Chip Seq
ChIP-seq peak calling and downstream interpretation with MACS3, signal track export, annotation, motif analysis, and differential binding review.
Bio Ppt Generate
Presentation generation (组会汇报 PPT)
Skills Hub
Browse and install community skills from the BioClaw Skills Hub. Use when a user's task is not covered by built-in skills, or when the user asks about available skills, advanced workflows, or specialized analysis pipelines. Triggers on "skills hub", "more skills", "install skill", "community skills", "find a skill for".
Bio Human Feedback
Phase 2.6: Human review checkpoint (人类反馈验证)
Bio Manuscript Common
Shared scripts and templates used by the bio-manuscript-* skill family (bio-manuscript-pipeline, bio-manuscript-refine, bio-manuscript-text). Do not invoke this skill directly — it is a resource container. Other bio-manuscript-* skills reference files here.
Bio Figure Design
Step 6: Figure design (Figure 详细设计)
Blast Search
Run BLAST sequence similarity searches. Use when the user asks to BLAST a sequence, find similar sequences, identify a gene/protein, or do homology search. Triggers on "blast", "sequence similarity", "homology", "identify sequence".
Solana
Query Solana blockchain data with USD pricing — wallet balances, token portfolios with values, transaction details, NFTs, whale detection, and live network stats. Uses Solana RPC + CoinGecko. No API key required.
Sec Report
SEC (size-exclusion chromatography) analysis with peak detection, oligomer classification, and publication-quality PDF report generation via Typst templates. Triggers on "SEC", "size exclusion", "chromatography", "oligomer analysis", "protein assembly", "SEC report".
Bio Task System
Step 2: Task system design (任务体系构建)
Query Opentarget
Query OpenTargets for drug targets, disease associations, and therapeutic evidence. Use when user asks about drug targets, disease mechanisms, target validation, or drug-disease associations. Triggers on "opentarget", "drug target", "target validation", "disease association", "therapeutic target", "drug for disease".
Proteomics
Mass spectrometry proteomics QC, quantification, comparative analysis, and export for DDA, DIA, and protein-level result tables.
Bio Manuscript Pipeline
End-to-end pipeline from structured research input to a full manuscript plan (一条龙 Pipeline)
Atac Seq
ATAC-seq processing with assay QC, MACS3 peak calling, consensus peak matrices, differential accessibility, and motif or footprint follow-up.
Query Stringdb
Query STRING for protein-protein interactions. Use when user asks about protein interactions, interaction networks, binding partners, or interactome. Triggers on "string", "protein interaction", "interaction network", "binding partners", "interactome", "PPI".
Meme Generation
Generate real meme images by picking a template and overlaying text with Pillow. Produces actual .png meme files.
Bio Metric System
Step 4: Metric system design (评价指标体系构建)
Query Kegg
Query KEGG for biological pathways and gene info. Use when user asks about metabolic pathways, signaling pathways, pathway genes, or KEGG IDs. Triggers on "kegg", "pathway", "metabolic pathway", "signaling pathway", "pathway genes".
Query Uniprot
Query UniProt protein database. Use when user asks about protein sequences, functions, annotations, domains, or protein identifiers. Triggers on "uniprot", "protein function", "protein sequence", "gene product", "protein info".
Bio Dataset Search
Step 3: Dataset search and task matching (数据集搜索与匹配)
Cell Annotation
Automated and marker-guided single-cell cell type annotation using CellTypist, marker review, reference transfer, and confidence-aware label curation.
Query Clinvar
Query ClinVar for clinical variant significance. Use when user asks about variant pathogenicity, genetic variants, clinical significance, or disease-causing mutations. Triggers on "clinvar", "pathogenic", "variant significance", "clinical significance", "disease variant", "mutation pathogenicity".
Blackbox
Delegate coding tasks to Blackbox AI CLI agent. Multi-model agent with built-in judge that runs tasks through multiple LLMs and picks the best result. Requires the blackbox CLI and a Blackbox AI API key.
Scrna Preprocessing Clustering
Standard scRNA-seq preprocessing and clustering with Scanpy. Use for QC, normalization, HVG selection, PCA, neighbor graph construction, UMAP, Leiden clustering, and export of an analysis-ready AnnData object.
Sequence Analysis
Analyze DNA/RNA/protein sequences. Use when the user provides a sequence and asks for analysis, translation, GC content, ORFs, motifs, restriction sites, or primer design. Triggers on "sequence", "translate", "GC content", "ORF", "primer", "restriction", "complement", "reverse complement".
