Use when you have paired mass-spectrometry spectral data (m/z and intensity arrays) with known molecular fingerprints or InChIKeys, and need to train a supervised deep learning…
Performs comprehensive, multi-layered research on any topic with structured analysis and synthesis of information from multiple sources.
Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurizat — from…
Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurizat — from…
Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
Use when when you have a trained BitterPredict classifier, a dataset of molecules with computed descriptors and known bitter/not-bitter labels, and want to understand which…
Design an acoustic levitation system that uses standing waves to trap and suspend small objects at pressure nodes.
Use when when you have microarray or RNA-seq expression data paired with phenotype/sample metadata describing experimental conditions, treatments, or group assignments, and you…
Use when targeting Developmental Cell or deciding whether a developmental or cell-biology manuscript fits this venue.
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design.
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design.
Diffusion-based molecular docking to predict 3D ligand–protein binding poses (blind docking) with confidence scoring; use when you need pose prediction for drug discovery or…
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design.
Use when you have fitted a linear model to gene expression data (microarray, RNA-seq, qPCR, or proteomics) across multiple samples and need to compute gene-level test statistics.
Use when when you have a collection of DNA adduct compound structures in SDF format that requires validation for structural integrity and completeness, and you need to generate…
Use when you have raw .idat files or beta-valued matrices from Illumina HumanMethylation450 (450K) or EPIC array experiments and need to import them into R for quality control and…
Use when you have loaded a raw GCIMS dataset and need to isolate the region of interest in drift time (typically 5–16 ms for small organic molecules) to exclude low-drift-time…
Pharmaceutical research assistant for drug discovery workflows. Search bioactive compounds on ChEMBL, calculate drug-likeness (Lipinski Ro5, QED, TPSA, synthetic accessibility),…
Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test framework, creating DGEList — from…
Molecular Electrostatics (dipole + partial charges) — When the user wants the dipole moment, atomic partial charges (Mulliken), or general electrostatic-character information…
Shared author-guideline skill for Elsevier food-science journals (Trends in Food Science & Technology, Food Hydrocolloids, LWT, Food Research International, Food Control, Meat…
Use when after a CNN model has generated predicted molecular embeddings from mass spectrometry data, and you need to identify the most likely candidate molecules from a r — from…
Use when you have a fitted linear model (lmFit object) from microarray or RNA-seq count data and need to compute stable variance estimates and differential expression sta — from…
Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines — from…
Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines — from…
Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines — from…
ENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types.
Use when after cloning or installing a peak-calling or genomic analysis tool from a repository, before using it on production data.
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic — from…
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic — from…
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic — from…
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic — from…
Computes DNA methylation age (DNAm age) and pace of aging by applying frozen elastic-net epigenetic clocks to a clean beta matrix with methylclock, dnaMethyAge, or methyl — from…
Use when you have predicted retention times from one or more machine learning models (DNN, Gaussian Process, or ensemble) applied to small-molecule chromatography data, along with…
Protein language models (ESM3, ESM C) for sequence generation, structure prediction, inverse folding, and embeddings.
Use when finalizing market research report appendix C (参考文献清单) before delivery; Use when verifying evidence/ folder PMID coverage matches the report's reference list; Use when…
Generate comprehensive, dense, exam-ready cheat sheets in DOCX or LaTeX/PDF format from lecture slides, textbook chapters, course PDFs, or notes.
Designing, running, and interpreting controlled experiments to decide whether a change is genuinely better — online A/B tests, randomized controlled trials, and offline hypothesis…
Creates beautiful, protein-focused weekly dinner menus for families with research capabilities. Generates printer-ready PDFs (8.5x11) with random design styles, identifies…
Use when after peak picking and sample alignment have produced an aligned feature table with m/z and retention time coordinates.
Counts RNA-seq reads overlapping GTF gene features. Takes sorted STAR BAMs plus GTF; outputs a per-gene tab-delimited matrix across samples.
Established figure and table patterns for ML / computational biology papers. Loaded by writing-brainstormer to ground figure suggestions in conventional patterns rather than…
Use when after RDKit generates multiple 3D conformers from ionized molecular structures using distance-geometry embedding, before filtering with ASE-ANI or submitting to quantum…
Use when when training or validating a deep learning model for molecular formula prediction from tandem MS/MS spectra, use this metric to track whether the model's predicted…
Author TOML-based Formula workflow templates that become Protomolecules and active Molecules in Gas Town's durable workflow system.
Use when you have calibrated m/z peak lists, configured adduct transformations (e.g., [M+H]+, [M+Na]+, [M-H]−), and need to annotate peaks with molecular formulae from KEGG,…
Use when when you have loaded a chemical database (e.g., HMDB pickle file) and need to understand how many distinct molecular formulas remain after filtering for a specific m/z…
Use when you have an observed m/z value from spatially-resolved mass spectrometry imaging and need to assign one or more plausible molecular formulae with confidence metrics.
Personalized cancer treatment navigation — maximal diagnostics, parallel therapy, therapeutic development, structure-based protein design.
Use when you have a collection of molecular fragments (e.g., from molecular decomposition, retrosynthesis, or synthetic planning) that must be matched to known fragment libraries…
Use when you have a tandem MS/MS spectrum of a structurally modified compound and a known reference structure (SMILES), and you need to annotate which fragment ions correspond to…
Use when you have tandem mass spectra for compounds with known binary or categorical molecular properties (e.
Use when code imports `freud` or `freud-analysis`, or user asks to analyze molecular simulation trajectories (RDF, MSD, order parameters, structure factor, PMFT, Voronoi,…
Use when you have received raw FT-ICR transient data from Bruker Solarix or ThermoFisher instruments and need to perform signal processing, apodization, calibration, or molecular…
Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundances from ASV tables.
Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from met — from…
Use when when you have abundance-normalized FT-ICR MS peak data with assigned molecular formulas and need to distinguish between richness (total number of distinct metabolites)…
Use when when you have experimental MS/MS spectra and want to discover structurally similar compounds beyond exact spectral library matches—particularly useful for identifying…
Galaxy tool discovery, intelligent recommendation, and execution — 8,000+ bioinformatics tools from usegalaxy.org with multi-signal scoring and workflow suggestions