> ## 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.

# Workflows

> Create and manage reusable research workflows

Create reusable workflows in OpenBio to automate repetitive research tasks. Save sequences of steps as templates, then execute them with different inputs—perfect for standardizing analyses and saving time on routine tasks.

<Info>
  **What is a Workflow?**
  A workflow is a saved sequence of research steps that you can execute repeatedly. Think of it as a recipe for common analyses like "Protein Structure Prediction Pipeline" or "Literature Review Protocol."

  It is a prompt that describes a sequence of steps to be executed. The more robust the workflow, the better the results will be.
</Info>

## Creating Workflows

### From an Existing Chat

The easiest way to create a workflow is from a successful conversation:

<Steps>
  <Step title="Complete Your Analysis">
    Have a chat conversation where you perform the steps you want to save as a workflow
  </Step>

  <Step title="Ask OpenBio to save as workflow">
    Ask OpenBio to save as workflow. Again, it is very important to be specific and describe the workflow in detail.

    <Tip>
      You can also ask OpenBio to ask questions to you to help you describe the workflow in detail.
    </Tip>
  </Step>

  <Step title="Review and Save">
    Review the workflow, ask OpenBio to make any changes, and save it will be saved to your workflow library automatically.
  </Step>
</Steps>

<Check>
  Your workflow is now available in the Workflows panel and can be referenced in any chat using `/workflow-name`
</Check>

### Creating from the Workflows Page

Build a new workflow without starting from a chat:

<Steps>
  <Step title="Go to Workflows Page">
    Click **"Workflows"** in the settings button in the top navigation bar
  </Step>

  <Step title="Create New Workflow">
    Click the **"+ Add Workflow"** button in the top-right corner of the Workflows page
  </Step>

  <Step title="Design Your Workflow">
    * **Name**: Give your workflow a descriptive title.
    * **Description**: Explain what it does and when to use it. Here's what makes a good description:
      * **Steps**: Add steps manually with clear instructions.
      * **Parameters**: Define input parameters that will change each time.
      * **Outputs**: Set up expected outputs and results.
      * **Helpful Descriptions**: Add helpful descriptions for each step.
  </Step>

  <Step title="Test and Refine">
    Test your workflow with sample inputs to ensure it works correctly
  </Step>
</Steps>

## Using Workflows

Reference workflows directly in your messages:

<Tabs>
  <Tab title="Simple Execution">
    ```
    Run /protein-analysis on this sequence: MKTAYIAKQRQ...
    ```
  </Tab>

  <Tab title="With Files">
    ```
    Execute /structure-prediction using @my_protein.fasta
    ```
  </Tab>

  <Tab title="Multiple Parameters">
    ```
    Run /literature-review for "CRISPR gene editing" with 10 papers from the last 5 years
    ```
  </Tab>
</Tabs>

<Tip>
  You can also use the workflow button (/) in the chat input to run a workflow.
</Tip>

## Workflow Examples

### Protein Structure Prediction Pipeline

**Purpose**: Complete structure analysis from sequence to visualization

**Steps**:

1. Validate the input protein sequence
2. Search for similar structures in the PDB database
3. Submit structure prediction using Boltz-2
4. Wait for prediction to complete
5. Visualize the predicted 3D structure
6. Analyze prediction quality and write a report

**Parameters**:

* `SEQUENCE`: Protein sequence to analyze
* `MODEL`: Prediction tool (Boltz-2, Chai-1, or SimpleFold)

### Literature Review Workflow

**Purpose**: Comprehensive literature search and summary

**Steps**:

1. Search PubMed for papers about `TOPIC` in last `YEARS` years
2. Filter results by relevance and journal impact factor
3. Retrieve the top `COUNT` most relevant papers
4. Extract key findings from each paper
5. Identify common themes and consensus
6. List any conflicting results or debates
7. Suggest potential research directions
8. Generate a formatted bibliography

**Parameters**:

* `TOPIC`: Research topic or question
* `YEARS`: Time range to search (default: 5 years)
* `COUNT`: Number of papers to analyze (default: 10)

## Editing Workflows

<Steps>
  <Step title="Open Workflow">
    On the Workflows page, click on the workflow name to open it
  </Step>

  <Step title="Edit Mode">
    Click the **"Edit"** button in the top-right corner of the workflow detail modal
  </Step>

  <Step title="Make Changes">
    * Modify workflow name or description
    * Add, remove, or reorder steps
    * Update parameter definitions
  </Step>

  <Step title="Save Changes">
    Click **"Save"** to update your workflow. You can also click **"Cancel"** to discard your changes.
  </Step>
</Steps>

<Tip>You can also ask OpenBio to update the workflow for you.</Tip>

## Workflow Visualization

OpenBio automatically generates Mermaid diagrams to visualize workflow structure. View flowcharts showing tool dependencies, data flow, and execution order.

To create a diagram, ask OpenBio to "visualize this workflow" or "show the workflow diagram." Diagrams update automatically as workflows change.

### Diagram Types

* Flowcharts for sequential workflows
* Dependency graphs for complex pipelines
* Swimlane diagrams for multi-stage processes

Export diagrams as images or Mermaid code for documentation.

## Workflow Best Practices

<AccordionGroup>
  <Accordion title="Start with Successful Chats">
    Always create workflows from conversations that worked well. Test your steps manually before saving them as a workflow.
  </Accordion>

  <Accordion title="Use Descriptive Names">
    "Protein-Ligand Docking with Chai-1" is much better than "Workflow 1". Include the key tools or methods in the name.
  </Accordion>

  <Accordion title="Document Everything">
    Explain what each step does, what inputs are needed, and what outputs to expect. Future you will thank you!
  </Accordion>

  <Accordion title="Handle Errors Gracefully">
    Include validation steps and error handling. What should happen if a file is missing or a search returns no results?
  </Accordion>

  <Accordion title="Test Before Trusting">
    Run new workflows with test data first. Verify each step works as expected before using on important research.
  </Accordion>

  <Accordion title="Keep Modular">
    Create smaller, focused workflows that can be combined rather than one giant workflow that tries to do everything.
  </Accordion>
</AccordionGroup>

## Troubleshooting

<AccordionGroup>
  <Accordion title="Can't find workflow in chat">
    **Solutions**:

    * Type `/` to see autocomplete suggestions
    * Check spelling of workflow name
    * Verify workflow is saved (check Workflows page)
  </Accordion>

  <Accordion title="Workflow takes too long">
    **Consider**:

    * Some steps (like structure prediction) inherently take time
    * Check if prediction jobs are queued (normal during busy periods)
    * Break complex workflows into smaller, faster ones
  </Accordion>
</AccordionGroup>

## Next Steps

<CardGroup cols={2}>
  <Card title="Predictions" href="/user-guide/features/predictions">
    Use workflows with AI prediction tools
  </Card>

  <Card title="Chat Guide" href="/user-guide/features/chat">
    Master chat to create better workflows
  </Card>

  <Card title="File Management" href="/user-guide/features/file-management">
    Organize files for workflow use
  </Card>

  <Card title="Projects" href="/user-guide/features/projects">
    Organize workflows by project
  </Card>
</CardGroup>

<Tip>
  **Power User Tip**: Create a "Workflow Development" project where you test and refine new workflows. Once they're working perfectly, move them to your main research projects.
</Tip>