Formal game theory for advisory file claims and repeated agent interactions. Analyze Nash equilibria in claim signaling games, apply the folk theorem to sustain cooperation under…
High school exam (Gaokao) AI tutor for Chinese students. Covers all subjects (Math, Chinese, English, Physics, Chemistry, Biology, History, Geography, Politi...
Manage multi-agent orchestrator for Claude Code. Use when user mentions gastown, gas town, gt commands, bd commands, convoys, polecats, crew, rigs, slinging work, multi-a — from…
Manage multi-agent orchestrator for Claude Code. Use when user mentions gastown, gas town, gt commands, bd commands, convoys, polecats, crew, rigs, slinging work, multi-a — from…
Use when when you have deconvolved GC-MS spectra (post-deconvolution output compatible with GNPS_GC input specification) and need to group them by chemical similarity to construct…
Use when building figures, tables, and the mandatory graphical abstract for a Global Change Biology (GCB) manuscript.
Use when preparing the data availability statement and the data/code archive for a Global Change Biology (GCB) manuscript.
Use when writing the response to a Global Change Biology (GCB) revise decision. A revision must address every reviewer point with evidence, defend the global-change mechanism and…
Use when designing the study behind a Global Change Biology (GCB) manuscript — manipulative experiments, observational/gradient studies, or process modelling of biological…
Use when deciding whether a research idea fits Global Change Biology (GCB) and how to frame its significance.
Use when drafting or polishing the prose of a Global Change Biology (GCB) manuscript so it reads for a broad ecology / biogeochemistry / Earth-system audience within the journal's…
Use when input GC-MS data (netCDF or mzML format) exhibits overlapping chromatographic peaks where multiple analytes co-elute at the same retention time, resulting in composite…
Use when you have antiSMASH v5.0.0 BGC predictions from a set of microbial genomes and you need to integrate those predictions with GNPS metabolomic data (MS2 spectra and…
Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annota — from…
Generates complete phenotype-scoring bioinformatics research designs for any disease context and any user-defined phenotype, pathway, process, signature, or molecular pro — from…
Use when you have raw Hi-C FASTQ files from a kilobase-resolution Hi-C experiment and need to produce a processed Hi-C contact map (.hic file) for visualization, loop calling, or…
Анализирует генетические данные пользователя из VCF файла. Используй когда пользователь спрашивает о своей генетике, наследственных признаках, предрасположенностях, метаболизме…
Use when when running metabologenomic RiPP detection pipelines (MetaMiner) on the same genomic dataset but with different input sequence formats (e.g., contigs.fasta vs.
基因组组装、注释和比较基因组 workflow skill。用于 short-read/long-read/HiFi assembly、polishing、scaffolding、BUSCO、contamination、Prokka、eukaryotic gene prediction、repeat/ncRNA/functional…
End-to-end genome assembly workflow from reads to polished assembly with QC. Supports short reads (SPAdes), long reads (Flye), and hybrid approaches.
Use when targeting Genome Biology or deciding whether a genomics or computational biology manuscript fits this venue.
Generate genome browser visualizations using pyGenomeTracks or IGV batch scripting for publication figures.
Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture
Use when a paired omics project JSON document contains genome identifiers (e.g. IMG IDs, NCBI accessions) but lacks corresponding organism names.
OneScience Evo2 基因组语言模型 skill。用于 Evo2 训练、推理、微调、长序列 DNA token、OpenGenome2 数据、FASTA/JSON 预处理、NeMo/Megatron batch、checkpoint 转换、variant effect 和 genome design 任务。
Use when you have filtered peak or chromatin accessibility counts and need to annotate each peak with the presence or absence of specific DNA sequence patterns—either predefined…
Use when you have assembled genomic DNA sequences (contigs in FASTA format, not antiSMASH or BOA output) and corresponding LC-MS/MS data (in MGF, mzXML, mzML, or mzData format)…
Create genome browser-style visualizations showing multiple data tracks (coverage, peaks, genes) using pyGenomeTracks, Gviz, and IGV.
