BioMed Skill Router
Find the most suitable skill for your biomedical task by analyzing your request and matching it against available skills.
When to Use
- User describes a biomedical task but doesn't know which skill to use
- User wants to discover what skills are available for a particular domain
- User needs help choosing between multiple skills for a similar task
- User asks "What can I do with OpenBioMed?" or "Which skill should I use for X?"
How It Works
The agent analyzes the user's natural language request and determines the most suitable skill based on:
- Understanding the user's intent and goal
- Identifying what data/inputs the user has
- Matching against available skill capabilities
Available Skills
Biochemistry & Drug Discovery
| Skill |
Description |
| drug-candidate-discovery |
Generate diverse druggable molecules for a given target or disease using AI-powered drug discovery tools. |
| drug-lead-analysis |
Analyze drug candidate molecules for drug-likeness (QED, Lipinski), ADMET properties, BBB penetration, and safety profiles. |
| target-based-lead-design |
Generate diverse lead compounds for a specific protein target using structure-based drug design with MolCraft. |
| admet-prediction |
Predict comprehensive ADMET properties (BBB penetration, side effects, Caco-2 permeability, half-life, LD50 toxicity). |
| retrosynthesis-planning |
Expert-in-the-loop retrosynthetic planning workflow for breaking down target molecules into available starting materials. |
| drug-drug-interaction-analysis |
Analyze potential drug-drug interactions (DDI) for up to 5 drugs using KEGG DDI database. |
| text-based-molecule-editing |
Modify molecules based on natural language descriptions using MolT5/BioT5 models. |
Protein Analysis & Engineering
| Skill |
Description |
| protein-mutation-analysis |
Analyze protein mutations by retrieving protein data, explaining mutation effects with MutaPLM, and predicting structure. |
| mutation-design-aav |
Design high-fitness and high-diversity mutants of AAV VP1 capsid protein. |
| mutation-design-gfp |
Design high-fluorescence and high-diversity GFP mutants. |
| functional-protein-design |
Generate functional protein sequences using CodeFP with Gene Ontology (GO) tag guidance. |
| similar-protein-retrieval |
Retrieve proteins with similar structures or sequences from UniProt, PDB, and AFDB databases. |
| structure-prediction-boltz-2 |
Predict protein complex structures and protein-ligand complexes with binding affinity using Boltz-2. |
| protein-structure-design-boltzgen |
All-atom protein design using BoltzGen diffusion model for binder design and peptide design. |
| antibody-structure-prediction-tfold |
Predict antibody/nanobody structures and antigen-antibody complex structures. |
| antibody-design-iggm |
Epitope-conditioned de novo antibody design and affinity maturation. |
| binding-affinity-prediction-prodigy |
Predict binding affinity scores for protein complexes using Prodigy. |
| protein-ligand-binding-analysis-plip |
Analyze protein-ligand interactions in PDB structures using PLIP (Protein-Ligand Interaction Profiler). |
| protein-function-prediction |
Predict protein function and properties from amino acid sequence using BioT5. |
| protein-subcellular-localization-prediction-biot5 |
Predict protein subcellular localization from amino acid sequence using BioT5. |
Single-Cell Omics Data Analysis
| Skill |
Description |
| single-cell-foundation-model-scrna-seq-geneformer |
Geneformer workflows for tokenization, cell/gene classification, embedding extraction, and perturbation analysis. |
| single-cell-foundation-model-scrna-seq-langcell |
LangCell for zero-shot and few-shot cell type annotation with multimodal cell-text matching. |
| single-cell-foundation-model-scrna-seq-scgpt |
scGPT for preprocessing, binning, cell embedding extraction, fine-tuning, and reference mapping. |
| spatial-transcriptomics-foundation-model-stofm |
SToFM for spatial transcriptomics preprocessing and cell embedding generation. |
| single-cell-scrna-seq-analysis-scanpy |
