OpenBio Special Agents are AI co-scientists designed to handle specific research workflows, providing expert guidance and automation for complex scientific tasks.Documentation Index
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What is an Agent?An Agent is your autonomous research collaborator for each workflow. It plans and executes tasks, runs tools, and iterates on results—handling complex multi-step research processes while keeping everything organized and reproducible.
Available Special Agents
General Agent
General-purpose research assistant for cross-domain tasks:- Multi-disciplinary research planning and coordination
- Cross-tool workflow automation and optimization
- General scientific data analysis and interpretation
- Research project management and documentation
Protein Design Agent
Specialized in protein-related workflows:- Structure prediction and analysis
- Protein design and engineering
- Folding and stability assessment
- Binding and interaction analysis
Drug Discovery Agent
Expert in pharmaceutical research:- Virtual screening and compound analysis
- Lead optimization and ADMET prediction
- Target identification and validation
- Molecular docking and dynamics
Molecular Biology Agent
Focused on DNA/RNA workflows:- PCR primer design and optimization
- Cloning strategy planning
- Restriction analysis and assembly
- Sequence analysis and annotation
Clinical Research Agent
Expert in biomedical data and regulatory information:- Drug safety and adverse event analysis with FDA databases
- Clinical trial data interpretation with ClinicalTrials.gov
- Regulatory compliance and labeling information
- Therapeutic target validation with OpenTargets
Literature Agent
Master of scientific literature:- Paper discovery and relevance scoring with PubMed and arXiv
- Citation network analysis and full-text retrieval
- Method extraction and comparison
- Research trend identification with bioRxiv
Data Analysis Agent
Expert in biological data processing:- Statistical analysis and testing with Jupyter environment
- Machine learning model training and validation
- Data visualization and plotting with integrated tools
- Bioinformatics pipeline automation
Genomics Agent
Specialized in genome-scale analysis:- DNA/RNA sequence retrieval and analysis from ENA
- Taxonomic classification and phylogenetics with MyTaxon
- Raw read processing and assembly with Ensembl
- Genome annotation and comparative analysis
Metabolomics Agent
Expert in metabolic pathway analysis:- Metabolite identification and quantification with NIH Metabolomics Workbench
- Mass spectrometry data analysis and m/z searches
- Pathway mapping and interpretation with KEGG
- Biomarker discovery and validation
Structure Prediction Agent
Master of 3D molecular structure modeling:- Protein structure prediction with AlphaFold and Boltz
- Ligand structure prediction with Boltz
- Protein-ligand complex modeling
- Structure confidence assessment and validation
Sequence Analysis Agent
Expert in biological sequence processing:- Multiple sequence alignment and conservation analysis
- Phylogenetic tree construction and analysis
- Motif discovery and pattern recognition
- Sequence similarity searches and database queries
Pathway Agent
Specialized in biological pathway analysis:- KEGG pathway mapping and analysis
- Reactome pathway enrichment and visualization
- Metabolic pathway reconstruction and simulation
- Signal transduction pathway analysis
Biomarker Discovery Agent
Focused on identifying disease-associated markers:- Differential expression analysis and statistical testing
- Biomarker validation and performance assessment
- Multi-omics biomarker integration and prioritization
- Clinical biomarker discovery and translation
Toxicology/Safety Agent
Expert in chemical and biological safety assessment:- Toxicity prediction and risk assessment
- Safety pharmacology and adverse effect analysis
- Environmental toxicology and ecotoxicity testing
- Regulatory toxicology and compliance evaluation
Custom Agent Builder
Create your own specialized AI assistant:- Combine tools from any workflow domain
- Set custom parameters and constraints
- Build domain-specific expertise
- Save and share agent configurations
Create your own Custom Agent
Location: Profile Settings → My Agents tab
Configure Tools and Parameters
- Select relevant tools from the OpenBio platform
- Set default parameters and constraints
Agent Workflow Examples
Structure Prediction Workflow
Ask your agent to run a workflow for you:- Analyzes sequence features and domains
- Selects optimal prediction method (AlphaFold/Boltz)
- Generates structure models with confidence scores
- Validates and refines predictions
- Provides structural analysis and interpretation