> ## 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.

# Utility Tools

> File management, notebooks, workflows, and system utilities

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

## 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"

## 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..."

## 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"

## 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"
* Generate Scientific illustrations

## 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
  <Tip>You can mention if you would like OpenBio to use a specific tool, or not to use a specific tool.</Tip>

## 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"

## Organization Tips

**File Structure**:

```
/Project
  /data (raw, processed)
  /sequences (proteins, dna)
  /results (predictions, analysis)
  /figures
  /protocols
  /literature
```

<Tip>You can tell OpenBio to organize the files in a specific way.</Tip>

**Naming Conventions**:

* Use descriptive names: `egfr_kinase_prediction.pdb`
* Include dates for experiments
* Avoid spaces (use `_` or `-`)
* Be consistent across projects