Generate ~5 actionable research topic recommendations by querying PubMed E-utilities; use when a user provides a research direction/constraints and needs evidence-backed topic…
Visualize, analyze, and render protein and molecular structures using PyMOL. Use when the user wants to create images of protein structures, perform structural alignments or…
Use when running molecular quantum chemistry calculations in Python. Computes single-point energies, optimized geometries, vibrational frequencies, and population analysis using…
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological — from…
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological — from…
Therapeutics Data Commons (TDC) AI-ready drug discovery datasets. Curated ADME, toxicity, DTI, DDI with scaffold/cold splits, standardized metrics, molecular oracles, and ADMET…
Use when when building a graph-based molecular property prediction model that must process both molecular structures (as heterogeneous graphs) and tabular metadata…
Use when after feature clustering has been applied to co-eluting LC-MS features and mass-to-charge ratio matching to KEGG has produced an annotated table with adduct assignments.
Query the QuickGO and Evidence & Conclusion Ontology (ECO) REST API. Use this when you need to map genes to biological processes, molecular functions, or cellular components, find…
Use when when annotating .msp mass spectrometry files with chemical structure metadata and you need fast, offline molecular transformations (SMILES↔InChI, canonical SMILES…
Computes all numeric RDKit molecular descriptors from SMILES strings, filtering out NaN, constant, and infinite values to produce a clean feature matrix.
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies — from…
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies — from…
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies — from…
Benchmark LLM reference recommendation capabilities by verifying every cited paper against Crossref, PubMed, arXiv, and DBLP.
Use when you have executed a structure annotation pipeline (like BAM) on a validation dataset for which ground-truth molecular structure annotations exist, and you need to assess…
调控注释数据库 skill。用于 ENCODE、ReMap、Cistrome、JASPAR、RegulomeDB、Roadmap Epigenomics、UCSC/Genome Browser tracks、TF motif、peak set 和 enhancer/promoter 注释查询交接。
Audit a rehabilitation or physical therapy platform end-to-end -- evaluate recovery metrics tracking (ROM, strength, balance, gait), patient-reported outcomes (DASH, LEFS, NDI,…
Run arbitrary scripts on KBase compute nodes via the CDM Task Service (CTS). Use when the user needs to move compute off their notebook or local machine — e.g., running…
Discovers, classifies, and masks repetitive elements and transposable elements with RepeatModeler2 (de novo family library), RepeatMasker (masking against a library), EDT — from…
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
Use when you have a normalized peak-abundance matrix from FT-ICR MS data (peaks as rows, samples as columns) and need to compare the number and diversity of detected molecular…
Use when after identifying precursor peptides from genome assemblies via BGC mining, when you need to enumerate the chemical space of PTM variants (lantibiotic, lassopeptide,…
Deterministic deep research via RivalSearchMCP. 9 tools: 5-engine web search (DuckDuckGo/Bing/Yahoo/Mojeek/Wikipedia), 9-platform social search…
Use when before constructing a DESeqDataSet from count data or tximport output, when you have raw RNA-seq samples that need to be annotated with experimental conditions, treatment…
Use when you have paired scATAC-seq and scRNA-seq data from the same cells (multiome experiment) and want to perform integrated analysis that leverages both chromatin…
Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline.
Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API.
Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API.
Use bioSkills to give an agent domain-specific bioinformatics procedures, tool choices, and guardrails for omics analysis workflows.
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
Use when targeting Science Signaling (Sci. Signal.) or deciding whether a cell-signaling, systems-biology, or signaling-pharmacology manuscript fits this AAAS venue.
Strategies for scientific computing, numerical methods, bioinformatics/DNA tasks, logic circuit design, algorithmic challenges, and ML training tasks.
Direct PubMed and NCBI E-utilities search workflows for biomedical literature, MeSH queries, PMID lookup, citation retrieval, and API-backed literature monitoring.
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design.
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.
gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.
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…
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.
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.