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    BIOVIAScientific Informatics

    Pipeline Pilot Fundamentals

    This curriculum familiarizes students with building and utilizing protocols in Pipeline Pilot. Protocols are pipelines of process steps you use to rapidly create, test, and publish scientific services and automate the process of accessing, analyzing, and reporting scientific data. This module covers the following topics:

    Level
    Fundamental
    Format
    eLearning

    Modules

    1. Fundamentals Introduction

      In Fundamentals you will learn the many uses of Pipeline Pilot, and how it helps automate everyday tasks. You’ll learn the interface layout, how to build protocols, and how to configure parameters on components so they work with the chosen data.

      • Exploring Pipeline Pilot
      • Exploring the Layout
      • Building a Protocol
      • Reviewing the Client-Server Architecture
    2. Manipulate Components

      Discover the basics of components and how you can work with them in a pipeline.

      • Exploring Components and Parameters
      • Adding Components to a Pipeline
      • Working with Existing Components
    3. Debug a Pipeline

      Learn how you can use Pipeline Pilot’s debugging capabilities.

      • Utilizing Checkpoints
      • Viewing Design Mode
      • Utilizing Debugging Tools
      • Managing Protocol Versions
      • Comparing Protocols
    4. Filter Data

      Explore how you can use filters to remove records from your data stream, separate records into two streams, and test that a property is present on your data record.

      • Browsing Filters
      • Filtering by the Value of a Property
      • Defining a Property
    5. Merge Data

      Learn to combine records based on one or more specified properties from the data stream, known as a key. You will also learn the different types of output you receive when you use the merge, join, and group components.

      • Browsing the Merge Components
      • Combining Data Records with a Key
      • Merging Properties of all Input Data Records
      • Comparing Merging, Joining, and Grouping
    6. Join Data

      Discover how to add properties to your data records from a reference cache or a file based on one or more specified properties from the data stream, known as a key. You will also learn the different types of output you will receive when you utilize the merge, join, and group components.

      • Adding Properties to Records on the Data Stream
      • Comparing Merging, Joining, and Grouping
    7. Group Data

      Learn how to reversibly aggregate data together either by number of records or by a key property. You will also learn the different types of output you will receive when you utilize the merge, join, and group components.

      • Grouping Data by a Tag
      • Filtering Grouped Data
      • Grouping Data by a Set Number of Records
      • Comparing Merging, Joining, and Grouping
    8. Utilize PilotScript

      PilotScript is the native scripting language in Pipeline Pilot that allows for the powerful manipulation of data records and control of data flow within pipelines. This course provides Instruction on how to use PilotScript, as well as how to add PilotScript to custom filters and custom manipulators.

      • Using the PilotScript Editor
      • Filtering Data Sets
      • Accessing Calculable Properties and Functions
      • Reviewing Comparisons, Variable Types, and Property Lists
    9. Create Subprotocols

      Learn to create a subprotocol to collapse one or more components into a single item. You’re also taught to add or expose parameters on a subprotocol, and share it as a reusable component. Discover the difference between the data flow in a subprotocol and a Run to Completion subprotocol, and how this can add functionality to your protocols.

      • Combining Components into a Subprotocol
      • Editing a Subprotocol
      • Saving and Sharing a Subprotocol
    10. Pass Data between Pipelines

      Explore the use of global variables, caches, files, and temporary files to pass data between multiple pipelines.

      • Running Multiple Pipelines
      • Passing Data with Global Variables, with Caches, and with Files
      • Reviewing File Locations
    11. Run and Automate Protocols Outside of Pipeline Pilot

      Discover Pipeline Pilot Web Port, a web-based application for running protocols in a browser. You are also taught to run protocols automatically through a command line prompt, and then schedule protocol execution through the Windows Task Scheduler, or via a cron job in Linux.

      • Working with Web Port
      • Running a Protocol from a Windows Command Line
      • Scheduling a Protocol Job

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