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OpenBio provides utility tools for managing files, organizing research notes, and creating workflows from the chat directly.

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File Management

Purpose: Organize and manage research files within projects Available operations:
  • Create, read, modify, delete files
  • Create and organize folders
  • Move/rename/copy files
  • Search files by name or content
  • Download files from trusted sources
  • Get file information and metadata
Example: “Create a file called analysis_results.txt”

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Notebook Tools

Purpose: Digital research notebook for notes and todos Notes Management:
  • Create, update, search, delete notes
  • Tag notes for organization
  • Rich text and Markdown support
  • Auto-timestamped
Todo Management:
  • Create, complete, update, delete tasks
  • Set due dates and priorities
  • Track completion status
Example: “Create a note: Today’s experiment showed…”

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Workflows

Purpose: Create and manage automated research workflows Available operations:
  • List, create, edit, delete workflows
  • Execute workflows with #workflow_name
  • Extract workflows from chat history
  • Ensure reproducible analyses
Example: “Create a workflow from this chat history”

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Visualization Tools

Purpose: Display structures and data Available tools:
  • Show 3D molecular structures (PDB, mmCIF, SDF)
  • Show 2D molecular structures (SMILES, InChI, MOL/SDF) Example: “Visualize @structure.pdb”

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Tool Management

OpenBio can manage the tools it has access to own its own. Available operations:
  • List available tools
  • Bind/unbind specialized tools
  • Manage chat context
    You can mention if you would like OpenBio to use a specific tool, or not to use a specific tool.

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Quick Examples

  • “Create a file called analysis_results.txt”
  • “Read the data in @experiment_results.csv”
  • “Create a note about protein expression results”
  • “Add a todo: Order primers for next experiment”
  • “Visualize @structure.pdb”
  • “Create a workflow from this chat”

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Organization Tips

File Structure: 
/Project
  /data (raw, processed)
  /sequences (proteins, dna)
  /results (predictions, analysis)
  /figures
  /protocols
  /literature
You can tell OpenBio to organize the files in a specific way.
Naming Conventions:
  • Use descriptive names: egfr_kinase_prediction.pdb
  • Include dates for experiments
  • Avoid spaces (use _ or -)
  • Be consistent across projects