Complete scRNA-seq analysis workflow with Scanpy including QC, normalization, clustering, and marker gene identification. |
| single-cell-multi-omics-analysis-scvi |
Probabilistic deep learning for single-cell multi-omics analysis including scVI, scANVI, totalVI. |
| cellxgene-census-query |
Query CZ CELLxGENE Census (61M+ cells) for single-cell expression data. |
| spatial-transcriptomics-spatial-data-io |
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms. |
| single-cell-atac-seq-qc-processing |
Trim adapters, align reads, remove duplicates, and evaluate chromatin accessibility data quality. |
| single-cell-atac-seq-peak-calling-annotaion |
Call accessible chromatin peaks with MACS2 and identify differentially accessible regions. |
| single-cell-proteomics-data-processing |
Load, inspect, centroid, and extract features from raw LC-MS/MS data files using pyOpenMS. |
| single-cell-proteomics-peptide-identification |
Search MS2 spectra against protein databases with MSFragger/Comet. |
| single-cell-multi-omics-data-harmonization |
Prepare multi-omics datasets for joint integration with normalization and batch correction. |
Data Retrieval & Knowledge
| Skill |
Description |
| pubchem-query |
Query PubChem database for chemical structures, similar compounds, and bioactivity data. |
| biomedical-literature-search |
Search PubMed and bioRxiv for biomedical research papers. |
| uniprot-query |
Query UniProt database for protein sequences, metadata, and search by criteria. |
| kegg-query |
Query KEGG database for drug information, pathway analysis, and disease-drug-target discovery. |
| ppi-string-query |
Query STRING database for protein-protein interactions with confidence scores. |
| chembl-query |
Query ChEMBL database for bioactivity data on drug-like compounds. |
Molecule Analysis
| Skill |
Description |
| iupac-name-identification-biot5 |
Identify the IUPAC name of a molecule using BioT5 question answering model. |
| molecule-biochemical-significance-query-biot5 |
Query a molecule's biochemical significance and roles in biology and chemistry. |
Disease & Target Analysis
| Skill |
Description |
| disease-drug-intelligence |
Comprehensive disease-to-innovative-drug analysis: targets, drugs, clinical progress, and mechanism trends. |
| target-drug-report |
Generate comprehensive drug development progress reports for disease therapeutic targets. |
Utilities
| Skill |
Description |
| biomed-skill-creator |
Create new biomedical skills or improve existing ones. |
Routing Process
When a user asks for help finding a skill:
- Understand the request - Analyze what the user wants to accomplish
- Identify available inputs - Determine what data the user has (molecule, protein, sequence, etc.)
- Match to skills - Select the most appropriate skill(s) based on the task
- Provide recommendation - Suggest the best skill and explain why
Example Interactions
User: "I want to design a drug for BCL2 protein"
Agent: Based on your request to design drugs for the BCL2 protein, I recommend:
target-based-lead-design - This skill generates diverse lead compounds for a specific protein target using structure-based drug design. You'll need a PDB ID for BCL2. Would you like me to help you find one?
User: "What can I use to analyze my scRNA-seq data?"
Agent: For scRNA-seq analysis, several skills are available depending on your goal:
single-cell-scrna-seq-analysis-scanpy - Complete analysis workflow (QC, clustering, marker genes)single-cell-foundation-model-scrna-seq-langcell - Cell type annotationsingle-cell-foundation-model-scrna-seq-geneformer - Embedding extraction and perturbation analysissingle-cell-foundation-model-scrna-seq-scgpt - Embedding extraction and reference mapping
What specific analysis do you want to perform?
User: "I have a molecule and want to check if it's toxic"
Agent: For toxicity analysis, use admet-prediction. This skill predicts comprehensive ADMET properties including toxicity (LD50), side effects, and BBB penetration. Please provide your molecule as a SMILES string.
