Protocol Exchange Overview

Last Updated: Oct 31, 2017 06:10AM PDT

Summary: The Protocol Exchange is a web portal that provides a way for Pipeline Pilot developers to publish and share protocols that are useful to the research community. This article describes the key features available to the community.

Covered Topics

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Key Features

The Exchange includes numerous key features that are beneficial to the research community. These features include:

  • Secure login using any of the following supported credentials: ScienceCloud guest, ScienceCloud registered user, LinkedIn (your password is not stored or shared). Note that the BIOVIA community log in option is currently disabled. If you have multiple identities, you can link them later to have a single identity for Exchange authentication purposes.  
  • Intuitive home page for finding and sorting protocols of interest
  • Search for protocols based on their names
  • Filter for protocols based on their keyword categories (e.g., Reporting, Generic, Table, etc.)
  • Sort dropdown list to view search results based on name or usage statistics (most relevant, most views, most downloads, most recent, highest rated)
  • Quick access to all protocols you previously downloaded or posted
  • Search Results pane for viewing protocol summary information, with one-click access to opening protocols on the Exchange to:
  • Download protocols posted by others and test them in Pipeline Pilot
  • Review and rate protocols
  • Comment on protocols to share ideas and ask questions

Logging In and Out

The Exchange offers a secure login using any of the following supported credentials:

  • ScienceCloud guest
  • ScienceCloud registered user
  • BIOVIA community (this option is currently disabled)
  • LinkedIn (your password is not stored or shared)

Note: If you have multiple identities, you can link them later to have a single identity for Exchange authentication purposes. For further information, see Exchange Authentication.

To log in to the Exchange:

  1. Point your browser to
  2. Select a sign-in option:
    • Sign in as ScienceCloud User
    • Sign in as Community User
    • Sign in with LinkedIn
    • Continue as Guest
  3. At the prompt, enter your Username and Password. (A username and password are not required for Guest login.)

To log out of the Exchange:

  • Click Sign Out.

Opening a Protocol

To open a protocol:

  • From the Search Results grid, select the protocol you want to open.

The protocol opens on a separate page and displays details and features for working with it on the Exchange. Information provided about a posted protocol can include:

  • Name
  • Usage statistics (Average Rating, status indictor showing if you rated the protocol or not, number of times protocol has been previously viewed an downloaded)
  • Protocol author name
  • Date posted
  • Description
  • Keywords
  • Required Collections
  • Required Data Files


Viewing a Protocol

You can view protocols on the Exchange to get an idea of how you can use them in Pipeline Pilot.

To view a protocol:

  • Click View Protocol.

The protocol, as it was designed in Pipeline Pilot, is displayed in a window that includes the following tabs:

  • Protocol Execution – Provides a graphical view of the components and pipelines used in the protocol.
  • Help – Displays details written by the protocol author about how to use the protocol in Pipeline Pilot.
  • Default Parameters – If the parent-level protocol contains any default parameters, they are listed here.


Downloading a Protocol

To download a protocol:

  1. Click Download.
  2. Use your browser's download features to import the protocol file into your local installation of Pipeline Pilot.

Tip: If a protocol requires data files, the filenames are listed in a Data Files section. To download the data file, click on the filename (or zip file).


Rating a Protocol

A protocol displays star icons across the top that you can use to assign it a rating. As you hover across the stars (from left to right), they are displayed in red to indicate the rating that will be applied when you click your mouse. The greater the number of stars that are highlighted, the higher the rating.

To rate a protocol:

  • Click the stars.

Adding Comments to a Protocol

Use the Comments feature to ask questions, share ideas, and offer feedback after testing protocols that you download from the Exchange in Pipeline Pilot.

To add comments:

  1. In the Comments text box, type your text.
  2. Click Submit.




Contribute Protocols to the Exchange

Documenting a Protocol for the Exchange

Exchange Authentication
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