Drafts an eCTD-compliant New Drug Application (NDA) for FDA submission under 21 CFR Part 314. Compiles clinical trial data, CMC documentation, nonclinical studies,…
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public data — from…
Dataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by channels; runs local, HPC (SLURM/SGE), cloud (AWS/GCP/Azure),…
Check if referenced bioinformatics software/code licenses allow commercial use (GPL vs MIT, etc.).
Submit compact AlphaFold Protein Structure Database API requests for prediction, UniProt summary, sequence summary, and annotation lookups.
Submit compact Human Protein Atlas requests for gene JSON, search downloads, and page-level tissue or cell-line lookups.
Submit, poll, and summarize NCBI BLAST Common URL API jobs (Blast.cgi) for nucleotide or protein sequences.
Clinical research outcome extraction for meta-analysis. Use when users need to extract outcome measures (binary, continuous, or survival data) from clinical research papers for…
Generates comprehensive academic introductions for biological pathways, including signaling processes, markers, and inhibitors.
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…
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…
6 pharmaceutical research skills. Trigger: drug discovery, pharmacology, clinical trial design, regulatory filing.
Run phi CLI commands for the dyno protein analysis platform: fetch structures, run folding/inverse-folding pipelines (ESMFold, AlphaFold2, ProteinMPNN), filter and score…
Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree.
Interactive scientific visualization with Plotly. Two APIs: plotly.express (px) for one-liner DataFrame plots, plotly.graph_objects (go) for trace-level control.
High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF…
Generates complete process-related diagnostic biomarker bioinformatics research designs from a user-provided disease context, gene-family or pathway theme, and validation — from…
Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline. Identifies CDS, rRNA, tRNA, tmRNA, signal peptides against Pfam, TIGRFAMs, RefSeq.
Structured, decision-ready review framework for AI/ML, computational biology, and bioscience proposals. Use when evaluating grant, project, or funding proposals.
Patterns for protein structure prediction using AlphaFold2/ColabFold, structural analysis, model quality assessment, and integration with experimental data.
protocols.io REST API: search and fetch wet-lab, bioinformatics, and clinical protocols by keyword, DOI, or category, with steps, reagents, materials, equipment, timing.
Search PubMed for scientific literature. Use when the user asks to find papers, search literature, look up research, find publications, or asks about recent studies.
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…
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…
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.
Audit a rehabilitation or physical therapy platform end-to-end -- evaluate recovery metrics tracking (ROM, strength, balance, gait), patient-reported outcomes (DASH, LEFS, NDI,…
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
Deterministic deep research via RivalSearchMCP. 9 tools: 5-engine web search (DuckDuckGo/Bing/Yahoo/Mojeek/Wikipedia), 9-platform social search…
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.
Direct PubMed and NCBI E-utilities search workflows for biomedical literature, MeSH queries, PMID lookup, citation retrieval, and API-backed literature monitoring.
Systematic strategies for searching scientific literature across PubMed, arXiv, Google Scholar, and AI-assisted tools.
gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.
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.
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…
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.
Splice-aware RNA-seq aligner producing sorted BAM and splice junction tables. Builds genome index, runs two-pass alignment for better junctions.
Set up your bio-research environment and explore available tools. Use when first getting oriented with the plugin, checking which literature, drug-discovery, or visualization MCP…
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for system — from…
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for system — from…
生物作业生成 Skill是面向班级作业的产品级 Hermes Skill，年级、册别、单元、知识点和难度通过参数传入。 Workflow: teacher_biology_homework_generation.run.
生物单元复习 Skill是面向单元复习的产品级 Hermes Skill，年级、册别、单元、知识点和难度通过参数传入。 Workflow: teacher_biology_unit_review.run.
Use when converting medical text between academic and patient-friendly tones, translating medical jargon for patients, adapting research papers for public audiences, or rewriting…
Discover novel small molecule binders for protein targets using structure-based and ligand-based approaches.
Provide comprehensive clinical interpretation of somatic mutations in cancer. Given a gene symbol + variant (e.g., EGFR L858R, BRAF V600E) and optional cancer type, performs…
AI-driven patient-to-trial matching for precision medicine and oncology. Given a patient profile (disease, molecular alterations, stage, prior treatments), discovers and ranks…
Generates comprehensive drug research reports with compound disambiguation, evidence grading, and mandatory completeness sections.
Production-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (CpG filtering, differential methylation, age-related CpG…
Comprehensive immune repertoire analysis for T-cell and B-cell receptor sequencing data. Analyze TCR/BCR repertoires to assess clonality, diversity, V(D)J gene usage, CDR3…
Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics.
Comprehensive patient stratification for precision medicine by integrating genomic, clinical, and therapeutic data.
Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved therapies, finds resistance…
Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles.