Use when you need to verify that an S4 replacement method (e.g., `mz<-`) in a bioinformatics backend class correctly validates input data using vectorized operations on…
Use when after MZmine feature detection and molecular networking on a single LC-MS/MS DDA sample, when you have a feature table (with retention time, m/z, fragmentation spectra)…
An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing
Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualizati — from…
Use when targeting Science Signaling (Sci. Signal.) or deciding whether a cell-signaling, systems-biology, or signaling-pharmacology manuscript fits this AAAS venue.
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expressi — from…
Use when planning multi-chapter scientific research analyses with expert consultation. Produces markdown analysis documents with pseudocode for RNA-seq, proteomics, or other data…
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3).
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez) — from…
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API — from…
Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR stu — from…
Strategies for scientific computing, numerical methods, bioinformatics/DNA tasks, logic circuit design, algorithmic challenges, and ML training tasks.
Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug d — from…
Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR s — from…
Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR s — from…
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided — 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…
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic — from…
Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and — from…
Direct PubMed and NCBI E-utilities search workflows for biomedical literature, MeSH queries, PMID lookup, citation retrieval, and API-backed literature monitoring.
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for system — from…
Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (uni — from…
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design.
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…
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakema — from…
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakema — from…
Systematic strategies for searching scientific literature across PubMed, arXiv, Google Scholar, and AI-assisted tools.
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3).
Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO.
Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell anal — from…
Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery — from…
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design.
gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
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…