See Also
skills_overview.md - Full skill catalog with detailed descriptionsbiomed-skill-creator - Create new skills when none match your needs
1---2name: biomed-skill-router3description: Find the most suitable skill for a given biomedical task. Use this skill when: (1) You are unsure which skill to use for a specific biomedical task, (2) You want to discover available skills for a particular domain, (3) You need to compare multiple skills for a given use case.4license: MIT5---67# BioMed Skill Router89Find the most suitable skill for your biomedical task by analyzing your request and matching it against available skills.1011## When to Use1213- User describes a biomedical task but doesn't know which skill to use14- User wants to discover what skills are available for a particular domain15- User needs help choosing between multiple skills for a similar task16- User asks "What can I do with OpenBioMed?" or "Which skill should I use for X?"1718## How It Works1920The agent analyzes the user's natural language request and determines the most suitable skill based on:211. Understanding the user's intent and goal222. Identifying what data/inputs the user has233. Matching against available skill capabilities2425## Available Skills2627### Biochemistry & Drug Discovery2829| Skill | Description |30|-------|-------------|31| drug-candidate-discovery | Generate diverse druggable molecules for a given target or disease using AI-powered drug discovery tools. |32| drug-lead-analysis | Analyze drug candidate molecules for drug-likeness (QED, Lipinski), ADMET properties, BBB penetration, and safety profiles. |33| target-based-lead-design | Generate diverse lead compounds for a specific protein target using structure-based drug design with MolCraft. |34| admet-prediction | Predict comprehensive ADMET properties (BBB penetration, side effects, Caco-2 permeability, half-life, LD50 toxicity). |35| retrosynthesis-planning | Expert-in-the-loop retrosynthetic planning workflow for breaking down target molecules into available starting materials. |36| drug-drug-interaction-analysis | Analyze potential drug-drug interactions (DDI) for up to 5 drugs using KEGG DDI database. |37| text-based-molecule-editing | Modify molecules based on natural language descriptions using MolT5/BioT5 models. |3839### Protein Analysis & Engineering4041| Skill | Description |42|-------|-------------|43| protein-mutation-analysis | Analyze protein mutations by retrieving protein data, explaining mutation effects with MutaPLM, and predicting structure. |44| mutation-design-aav | Design high-fitness and high-diversity mutants of AAV VP1 capsid protein. |45| mutation-design-gfp | Design high-fluorescence and high-diversity GFP mutants. |46| functional-protein-design | Generate functional protein sequences using CodeFP with Gene Ontology (GO) tag guidance. |47| similar-protein-retrieval | Retrieve proteins with similar structures or sequences from UniProt, PDB, and AFDB databases. |48| structure-prediction-boltz-2 | Predict protein complex structures and protein-ligand complexes with binding affinity using Boltz-2. |49| protein-structure-design-boltzgen | All-atom protein design using BoltzGen diffusion model for binder design and peptide design. |50| antibody-structure-prediction-tfold | Predict antibody/nanobody structures and antigen-antibody complex structures. |51| antibody-design-iggm | Epitope-conditioned de novo antibody design and affinity maturation. |52| binding-affinity-prediction-prodigy | Predict binding affinity scores for protein complexes using Prodigy. |53| protein-ligand-binding-analysis-plip | Analyze protein-ligand interactions in PDB structures using PLIP (Protein-Ligand Interaction Profiler). |54| protein-function-prediction | Predict protein function and properties from amino acid sequence using BioT5. |55| protein-subcellular-localization-prediction-biot5 | Predict protein subcellular localization from amino acid sequence using BioT5. |5657### Single-Cell Omics Data Analysis5859| Skill | Description |60|-------|-------------|61| single-cell-foundation-model-scrna-seq-geneformer | Geneformer workflows for tokenization, cell/gene classification, embedding extraction, and perturbation analysis. |62| single-cell-foundation-model-scrna-seq-langcell | LangCell for zero-shot and few-shot cell type annotation with multimodal cell-text matching. |63| single-cell-foundation-model-scrna-seq-scgpt | scGPT for preprocessing, binning, cell embedding extraction, fine-tuning, and reference mapping. |64| spatial-transcriptomics-foundation-model-stofm | SToFM for spatial transcriptomics preprocessing and cell embedding