PyTorch-native Graph Neural Network framework for molecules and proteins. Suitable for building custom GNN architectures for drug discovery, protein modeling, or knowledge graph…
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…
Use when you have collected liquid chromatography (LC) spectra and retention time labels for your in-house molecular database, and you want to leverage a pretrained GNN-RT model…
Use when you have raw or processed arrival-time data from a TWIM-MS instrument and need to convert it to CCS values for comparison across experiments or biomolecular classes.
Use when you have TWIM-MS data (arrival time and m/z values) from a multi-omic sample and need to: (1) establish a CCS calibration curve from known standards, (2) assign…
Query UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies.
Atomic-design guidance for Molecules — functional groups of atoms (SearchBar = input + button + icon; FormField = label + input + error) with a single cohesive purpose.
This pipeline performs genome-wide segmentation of CpG methylation profiles to identify Unmethylated Regions (UMRs), Low-Methylated Regions (LMRs), and Partially Methylat — from…
Use when when you have parallel mass spectra and molecular structure data (e.g., CANOPUS or MassSpecGym datasets) and aim to train a single encoder-decoder model (e.g., BART) that…
Use when when you have a ranked list of GCF-MF (genomic cluster family–molecular feature) link predictions from one or more scoring functions, a curated set of known validated…
Use when when you have scored GCF-MF (gene cluster family–molecular family) links using two or more complementary scoring approaches (e.g., standardised strain correlation and…
变异与区间文件处理 skill。用于 VCF/BCF、BED、GFF/GTF、interval_list、peak、DMR、loop、genomic ranges 的过滤、合并、交集、注释、坐标系转换和 genome build 一致性检查。
Search PubMed with veterinary-specific filters and MeSH terms to find relevant animal health research. Handles the sparse, multi-species nature of veterinary literature.
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…
Waddington's epigenetic landscape: cell fate as gradient flow on potential surfaces, connecting developmental biology to dynamical systems, Schrödinger bridges, and fractional…
Use when when you have a parsed mass spectrum (precursor m/z, ionization mode, collision energy, and fragment peak list as m/z–intensity pairs) and need to obtain molecular…
Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (U — from…
Use when when you have pre-processed MS/MS spectra and a pre-trained Word2Vec model, and need to compute fast, scalable similarity scores for library matching or molecular…
Use when when comparing large numbers of MS/MS spectra against spectral libraries or in molecular networking, particularly when molecules differ by multiple structural…
Use when when applying a pre-trained Word2Vec model to mass spectra at inference time (e.g., library matching or molecular networking), especially when the query spectra may…
Decompose goals into MEOWs (Molecular Expressions of Work) - trackable atomic units following Gas Town's bead-based work model.
Use when when you have a multi-step computational chemistry or molecular modeling pipeline (3+ sequential or parallel stages) that must process many molecules, each requiring…
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.
Use when interacting with a ZnDraw molecular visualization server — reading frames, navigating trajectories, selecting atoms, bookmarking, creating plots, running extensions, or…
How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval.
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.
Convert between .h5ad (AnnData) files and R single-cell data formats (Seurat, SingleCellExperiment) using anndataR.
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 bi — from…
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 bi — from…
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.
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.
Use this skill for MolMIM, NVIDIA's BioNeMo NIM microservice for small-molecule latent-space generation and optimization.
Use this skill for OpenFold3, NVIDIA's BioNeMo NIM microservice for biomolecular structure prediction.
Structure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor. Use this skill when: (1) Predicting protein complex structures, (2) Validating desig — from…
Structure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor. Use this skill when: (1) Predicting protein complex structures, (2) Validating desig — from…
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 liga — from…
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 liga — from…
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 liga — from…
Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi. Use this skill when: (1) Scoring the regulatory effect of a variant on…
Structure prediction using Chai-1, a foundation model for molecular structure. Use this skill when: (1) Predicting protein-protein complex structures, (2) Validating desi — from…
Structure prediction using Chai-1, a foundation model for molecular structure. Use this skill when: (1) Predicting protein-protein complex structures, (2) Validating desi — from…
Structure prediction for protein, nucleic-acid, and small-molecule complexes with the Chai-1 foundation model (Chai Discovery 2024, github.com/chaidiscovery/chai-lab).
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…
Performs ChIP-specific biological validation. It calculates metrics unique to protein-binding assays, such as Cross-correlation (NSC/RSC) and FRiP.
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]",…
Builds the full component hierarchy from the raw design tree — mapping Figma components to atoms, molecules, and sections.
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.
Extract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyze how someone thinks, understand cognitive style, profile — from…
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 pharmaco — from…
This skill should be used when the user asks about "Elnora agent capabilities", "what can the agent do", "agent tools", "web search", "academic search", "PubMed", "ArXiv", "Exa",…
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…