LAMMPS molecular dynamics skill for nanoscale system simulation with force field management
LAMMPS molecular dynamics simulation skill for atomistic simulations, force field setup, and large-scale parallel computations
Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser.
Write comprehensive literature reviews for medical imaging AI research. Use when writing survey papers, systematic reviews, or literature analyses on topics like segmentation,…
AI-powered molecular glue discovery for targeted protein degradation, enabling neo-substrate recruitment and undruggable target degradation through E3 ligase interface modulation.
Ultra-sensitive AI-powered molecular residual disease detection using MRD-EDGE deep learning for sub-0.001% VAF ctDNA detection and early relapse prediction.
Time-of-Flight Secondary Ion Mass Spectrometry skill for molecular surface analysis and imaging
AI-powered ternary complex prediction for targeted protein degradation, modeling POI-degrader-E3 ligase assemblies to optimize PROTAC and molecular glue efficacy.
UCSC Genome Browser query skill for genome annotation retrieval and track data access
Compare Figma design system components against the Breeze design graph component registry. First builds existingcomponents.json by iteratively fetching all Component nodes from…
Run eggNOG-mapper on genome protein FASTA files to generate functional annotations (COG, GO, KEGG, EC, PFAMs).
Run `@metaharness/darwin evolve ` to mutate a harness's seven policy surfaces (planner/contextBuilder/reviewer/retryPolicy/toolPolicy/memoryPolicy/scorePolicy),…
7-section repo readiness report from `metaharness genome
`. Returns repo_type / agent_topology / risk_score / mcp_surface / test_confidence / publish_readiness.
Run a GEPA learning cycle via `metaharness learn` (upstream ADR-235,
[email protected]) — optimizes a harness genome against a SWE-bench-style slice manifest.
ADR-152 — weighted similarity between two harness fingerprints (genome + score JSON). Returns overall score in [0,1] plus per-component breakdown (cosine over 9 numerics,…
Research scientific papers from the last 30 days across OpenAlex, Semantic Scholar, PubMed, arXiv, and HuggingFace
Genome in a Bottle benchmark validation skill for pipeline accuracy assessment
IGV integration skill for interactive genome visualization and review
MEGAHIT metagenomic assembly skill for reconstructing genomes from short reads
Nextflow workflow management skill for reproducible bioinformatics pipelines
Molecular Hamiltonian construction skill using OpenFermion
PyMOL molecular visualization skill for structure rendering and analysis
This pipeline performs genome-wide segmentation of CpG methylation profiles to identify Unmethylated Regions (UMRs), Low-Methylated Regions (LMRs), and Partially Methylated…
Use when after running inference on a trained structure prediction model with one or more input modalities (1H NMR, 13C NMR, or combined), you have generated predicted molecular…
Use when after peak detection and MS1 feature extraction from FIA-MS, GC-MS, LC-MS(/MS), or CE-MS data, when you need to identify unknown metabolites by matching observed m/z…
Use when you have preprocessed metabolite intensity data (log2-transformed, zero-mean unit-variance standardized) mapped to compound annotations, and you need to derive activity…
Use when after computing PLAGE-derived activity scores for pathways or metabolite sets (Molecular Families, Mass2Motifs) from log2-standardized metabolomics intensity data.
Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded Cu — from…
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expressi — from…
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expressi — from…
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expressi — from…
表面への分子吸着を扱うスキルです。 吸着エネルギー, adsorption energy, 吸着構造, adsorption structure, 吸着サイト探索, adsorption site search, add_adsorbate, ontop, bridge, fcc, hcp, 吸着サイト, slab+molecule, FixAtoms,…
Drafts an Adverse Event Reporting Policy compliant with 21 CFR 312.32 (IND safety reporting), 21 CFR 314.80 (postmarketing), and ICH E2A, with multi-jurisdictional overlays (EMA,…
Agente especialista em Biologia para FUVEST — 1ª fase. Biologia tem presença consistente nas 90 questões objetivas, especialmente Genética e Ecologia, que são os tópicos favoritos…
Use when when you need to evaluate how a specific algorithm parameter (such as SearchMolecularFormulas first_hit mode) affects the quantity and quality of molecular formula…
Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery…
Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery…
Access AlphaFold DB's 200M+ predicted structures by UniProt ID. Download PDB/mmCIF, analyze pLDDT/PAE, bulk-fetch proteomes via Google Cloud.
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants.
Detect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context.
Analyze a tensegrity system by identifying compression struts and tension cables, classifying type (class 1/2, biological/architectural), computing prestress equilibrium,…
Structures clinical data warehouse queries for quality measurement, research, and operational analytics.
Structures clinical trial data analysis with primary endpoint evaluation and safety reporting. Use when analyzing trial results, evaluating endpoints, or preparing statistical…
Search arXiv preprint repository for papers in physics, mathematics, computer science, quantitative biology, and related fields. — from langchain-ai/deepagentsjs
Search arXiv preprint repository for papers in physics, mathematics, computer science, quantitative biology, and related fields — from bg-szy/TOP-SKILLS
ASE (Atomic Simulation Environment) の基礎操作を扱うスキルです。 Atoms オブジェクトの生成・編集、ase.build.molecule, ase.build.bulk, repeat, supercell, PBC (periodic boundary conditions), cell, positions,…
Polish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka).
Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers.
Use when you have a batch of mass spectra records in .msp format that lack standardized metadata fields (SMILES, InChI, CAS numbers, molecular formula, IUPAC names) and need to…
Interact with atomCAD node networks programmatically. Query, edit, and replace CAD geometry nodes for atomic/molecular structure design.
Atomic Design methodology for React component architecture. Use for structuring component libraries, organizing UI hierarchies, and creating scalable design systems.
Expert Atomic Design decisions for iOS/tvOS: when component hierarchy adds value vs overkill, atom vs molecule boundary judgment, design token management trade-offs, and component…
Molecular docking with AutoDock Vina (Python API). Receptor/ligand prep (Meeko + RDKit), grid box, docking, pose and binding energy analysis, and batch virtual screening.
Use when you have high-resolution tandem mass spectrometry (MS2) data in .ms2 format and need to systematically identify and annotate lipid A molecular structures.
Annotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. Identifies CDS, ncRNA, tRNA, rRNA, tmRNA, sORFs, CRISPR arrays, oriC/oriV/oriT,…
Use when you have a coordinate-sorted BAM file from a single-cell ATAC-seq experiment (especially 10X Genomics platforms) and need to extract per-fragment information including…
Use when when you have a trained molecular classifier (like BitterPredict) that accepts structured descriptor input, and you need to understand which chemical descriptor subgroups…
Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtures for external data bo — from…
Use when you have extracted quantitative genomic features (e.g., insulation scores, boundary annotations) as a pandas DataFrame with bin coordinates and boolean or numeric…