generation. |65| single-cell-scrna-seq-analysis-scanpy | Complete scRNA-seq analysis workflow with Scanpy including QC, normalization, clustering, and marker gene identification. |66| single-cell-multi-omics-analysis-scvi | Probabilistic deep learning for single-cell multi-omics analysis including scVI, scANVI, totalVI. |67| cellxgene-census-query | Query CZ CELLxGENE Census (61M+ cells) for single-cell expression data. |68| spatial-transcriptomics-spatial-data-io | Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms. |69| single-cell-atac-seq-qc-processing | Trim adapters, align reads, remove duplicates, and evaluate chromatin accessibility data quality. |70| single-cell-atac-seq-peak-calling-annotaion | Call accessible chromatin peaks with MACS2 and identify differentially accessible regions. |71| single-cell-proteomics-data-processing | Load, inspect, centroid, and extract features from raw LC-MS/MS data files using pyOpenMS. |72| single-cell-proteomics-peptide-identification | Search MS2 spectra against protein databases with MSFragger/Comet. |73| single-cell-multi-omics-data-harmonization | Prepare multi-omics datasets for joint integration with normalization and batch correction. |7475### Data Retrieval & Knowledge7677| Skill | Description |78|-------|-------------|79| pubchem-query | Query PubChem database for chemical structures, similar compounds, and bioactivity data. |80| biomedical-literature-search | Search PubMed and bioRxiv for biomedical research papers. |81| uniprot-query | Query UniProt database for protein sequences, metadata, and search by criteria. |82| kegg-query | Query KEGG database for drug information, pathway analysis, and disease-drug-target discovery. |83| ppi-string-query | Query STRING database for protein-protein interactions with confidence scores. |84| chembl-query | Query ChEMBL database for bioactivity data on drug-like compounds. |8586### Molecule Analysis8788| Skill | Description |89|-------|-------------|90| iupac-name-identification-biot5 | Identify the IUPAC name of a molecule using BioT5 question answering model. |91| molecule-biochemical-significance-query-biot5 | Query a molecule's biochemical significance and roles in biology and chemistry. |9293### Disease & Target Analysis9495| Skill | Description |96|-------|-------------|97| disease-drug-intelligence | Comprehensive disease-to-innovative-drug analysis: targets, drugs, clinical progress, and mechanism trends. |98| target-drug-report | Generate comprehensive drug development progress reports for disease therapeutic targets. |99100### Utilities101102| Skill | Description |103|-------|-------------|104| biomed-skill-creator | Create new biomedical skills or improve existing ones. |105106## Routing Process107108When a user asks for help finding a skill:1091101. **Understand the request** - Analyze what the user wants to accomplish1112. **Identify available inputs** - Determine what data the user has (molecule, protein, sequence, etc.)1123. **Match to skills** - Select the most appropriate skill(s) based on the task1134. **Provide recommendation** - Suggest the best skill and explain why114115## Example Interactions116117**User:** "I want to design a drug for BCL2 protein"118119**Agent:** Based on your request to design drugs for the BCL2 protein, I recommend:120121**`target-based-lead-design`** - This skill generates diverse lead compounds for a specific protein target using structure-based drug design. You'll need a PDB ID for BCL2. Would you like me to help you find one?122123---124125**User:** "What can I use to analyze my scRNA-seq data?"126127**Agent:** For scRNA-seq analysis, several skills are available depending on your goal:128129- **`single-cell-scrna-seq-analysis-scanpy`** - Complete analysis workflow (QC, clustering, marker genes)130- **`single-cell-foundation-model-scrna-seq-langcell`** - Cell type annotation131- **`single-cell-foundation-model-scrna-seq-geneformer`** - Embedding extraction and perturbation analysis132- **`single-cell-foundation-model-scrna-seq-scgpt`** - Embedding extraction and reference mapping133134What specific analysis do you want to perform?135136---137138**User:** "I have a molecule and want to check if it's toxic"139140**Agent:** For toxicity analysis, use **`admet-prediction`**. This skill predicts comprehensive ADMET properties including toxicity (LD50), side effects, and BBB penetration. Please provide your molecule as a SMILES string.141142## See Also143144- `skills_overview.md` - Full skill catalog with detailed descriptions145- `biomed-skill-creator` - Create new skills when none match your needs
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