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
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…
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…
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…
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
Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers.
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.
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,…
Genomic interval ops on BED/BAM/GFF/VCF. Find overlaps, merge intervals, compute coverage, extract FASTA, find nearest features.
Biological foundations of behavior and mental processes. Covers brain structure and function (cerebral cortex, limbic system, brainstem, cerebellum, lateralization),…
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data m — from…
Evidence-based medical knowledge and research mentor grounded in the Bian Que tradition. Covers clinical reasoning, diagnostic thinking (望闻问切), pharmacology, pathology,…
Create and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC — from…
Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program…
Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package.
Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-step / MVMR mediation, or…
Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data.
Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective…
Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks.
Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R…
Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded…
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 borrowing,…
Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, Boschloo, Cochran-Mantel-Haenszel, and modern McNemar variants with calibrated…
Reads, validates, and prepares CDISC SDTM and ADaM clinical trial data for analysis. Covers SDTM domain joins (DM, AE, EX, VS, LB, DS), ADaM architecture (ADSL, BDS, OCCDS, ADTTE)…
Computes and interprets treatment effect measures (OR, RR, RD, HR, NNT) with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen, MOVER, profile likelihood,…
Performs logistic regression for clinical trial outcomes (binary, ordinal, multinomial) with marginal-vs-conditional estimand reporting per FDA 2023 covariate adjustment guidance,…
Implements missing-data sensitivity analyses for confirmatory clinical trials including MMRM under MAR (with Kenward-Roger correction), reference-based multiple imputation (J2R,…
Implements multiplicity control for confirmatory clinical trials using graphical procedures (Bretz-Maurer-Hommel), gatekeeping (parallel, serial, mixed), Hochberg/Hommel/Holm with…
Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints; superiority, non-inferiority, and equivalence designs; FDA 2016…
Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RERI for…
Performs time-to-event analysis for clinical trials including Cox proportional hazards regression with PH diagnostics, restricted mean survival time (RMST) under non-PH, competing…