> ## Documentation Index
> Fetch the complete documentation index at: https://docs.openbio.tech/llms.txt
> Use this file to discover all available pages before exploring further.

# Agents

> Automate complex research workflows with specialized agents designed for specific biological tasks.

OpenBio Special Agents are AI co-scientists designed to handle specific research workflows, providing expert guidance and automation for complex scientific tasks.

<Info>
  **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.
</Info>

Watch a demo of Agents in action:

<iframe className="w-full aspect-video rounded-xl" src="https://www.youtube.com/embed/2W17zRXQoCo" title="Agents Demo" frameBorder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerPolicy="strict-origin-when-cross-origin" allowFullScreen />

## 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

<Info>
  **Location**: Profile Settings → My Agents tab
</Info>

<Steps>
  <Step title="Open Agents Settings">
    Navigate to Profile → Settings → My Agent → Create Agent
  </Step>

  <Step title="Create Agent">
    Click the **"Create Agent"** button
  </Step>

  <Step title="Define your Agent">
    * Name your agent
    * Describe what the agent will do
  </Step>

  <Step title="Configure Tools and Parameters">
    * Select relevant tools from the OpenBio platform
    * Set default parameters and constraints
  </Step>

  <Step title="Save your Agent">
    * Configure the Agent details
    * Select an icon and color for your agent and save the agent
  </Step>
</Steps>

## Agent Workflow Examples

### Structure Prediction Workflow

Ask your agent to run a workflow for you:

```
"Predict the 3D structure of this protein sequence"
```

Structure Prediction Agent:

1. Analyzes sequence features and domains
2. Selects optimal prediction method (AlphaFold/Boltz)
3. Generates structure models with confidence scores
4. Validates and refines predictions
5. Provides structural analysis and interpretation