Wikis

Overview

Wikis are available in Synapse both on the Project level and on Files/Folders to provide a space to build narrative content to describe the research. Every project has a Wiki tab where you can build pages and a hierarchy of subpages as you would with any website. These pages can be reordered through the Edit Order button below the Wiki pages, to change both the hierarchy and the order of pages within a particular level.

Wikis can also be added to Folders and Files allowing additional content documentation. Wikis, whether they are under the Wiki tab or on a folder, are built in the same way and enables incorporation of highly customized content including, but not limited to: images, tables, code blocks, LaTeX formatted equations, and scholarly references. In addition, Synapse-specific widgets lets you embed dynamic content based on other resources stored in Synapse.

Creating, editing, and deleting a Wiki

Using the Synapse web portal

After creating a new project, select the Wiki tab. Start a Wiki through the Tools menu by selecting the ‘Edit Project Wiki’ function. Content in this first Wiki becomes your Project’s home page. Go to the Tools menu to add subpages to your Wiki. These will appear as links on the left side of your home page. Adding a Wiki to a Folder or File is done in a similar manner by selecting ‘Edit Folder/File Wiki’. Content added to a Wiki can be previewed before saving. Each version of a saved Wiki is visible under Wiki History where older versions can be restored. To delete a Wiki select ‘Delete Wiki Page’ under Tools.

Select Tools then select Edit Project/Folder/File wiki

Using R/Python

 
The command line client does not support the creation of Wiki content. We suggest using (to get to the webpage of the project) `synapse onweb syn###` where `syn###` is the Synapse Id of your created project. Then editing the Wiki using the web client. 

Governance

Wiki pages do not have Conditions for Use as a feature. Therefore, do not put any protected human data (Controlled Data) in Synapse Wikis. See the Synapse Data Use Procedure document for details.

Wiki Features

Markdown language

The layout and text of a Wiki can be customized using Wiki markdown language. A Formatting Guide is available within the Wiki editing window. For additional markdown functions see Markdown in Synapse. Useful markdown shortcuts are available as separate tools, including: heading, bold, italic, strike-through, code block, sub and superscript.

Tables in Markdown

To create a table you separate the columns by the pipe character (|). A Header can be added by separating the first row by dashes (-). A header allows the table to be sorted by each column. A simple table would be created by the following markdown.

````
 Header 1 | Header 2 | Header 3 |
--- | --- | --- |
 a  |  b  |  c  |
````

For more table settings see the formatting guide at the top of the wiki editor.

synapse logo Tip: To insert large amounts of text, use the widget "Table: Paste tabular data" (see all widgets below).

Files, images and videos can be attached to a Wiki. This may be content on from the web, your desktop, or Files already uploaded to Synapse. Links can be added to content available from any source with a url or to a Synapse users profile through the Tag someone widget, or by typing @ - just enter the Synapse username in the dialog that appears.

Additional Widgets

On the project Wiki page, go to ‘Tools’ and click on ‘Edit Project Wiki’

See the ‘Insert’ list for the following widgets to customize your Wiki design.

synapse logo Tip: To edit widgets after they have been added to the wiki, see the widget edit button in the upper left hand corner of the Wiki editing window.
Widget Hover over the image to see what the widget will look like when embedded in your project
References
Create a reference list by linking to papers using the References widget
File Preview
Embeds a preview window for csv, txt and image files
 
Provenance
Embeds the provenance graph created for a file
Table of Contents
Creates a content list that links to sections of the wiki based on headers and subheaders
Entity List
A list of Synapse Folders, Files or Tables can be easily created by browsing to the Synapse location or searching by entity name or Synapse ID. The table lists entity name, date entity was created, who created it, and for Files and Tables - version and version notes
Table: Paste tabular data
A table can be created of any data by pasting tab delimited content into this widget window.
Table: Query on a Synapse Table
Provides a Query for any Synapse Table and displays the information in theWiki.
Query on Files/Folders
Provides a Query based an annotations (need link) added to Files and Folders. Columns in the Query table can be renamed and ordered through the ‘Add Column Renderer’
Button Link
Insert a button that links to content within Synapse or elsewhere. Tip: buttons can be colored purple by adding '&highlight=true' to the end of the widget markdown
Join Team Button
Provide a button for people to join Synapse Teams
Team Badge
Creates a link to the Team profile
Genome Browser
You can add a Biodalliance genome browser using tracks from files uploaded to Synapse or from external sources. Choose between Human or Mouse and adjust your tracks for height and color. See the Biodalliance Setup page for more information
Video
Video, Vimeo Video, and YouTube Video insert a video from various sources.


See Also

Discussion

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