User’s Guide

Preliminary Pages

• Preface

An Introduction to VisTrails

• What Is VisTrails?
  • Important Features
  • Obtaining the software
• Getting Started
  • Installation
  • Quick Start
  • Installing additional packages
  • The Vistrails Builder Window
  • Manipulating VisTrails Files
  • VisTrails Basics
  • VisTrails Interaction

Learning VisTrails By Example

• Creating and Modifying Workflows
  • Working with Modules
  • Adding and Deleting Modules
  • Connecting Modules
  • Changing Module Parameters
  • Using Global Variables
  • Configuring Module Labels
  • Configuring Module Ports
  • Basic Modules
• Groups and Subworkflows
  • Grouping Modules
  • Subworkflows and Group Modules
  • Subworkflows
• Interacting with the Version Tree
  • Version Tree View
  • Adding and Deleting Tags
  • Upgrading Versions
  • Adding Version Annotations
  • Navigating Versions
  • Comparing Versions
• Merging Two Version Trees
  • Example
• Querying the Version Tree
  • Query By Example
  • Textual Queries
• Spreadsheet
  • The Spreadsheet Layout
  • Sending Output to the Spreadsheet
  • Interacting with the Spreadsheet
  • Launching a Web Browser
  • Saving a Spreadsheet
• Tabular data package
• Using Analogies to Update Workflows
  • Visualization by Analogy
  • Using the Visual Diff Window
  • Using the Spreadsheet
  • Notes
• Parameter Exploration
  • Creating a Parameter Exploration
  • Alternatives to Linear Interpolation
  • Saving Parameter Explorations
  • “Virtual Cell” Layout
• Provenance Browser
• Mashups
  • Creating Parameter Aliases
  • Configuring Parameter Aliases
  • Saving a Mashup
  • Managing Multiple Mashups
  • A Simple Example
• Module Descriptions and Examples
  • VisTrails VTK modules
  • Modules and Corresponding Examples

Intermediate Concepts and VisTrails Packages

• Parameter Widgets
  • Introduction to Parameter Widgets
• Control Flow in VisTrails
  • The Map operator
  • Filtering results
  • Conditional module
  • While loop
  • For loop
  • Boolean operations
  • Vector operations
• The Control Flow Assistant
  • Using the Control Flow Assistant (CFA)
• List Handling in VisTrails
  • The List type
  • Iterating over lists
• Streaming in VisTrails
  • Using Streaming
• Parallel Flow in VisTrails
  • Setting up an IPython cluster
  • Interacting with the cluster
  • The Map module
• Connecting to a Database
  • Setup
  • Opening from a database
  • Saving to a database
  • Known Issues
• Example: Web Services
  • Enabling the SUDSWebServices Package
  • Adding Web Service Packages
  • Creating a new vistrail
  • Executing the workflow
• Example: ITK
  • Introduction to ITK
  • Preparing ITK
  • ITK and VisTrails
• Persistence in VisTrails
  • Getting Started With Persistence
  • Managing the store
  • Examples
• Running commands on a remote server
  • Referencing a queue
  • Submitting a job
  • Downloading output files
  • Example
  • Setting up ssh keys
• VisTrails Server Setup
  • Using Xvfb
  • Connecting to X server directly
  • Basic Configuration
• Embedding VisTrails Files Via Latex
  • Latex Setup and Commands
  • Including VisTrails Results in Latex
  • Including crowdlabs.org workflow results in Latex
• Example: scikit-learn
  • Introduction to scikit-Learn
  • Installing scikit-learn
  • Using scikit-learn via VisTrails