Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological — from…
Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep lear — from…
Graph-based drug discovery toolkit. Molecular property prediction (ADMET), protein modeling, knowledge graph reasoning, molecular generation, retrosynthesis, GNNs (GIN, G — from…
Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelin — from…
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological — from…
Use for scientific or scholarly research with source traceability, literature reviews, paper discovery, arXiv/OpenAlex/Crossref/Europe PMC/Semantic Scholar/PubMed queries, corpus…
Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or mul — from…
Comprehensive scientific research toolkit with 139 specialized skills for biology, chemistry, medicine, data science, and computational research.
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for system — from…
PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reaso — from…
Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or mul — from…
Search academic paper databases (PubMed, arXiv, bioRxiv) and retrieve paper metadata including DOIs
Use when before executing a bioinformatics pipeline that depends on multiple R packages with strict version constraints (e.g., DaDIA, which requires R ≥4.0, XCMS ≥3.11.4, and…
北师大版高中生物同步 Skill是面向课前预习、课后作业、同步巩固、单元复习、错题巩固、期中期末复习、高考复习的产品级 Hermes Skill，年级、册别、单元、知识点和难度通过参数传入。 Workflow: senior_biology_bs_textbook_sync.run.
高中生物快速巩固 Skill是面向每日打卡、同步巩固的产品级 Hermes Skill，年级、册别、单元、知识点和难度通过参数传入。 Workflow: senior_biology_quick_practice.run.
人教版高中生物同步 Skill是面向课前预习、课后作业、同步巩固、单元复习、错题巩固、期中期末复习、高考复习的产品级 Hermes Skill，年级、册别、单元、知识点和难度通过参数传入。 Workflow: senior_biology_rj_textbook_sync.run.
Use when after computing activity scores for a collection of metabolite sets (pathways, GNPS Molecular Families, or MS2LDA Mass2Motifs) from intensity and annotation data.
Autonomous pipeline monitor using sense-think-act loop. Watches snakemake/nextflow jobs, detects errors, applies fixes from memory, restarts on failure.
Use when you have a collection of cleaned MS/MS spectra (in formats like mzML, mgf, msp, mzxml, or json) and need to predict molecular structural similarities between spectrum…
Use when after training contrastive embeddings that unify MS/MS spectra and molecular structures into a shared embedding space.
Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymm — from…
Use when you have aligned single-cell ATAC-seq data as BAM files or fragment files (TSV format with genomic coordinates) and need to prepare it for spectral embedding, clustering,…
Use when after loading fragment counts into a SummarizedExperiment object (e.g., via getCounts) but before motif matching or deviation computation.
Qualify a single-cell Perturb-seq screen's no-phenotype calls with karyon — flag perturbations called "no effect" where the guide never actually knocked the target down (a silent…
Use when when you have processed LC-MS/MS data with precursor m/z, ionization mode, collision energy (if available), and fragment peak lists (m/z and intensity pairs), and need to…
Biología Celular — Estructura celular, genética, evolución, ecología y división celular para nivel secundaria/bachillerato/1º universidad.
Use when when you have ionized adduct structures (SMILES or MOL format) from a prior ionization-state determination step and need to create multiple low-energy 3D conformations…
Use when when you have a set of small molecule structures (as SMILES or molecular graphs) and need to predict their elution order in RPLC systems with eluent pH around 2.
Use when you have observed compounds (from LC-MS, GC-MS, or spectroscopy) and a set of predicted metabolite structures from BioTransformer, and need to assign identities to the…
Use when you have SMILES strings for candidate novel psychoactive substance structures and need to convert them into a machine-readable molecular representation before computing…
Use when when you have a dataset of molecular structures encoded as SMILES strings that will be processed downstream (e.
Use when you have raw molecular structures in SMILES or SDF format that will feed into BitterPredict.m or other structure-based classifiers.
Use when you have a SMILES input file of small organic molecules and need to predict their collision cross sections or other molecular properties via quantum mechanics.
smina molecular docking CLI. AutoDock Vina fork with customizable scoring functions, native SDF/MOL2/PDB ligand input, autoboxing, local energy minimization, and per-atom score…
Workflow management system for bioinformatics. Use for creating reproducible and scalable computational biology pipelines.
Run SnpEff, a variant annotation and effect prediction tool for genomic variants. Use when the user wants to annotate VCF files, build genome databases, or use SnpEff utilities.
Use when you have a bioinformatics pipeline (like HiC-Pro) with mixed Python, R, and compiled tool dependencies, and you need to ensure consistent reproducibility across machines…
Use when you need to determine the full scope of hardware and methodological compatibility for a bioinformatics tool before designing an analytical workflow.
Use when targeting Soil Biology & Biochemistry or deciding whether a soil-science manuscript fits this venue.
Route questions at the experimental frontier of wine knowledge — synesthetic tasting notes, coached blind tasting practice, climate change projections for wine regions, and…
Use when when you need to reverse-engineer or formally document the computational steps within a closed or under-documented scientific software module—particularly when the…
Use when when you have loaded a dataset of molecular fingerprint vectors (such as biosynfoni fingerprints from a Zenodo deposit) and need to quantify how sparse the…
Use when when you have spatial molecular data (e.g., Visium, imaging-based cytometry) stored in an AnnData object with coordinate information in .
Use when you have paired MS/MS spectra (known compound and its structural analog) with assigned precursor m/z, charge, and SMILES; you want to quantify which parts of the…
Use when after running GNPS molecular networking, SIRIUS compound identification,
Use when you have deconvolved GC-MS spectra in GNPS_GC input-compatible format and want to construct a molecular network to identify relationships between unknown compounds and…
Use when when you have raw LC-MS/MS DDA spectral data (positive and/or negative ionization modes) paired with sample metadata (originating taxon), and you need to detect molecular…
Use when you have completed a GNPS1 (METABOLOMICS-SNETS, METABOLOMICS-SNETS-V2, FEATURE-BASED-MOLECULAR-NETWORKING) or GNPS2 (classical_networking_workflow,…
Use when when you have a trained or untrained chemprop base model (graph convolution + readout layers) and need to extend it to predict infrared spectral properties rather than…
Use when you have a high-resolution LC-MS/MS spectrum or pre-computed molecular fingerprint from a small-molecule sample and need to retrieve a systematic structural…
Use when when you have metabolomics intensity data with metabolites grouped by fragmentation spectral similarity (Molecular Families or Mass2Motifs) and need to rank or score…
Use when you have deconvolved GC-MS spectra (from overlapping chromatographic peaks) in MGF or mzTab format and want to group chemically related compounds, visualize their…
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 MS/MS spectra in MGF or similar format and a reference library of molecular structures (SMILES or SDF), and your goal is to retrieve the most likely structures…
Use when when you have aligned peak-alignment data from a preceding molecular networking task (structured as a table with peak intensity, m/z, retention time, and alignment…
Use when you have a molecular structure (SMILES, InChI, or chemical formula) and need to predict which fragments will appear with high intensity in a tandem MS spectrum, or when…
Use when you have extracted MS1 and MS2 scans in mzML/mzXML format from raw chromatogram files and a structured metadata file (containing retention time, m/z, compound name,…
Use when you have preprocessed 1D ¹H and/or ¹³C NMR spectra from an unknown organic compound with ≤19 heavy atoms, and you need to recover its molecular structure (both formula…
Use when when you need to prepare mass spectra and molecular structures for joint modeling in a BART or transformer-based sequence model, and you lack a unified representation…