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 — from…
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 — from…
Use when targeting Global Change Biology or deciding whether a biology/ecology manuscript fits this venue.
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…
Use when you receive mass spectrometry data through heterogeneous identifier formats—specifically when the input could be a GNPS Task ID, a Universal Spectrum Identifier (USI), or…
Use when you have experimental MS/MS spectra and need to assign definitive molecular identities by matching against a curated spectral library.
Use when user requests medical/pharmaceutical market sizing, Chinese clinical pathway reconstruction, patient flow waterfall charts, drug usage composition analysis, unmet need…
Implement a generative diffusion model (DDPM or score-based) with noise scheduling, U-Net architecture, training loop, and sampling procedures including DDIM acceleration.
Use when augmenting mass spectrometry ion images in ISO mode (isotope ions from the same molecule) and you need to simulate intensity-dependent data loss that reflects real…
Use when when you have loaded aligned peak data (from a preceding molecular networking alignment task) as a structured table with peak intensity, m/z, retention time, and…
Systematically interpret nuclear magnetic resonance spectra (1H, 13C, DEPT, and 2D experiments) to elucidate molecular structure.
Structures microbiology result interpretation with susceptibility patterns and resistance mechanisms.
Structures molecular test interpretation including NGS panels, FISH, and PCR-based assays. Use when interpreting molecular results, reporting genetic variants, or documenting…
Identify domains, families, and sites in proteins; find all proteins in a family or sharing a domain; explore species distribution for a domain; annotate genomes with protein…
Use when when preparing ion image data from mass spectrometry imaging for contrastive self-supervised representation learning, and you need to generate augmented image pairs that…
Use when training a contrastive encoder on mass spectrometry imaging (MSI) data in ISO mode (isotope ions from the same molecule).
Use when you have TWIM-MS experimental data with assigned biomolecular class labels (e.g., peptides, lipids, carbohydrates) and arrival time measurements, and you need to compute…
Use when you have a curated dataset of molecular structures (or molecular descriptors) paired with experimentally measured or reference collision cross section values, and you…
Use when when you have SMILES strings representing neutral organic molecules and need to enumerate the likely protonated (e.g., [M+H]+) and deprotonated (e.
Designs and analyzes stable-isotope-resolved metabolomics (SIRM / isotope tracing / fluxomics) experiments that measure metabolic ACTIVITY via 13C/15N/2H tracers, distinc — from…
Use when targeting JAMA Neurology or deciding whether a clinical-neurology study fits this venue. Encodes the journal's fit, the neurological-trial and observational evidence bar,…
Use when targeting JAMA Oncology or deciding whether a clinical-oncology study fits this venue. Encodes the journal's fit, the cancer-trial and outcomes-research evidence bar,…
Use when targeting JAMA Psychiatry or deciding whether a clinical-psychiatry or mental-health study fits this venue.