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AI Agents & Collaborative Intelligence

Unlike generic chatbots, CodeXomics is powered by a Multi-Agent System (MAS)—a network of 7 specialized AI agents working together behind the scenes to perform complex genome analysis safely and effectively.

🧠 Meet the Agents

When you send a request in the CodeXomics ChatBox, you aren't just talking to a single LLM; you are submitting a task to the agent swarm:

  1. CoordinatorAgent: The manager. It breaks down your prompt into sub-tasks and delegates them to the most suitable specialized agents.
  2. AnalysisAgent: The mathematician. Handles sequence motif searching, GC content calculations, primer formulation, and deep string manipulations.
  3. DataAgent: The librarian. Specializes in formatting sequences, exporting files (FASTA/GenBank), and retrieving external public databases.
  4. NavigationAgent: The navigator. Interprets positional commands ("Go to the start of the BRCA1 gene") and manipulates the main visualization UI.
  5. PluginAgent: The integrator. Specifically trained to handle execution flows for any installed third-party plugins from the Marketplace.
  6. ExternalAgent: The protocol agent. Responsible for executing tasks that require communicating with remote MCP servers.
  7. DeepResearchAgent: The researcher. A highly capable agent specifically spun up for unbounded research loops requiring multi-step web and database probing.

🪄 Smart Execution Flow

When you ask: "Analyze the sequence from chromosome 1 and jump to the longest open reading frame":

  1. Routing Strategy: The CoordinatorAgent scores the prompt using calculateAgentScore.
  2. Phase 1 (Analysis): The AnalysisAgent runs the analyze_sequence tool in the background to return reading frames.
  3. Phase 2 (Navigation): The NavigationAgent takes the resulting output bounds and natively moves your camera position to the exact nucleotides on the screen.
  4. Caching: If you ask a similar identical question later, the agents instantly respond via memory blocks rather than burning token usage repeating execution.

💬 Monitoring Agent Thoughts

You can observe these agents collaborating in real time! Inside the AI chat panel, click the Thinking Process dropdown on a message block to trace exactly which agent picked up the task, which tools they used, and how they passed information back and forth.