Document a Protocol for the Exchange

Last Updated: Nov 21, 2015 10:01PM PST

Summary: Good protocol design includes assigning an intelligent name that can help users find your protocol when searching the Exchange. Protocol usability is also enhanced by the use of Sticky Notes and adding descriptive help text and summary information.

Covered Topics

Clicking a link will scroll the page to the relevant section.

Protocol Names

Protocol names deserve extra consideration. The Save Protocol dialog provides a way for you to assign a naming convention (Name) plus background details about the purpose of the protocol (summary). This information is used by the Exchange to mine keywords for protocol searching.

To yield good search results, add a concise summary with text that will help identify your protocol in the search results.

 save protocol dialog.png

Sticky Notes

A Sticky Note is a digital version of a Post-it type note. You can embed these colorful notes directly into your pipelines at the protocol, component, and subprotocol levels.

Use Sticky Notes to document specific sections in your protocol. They can help you capture ideas and organize thoughts about what you build in the exact place where they matter in a pipeline.

When used appropriately, these notes can greatly enhance the usability of your protocols.

 sticky notes overview.png

Adding a Sticky Note in Pipeline Pilot

  1. Open the protocol in Pipeline Pilot.
  2. Right-click where you want to add the note and select Add Sticky Note.
  3. Type your note text.
    sticky notes add.png
  4. Click anywhere outside the note to close it.

Tip: You can resize notes and apply different colors and shading. Right-click the note and select an option.

Help Text

When you design a protocol in Pipeline Pilot, it is good practice to include some helpful text that explains how to use it. This is especially important if you share your files with other users on the Exchange.

Adding Help Text

  1. Open the protocol in Pipeline Pilot.
  2. Right-click and select Edit Protocol to open the editor.
  3. In Summary, add a one-line synopsis that captures the essence of your protocol.
  4. In Description, add the following information:
    • Use hash tags to flag keywords.
    • Optionally, include additional keywords on a separate line.
    • Enter text that provides more detail about your protocol. Be thorough in documenting its use and include details on the type of data it is designed to process. This is also a good place to highlight key parameters and describe how different settings control behavior and performance.

 document protocol.png
The following illustration shows what this well-documented protocol looks like on the Exchange. 
exchange view of protocol.png


Contribute Protocols to the Exchange

Exchange Authentication

ScienceCloud Exchange (Community Overview)
seconds ago
a minute ago
minutes ago
an hour ago
hours ago
a day ago
days ago
Invalid characters found