Wikis provide a space to write narrative content to describe a project or content within the project. They are available in Synapse on
Project has a separate Wiki tab where you can create pages and a hierarchy of sub-pages.
Wikis can also be added to
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.
Wikis inherit their sharing settings from the object they are associated with (a Project, Folder, or File), and cannot have separate sharing settings from that object. Anyone (including viewers who are not logged into Synapse if the Project is shared with the public) who has ‘View’ permissions or greater can see the content of the Wiki page if the object is shared with them.
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
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.
Use the Tools menu and then select Edit Project/Folder/File wiki
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.
projWiki = Wiki(title='Data Summary', owner = myProj) markdownText = '''* Cell growth look normally distributed. There is evidence of inverse growth between these two cell lines ''' projWiki['markdown'] = markdownText projWiki = syn.store(projWiki)
library(synapser) synLogin() markdownText <- "* Cell growth look normally distributed\n* There is evidence of inverse growth between these two cell lines." wiki <- Wiki(owner="syn123", title="Analysis summary", markdown=markdownText) wiki <- synStore(wiki)
Project Wiki can have subpages, which will appear nested below the main Wiki page. This will also create a navigation bar on the right side of the page that lists the Wiki subpages in the order they were created. Links to wiki subpages include the
Project ID, the wiki path, and the ID of the wiki page, e.g. https://www.synapse.org/#!Synapse:syn150935/wiki/27376. The subpage ID can be found in the browser URL bar when the subpage is viewed.
To add a subpage, use the Tools menu and then click “Add Wiki Subpage”. You can then edit this sub-page like any other Wiki page through the Tools menu and “Edit Project Wiki”.
These pages can be reordered through the Edit Order button below the Wiki page navigation bar to change both the hierarchy and the order of pages within a particular level.
The layout and text of a
Wiki can be customized using standard Markdown notation. A Formatting Guide is available within the Wiki editing window. For a reference of Markdown formatting see the Markdown Formatting Guide. Useful Markdown shortcuts are available in the Wiki Editor in a tool bar including: heading, bold, italic, strike-through, code block, sub and superscript. Links can be added to content available from any source with a URL.
Widgets are Synapse features that supplement the Markdown text that can be typed into the Wiki editor. These include inserting images, tagging individuals, querying tables, and many more. See the ‘Insert’ menu while in the Wiki editor for the list of widgets to customize your Wiki.
See the ‘Insert’ list for the following widgets to customize your Wiki design.
|Widget||Hover over the image to see what the widget will look like when embedded in your project|
Create a reference list by linking to papers using the References widget
Embeds a preview window for csv, txt and image files
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
A list of Synapse
|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
Provides a Query for any Synapse
Provides a Query based an annotations (need link) added to
Insert a button that links to content within Synapse or elsewhere. Tip: buttons can be colored purple by adding
|Join Team Button
Provide a button for people to join Synapse Teams
Creates a link to the
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, Vimeo Video, and YouTube Video insert a video from various sources.
A Synapse user can be tagged by using the ‘Tag someone’ Widget from the ‘Insert’ menu. This displays a user badge which can be clicked on to visit the users’ profile page. You can also do this by typing ‘@’ while editing a Wiki by entering the Synapse username or part of their full name in the dialog that appears.
See the Synapse Data Use Procedure document for details.