Patterns for building robust, reproducible genomics analysis pipelines. Covers workflow managers, NGS data processing, variant calling, RNA-seq, and common bioinformatics…
Bengio's GFlowNets: Generative Flow Networks that sample proportionally to reward. Diversity over maximization for causal discovery and molecule design.
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis.
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis.
CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr,…
Use when you have a pre-trained GNN model checkpoint, a test dataset with molecular representations (SMILES, 3D coordinates, adducts) and ground-truth labels, and need to quantify…
Query the Genome Aggregation Database (gnomAD). Use when determining the rarity or allele frequency of specific genetic variants, retrieving gene constraint metrics (pLI, LOEUF)…
Use when you have extracted MS1 and MS2 scans (in mzML/mzXML format) from raw chromatogram files and possess user-provided metadata (retention time, m/z, compound name, m — from…
Use when you have computed frequent fragmentation patterns from a collection of MS/MS spectra using mineMS2, and you want to focus pattern interpretation on subsets of spectra…
Use when you have downloaded a GNPS archive from either GNPS1 (https://gnps.ucsd.edu) — from HolobiomicsLab/asb-skill-collections
Use when you have generated a GNPS mass spectral molecular network (in classical or feature-based mode) and want to annotate network nodes with substructural motifs from MS2LDA or…
Use when you have a trained graph neural network model for CCS prediction and need to identify which molecular structural features drive individual predictions or systematic…
Use when you have a collection of MS/MS spectra (stored as Spectrum2 objects in an ms2Lib class) and need to identify which spectra share identical fragmentation…
Use when you have spatial molecular data (e.g., coordinates from microscopy or sequencing assays stored in an AnnData object), you need to compute a k-nearest-neighbor graph for…
Use when you have a GNPS mass spectral molecular network and wish to annotate its nodes with both chemical class assignments (from GNPS public library matches) and MS2LDA-derived…
Use when you have molecular structures (SMILES or SDF format) that need to be matched against MS/MS spectra, or you need to compute similarity between query spectra and a…
Design guide RNAs for CRISPR-Cas9/Cas12a experiments using CRISPRscan and local scoring algorithms. Score guides for on-target activity using Rule Set 2 and Azimuth model — from…
Use when working on biomolecular molecular dynamics with GROMACS, including system setup, equilibration, production runs, trajectory analysis, or MM/PBSA-style post-processing.
Parse, query, and convert GTF and GFF3 annotation files. Extract gene, transcript, and exon coordinates using gffread, gtfparse, and gffutils.
End-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and association testing for case-control or quantitative trait — from…
Harmony batch correction for scRNA-seq and other omics. Removes batch effects from PCA embeddings while preserving biology. Run after PCA, before UMAP.
Résume prudemment des articles, recommandations ou contenus médicaux. À utiliser quand l'utilisateur demande une synthèse scientifique, une revue rapide, ou veut comprend — from…
Build, evaluate, and document per-measure HEDIS extraction pipelines (NLP engineering, not chart review).
Use when when building a Graph Transformer model for continuous property prediction on molecules with associated experimental or instrumental metadata (e.g., retention time…
Detect horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath- — from…
Use when you have a cooler file (.cool or .mcool) from a Hi-C experiment and need to generate a genome-wide track of per-bin sequencing depth to assess coverage uniformity,…
Use when you have a cooler-format Hi-C contact matrix and need to establish a genome-wide baseline contact frequency by genomic distance.
Use when immediately after parsing and validating raw LC-MS/MS data files (mzML, mzXML, or vendor formats) when you need to prepare spectral data for fragmentation tree…
Use when you have high-resolution MS2 data in .ms2 format from lipid A samples and need to perform automated structure annotation to identify lipid A molecular variants and their…
Use when when you need to establish a reproducible inventory of compounds for LC-MS/MS simulation studies, particularly to determine how many unique molecular formulas fall within…
De novo and known TF motif enrichment in ChIP-seq/ATAC-seq peaks via HOMER. findMotifsGenome.pl finds over-represented patterns vs background; annotatePeaks.pl assigns context…
Use when when you have raw strain correlation scores (or similar overlap-based metrics) computed across genomic cluster family (GCF) and molecular family (MF) pairs of varying…