Query Geo
Query NCBI GEO for gene expression datasets. Use when user asks about RNA-seq datasets, microarray data, expression data, GEO accessions, or finding public datasets. Triggers on "geo", "gene expression omnibus", "expression dataset", "RNA-seq dataset", "microarray dataset", "GSE", "GDS".
Report Template
Publication-quality PDF report generation using Typst templates. Produces professional scientific reports with colored section bands, styled tables, figure captions, callout boxes, and page headers/footers.
Metagenomics
Shotgun metagenomics workflow with host-depletion-aware QC, taxonomic profiling, functional profiling, AMR follow-up, and reproducible community output tables.
Bio Analysis System
Step 5: Analysis system design (分析方法体系构建)
Base
Query Base (Ethereum L2) blockchain data with USD pricing — wallet balances, token info, transaction details, gas analysis, contract inspection, whale detection, and live network stats. Uses Base RPC + CoinGecko. No API key required.
Pubmed Search
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. Triggers on "pubmed", "papers", "literature", "publications", "research on", "studies about".
Honcho
Configure and use Honcho memory with Hermes -- cross-session user modeling, multi-profile peer isolation, observation config, dialectic reasoning, session summaries, and context budget enforcement. Use when setting up Honcho, troubleshooting memory, managing profiles with Honcho peers, or tuning observation, recall, and dialectic settings.
Bio Manuscript Text
Step 7: Manuscript drafting (论文文案生成)
Query Alphafold
Query AlphaFold protein structure predictions. Use when user asks about protein structure, 3D structure, protein folding, or structure prediction. Triggers on "alphafold", "protein structure", "3D structure", "folding", "pLDDT", "structure prediction".
Differential Expression
Bulk transcriptomics differential expression with count-aware modeling, design validation, contrast handling, thresholded exports, and publication-ready DE figures.
Query Interpro
Query InterPro for protein domains and families. Use when user asks about protein domains, functional sites, protein families, domain architecture, or motifs. Triggers on "interpro", "protein domain", "domain architecture", "protein family", "functional site", "motif".
Bio Innovation Check
Step 1: Innovation assessment (创新性检测)
Blender Mcp
Control Blender directly from Hermes via socket connection to the blender-mcp addon. Create 3D objects, materials, animations, and run arbitrary Blender Python (bpy) code. Use when user wants to create or modify anything in Blender.
Sds Gel Review
Review SDS-PAGE or protein purification gel images using DNA sequence, protein sequence, base-pair length, expected protein size, and lane labels. Use when the user wants to judge whether a gel ran well, whether the main band matches the expected product, or whether there may be impurities, degradation, aggregation, or low expression.
Query Reactome
Query Reactome for biological pathways and reactions. Use when user asks about signaling cascades, biological processes, pathway diagrams, or reaction details. Triggers on "reactome", "signaling cascade", "biological pathway", "pathway diagram", "reaction mechanism".
Touchdesigner Mcp
Control a running TouchDesigner instance via twozero MCP — create operators, set parameters, wire connections, execute Python, build real-time visuals. 36 native tools.
Bio Tools
Biology research tools reference. Always available inside agent containers.
Bio Manuscript Refine
Refine loop: three-reviewer iterative refinement (三审稿人迭代优化)
Query Pdb
Query RCSB PDB for experimental protein structures. Use when user asks about crystal structures, X-ray, cryo-EM, NMR structures, or PDB IDs. Triggers on "pdb", "crystal structure", "cryo-em", "x-ray structure", "protein crystal", "experimental structure".
Concept Diagrams
Generate flat, minimal light/dark-aware SVG diagrams as standalone HTML files, using a unified educational visual language with 9 semantic color ramps, sentence-case typography, and automatic dark mode. Best suited for educational and non-software visuals — physics setups, chemistry mechanisms, math curves, physical objects (aircraft, turbines, smartphones, mechanical watches), anatomy, floor pla…
Structural Biology
Structure retrieval, confidence-aware AlphaFold DB usage, coordinate download, PAE and pLDDT interpretation, and structure-guided biological annotation.
Query Ensembl
Query Ensembl for genomic data. Use when user asks about gene coordinates, genomic sequences, variants, gene structure, exons, transcripts, or species comparison. Triggers on "ensembl", "gene coordinates", "genomic location", "exon", "transcript", "variant location", "rsid", "rs number".