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.
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…
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…
This skill should be used when working with genomic interval data (BED files) for machine learning tasks.
This skill performs genome-wide DNA methylation profiling. It supports single-sample and multi-sample workflows to compute methylation density distributions, genomic feature…
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.
Use when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate, genomics, materials, medicine, ecology, energy, engineering,…
Binder design ranking using ipSAE (interprotein Score from Aligned Errors). Use this skill when: (1) Ranking binder designs for experimental testing, (2) Filtering BindCr — from…
Binder design ranking using ipSAE (interprotein Score from Aligned Errors). Use this skill when: (1) Ranking binder designs for experimental testing, (2) Filtering BindCr — from…
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 bind — from…
Ligand-aware protein sequence design using LigandMPNN. Use this skill when: (1) Designing sequences around small molecules, (2) Enzyme active site design, (3) Ligand bind — from…
Analyze biological data using Lobster AI — single-cell RNA-seq, bulk RNA-seq, literature mining, dataset discovery, quality control, and visualization.
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.