundaries, and quality standards…
Build and save a structured organizational genome — 7 markdown files across identity, decision architecture, and quality standards directories in $HOME/.ai-first-kit/ — that…
This skill should be used when the user asks to "create a packmol input", "pack molecules with packmol", "solvate a protein", "build an initial configuration", "setup molecular…
Query PubChem database for chemical structures, similar compounds, and bioactivity data. Use this skill when: (1) Converting drug name to molecular structure (SMILES, SDF), (2)…
Designs QTL colocalization studies that connect eQTL, pQTL, sQTL, or related molecular QTL signals with GWAS loci.
Designs complete single-cell research plans from a user-provided biomedical direction. Always use this skill whenever a user wants to design, scope, or structure a single — from…
Rapidly maps the evidence landscape around a medical topic by organizing major research streams, target populations, endpoints, methods, evidence density, and thin areas.
Extracts concrete unmet clinical needs from guidelines, reviews, real-world studies, and clinical-practice evidence.
Generate photorealistic rendering scripts for PyMOL and UCSF ChimeraX.
Assemble genomes/metagenomes and produce assembly QC artifacts.
Cluster proteins into orthogroups and derive pangenome matrices.
Preprint server API for biology and medicine papers
PNNL cheminformatics LLM agent for molecular analysis