Generates complete cross-disease shared-biomarker bioinformatics research designs from a user-provided disease pair and validation direction.
Use when when you have calculated molecular descriptors from validated chemical structures and need to prepare them for BitterPredict.m classification.
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…
Biohub ESMFold2 / ESMFold2-Fast all-atom co-folding (Candido et al. 2026, github.com/Biohub/esm). Single-sequence and MSA modes; protein, DNA, RNA, ligand (CCD/SMILES), modified…
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…
Use when your project JSON document contains genome identifiers but lacks organism name or taxonomic annotations.
Generates complete FAERS-style pharmacovigilance disproportionality research designs from a user-provided drug class, comparator strategy, adverse-event domain, and patie — from…
Full Protein Characterization - Complete protein characterization: validate sequence, compute all properties, predict structure, and analyze pockets.
Use when you have a gene expression matrix (RNA-seq counts, microarray intensities, or normalized expression values) and need to perform gene set enrichment analysis on preranked…
Design and save a complete governance ecosystem for agentic operations — 6 structured documents (authority matrix, hard boundaries, escalation protocols, policy generation loop,…
Use for any task involving the HDMA (Human Development Multiomic Atlas) repository — using its data (fragments, count matrices, Seurat/ArchR/BPCells objects, ChromBPNet models,…
Use when you have a cooler-format Hi-C contact matrix and need to identify TAD boundaries and insulation strength along the genome.
Evidence-based medical knowledge and research mentor. Trigger this skill when users ask any question related to medicine, clinical science, pharmacology, pathology, epidemiology,…
Use when when you have raw HPLC column specifications from RepoRT or similar metadata repositories and need to prepare them as input features for machine learning models.
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.
LAMMPS molecular dynamics with DeepMD/DPA machine-learning potentials ONLY. This skill generates LAMMPS input files (in.lammps) using pair_style deepmd.
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…
Use when after molecular formula assignment has been performed on calibrated m/z values. Apply this skill when you need to quantify the accuracy of formula-to-peak matching,…
Guide for writing Python code using Matlantis, PFN's cloud-based atomistic simulation platform powered by neural network potentials (PFP).
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.
Microbiome Genomics Analysis - Analyze microbial genome: NCBI genome data, taxonomy, KEGG metabolic pathways, and annotation.
Use when when you have molecular structures (SMILES or graph formats) and need to predict a physicochemical or spectral property (e.g., infrared spectra) using a graph neural…
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.
中国药品权威数据库查询 — NMPA(国家药监局) + CDE(药品审评中心) + DrugBank(英文名/ATC) + PubChem(化学结构) 多源融合,提供(通用名 ↔ 商品名 ↔ 英文名 ↔ 适应症 ↔ NMPA 批文号 ↔ 上市日期)精确映射。Make sure to use this skill whenever the user…
Use this skill for "search for papers", "find citations", "look up a DOI", "get BibTeX", "download PDF", "convert PDF to markdown", "find canonical papers", "convert identifiers",…
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…
Pharmacokinetics Profile Builder - Build a PK profile: FDA pharmacokinetics, clinical pharmacology, dosage info, and molecular properties.
Find open PhD positions, funded studentships, fellowships, or labs actively recruiting students that match the applicant's profile.
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)…
Search PubMed and retrieve structured biomedical literature with PMID lists, abstracts, MeSH terms, publication types, and PMC IDs for full-text access.
Designs QTL colocalization studies that connect eQTL, pQTL, sQTL, or related molecular QTL signals with GWAS loci.
Use when after a CNN model has generated predicted molecular embeddings from mass spectrometry data, use this skill to match those predictions against a curated reference — from…
Use when when you need to confirm that a documented web service endpoint is deployed and accessible before using it for analysis, or when troubleshooting tool availability in a…
Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology.
Enforce evidence-based responses for any science-related discussion. Use this skill whenever the conversation involves ANY scientific topic — including but not limited to physics,…
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis.
Use when after computing pairwise similarity scores across a collection of preprocessed mass spectra using matchms similarity measures (Cosine-related, molecular…
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…
Use when you have an ArchR project with clustered single-cell ATAC-seq cells and want to reconstruct developmental or cellular transition trajectories.
Use when when you have SMILES structures of small organic molecules and need to predict CCS values for metabolite annotation in untargeted mass spectrometry workflows.
Use when after identifying candidate parent–adduct mass-difference pairs (via massdiff, histogram binning, and adductMatch), apply this skill to discriminate true molecular…
Use when after computing pairwise similarity scores between query molecular embeddings and a reference database, apply this skill when you need to distinguish high-confidence…
Use this skill when working with scientific research tools and workflows across bioinformatics, cheminformatics, genomics, structural biology, proteomics, and drug discovery.
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