Wikis provide Wikis provide a space to write narrative content to describe a project or content within the project. They are available in Synapse on Projectson Projects, Folders Folders, and Filesand Files. Every Project has a separate Wiki tab where you can create pages and a hierarchy of sub-pages.
Wiki pages can be written using text, Markdown, or basic HTML. Additionally, you can embed dynamic content based on other resources stored in Synapse.
A Wiki inherits it’s its sharing settings from the Project, Folder, or File it is associated with, and it cannot have separate sharing settings. Anyone with ‘view’ permissions or greater can see the content of the Wiki page. When a Project, Folder or File is shared with the public, the associated Wiki is visible to viewers who are not logged in to Synapse.
Creating, Editing, and Deleting a Wiki
Through a Web Browser
After creating Create a new projectProject, then select the Wiki tab. Start a Wiki through the Navigate to the Wiki Tools menu by selecting and select the Edit Project Wiki function. Content in this first Wiki becomes your Project’s home page. Go to the Wiki Tools menu to add subpages to your Wiki. These will appear as links on the left side of your home page. Adding
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To add a Wiki to a Folder or File is done in a similar manner by selecting ‘Edit Folder/File Wiki’, navigate to the Folder or File and select Edit Wiki from the Tools menu. Content added to a Wiki can be previewed before saving. Each version of a saved Wiki is visible under Wiki Revision History where older versions can be restored. To delete a Wiki select a Wiki select Delete Wiki Page under the Wiki Tools.
Use the Tools menu and then select Edit Project/Folder/File wiki
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menu.
Command Line
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.
Python
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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) |
R
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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) |
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A 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 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 the Wiki Tools menu and then click Add Wiki Subpage. You can then edit this sub-page like any other Wiki page through the Tools menu Wiki 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. Click Edit Order, and then select the page you want to move. Use the arrow buttons to move the page up or down in your page tree. Use the left and right arrows to create or promote subpages. When you are finished, click Done to save your work.
Wiki Markdown Language
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 also available in the Wiki Editor in a tool bar, including: heading, bold, italic, strike-through, code block, sub subscript and superscript. Links can be added to content available from any source with a URLYou can also insert links to any URL source.
Wiki Widgets
Widgets are Synapse features that can be added to supplement the any Markdown text that can be typed into the Wiki editorand customize your Wiki. These include inserting images, tagging individuals, querying tables, and many more. See Use the ‘Insert’ menu while in Insert menu at the top of 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.
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Tip: To window to select a widget. Each of these widgets is described in the following table.
To edit widgets after they have been added to the wiki, see the widget edit use the Edit Synapse Widget button in the upper left hand corner of the Wiki editing window. Click on the Markdown text for a widget, and then click Edit Synapse Widget to view the widget configuration window again.
Widget | Hover over the image to see what the widget will look like when embedded in your project | ReferenceDescription | ||||
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Attachment | Attach a file from your local computer to the Wiki. | |||||
Button Link | Insert a button that links to content within Synapse or elsewhere. Tip: buttons can be colored purple by adding | |||||
Collapsible Section (Details/Summary) | Insert a label or heading that you can click to expand and reveal additional text. | |||||
Entity List | A list of Synapse Folders, Files or Tables can be 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 version and version notes (if selecting Files, Tables, or Views). | |||||
File Preview | Embeds a preview window for .csv, .txt, and image files | |||||
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. | |||||
Image | Embeds Embeds an JPG, PNG, GIF or SVG. The image can be uploaded, from the web, or from a Synapse file. Note: Images file names that have certain words (ie, ‘ad’) could be blocked if you are using an adblocker. . | |||||
Join Team Button | Provide a button for people to join Synapse Teams. | |||||
Leaderboard | ||||||
Link | Insert a URL or Synapse ID linked to text. | |||||
Provenance Graph | Embeds the provenance graph created for a file. | |||||
Table of ContentsReference | Create a content reference list that links to sections of the wiki based on headers and subheadersEntity List | |||||
Simple Plot | Insert a simple bar chart from a File or Table. | |||||
Submit to Evaluation | Create a button for users to submit their entries to a Challenge. | |||||
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 Table or View and displays the information in the Wiki. | Button Link | Join Team Button | Team Badge | Genome Browser | Video |
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Tagging Synapse Users
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Table of Contents | Creates a content list that links to sections of the wiki based on headers and subheaders |
Team Badge | Creates a link to the Team profile. |
Team Member Count | Select a Team to display the team member count. |
Team Members List | Select a Team to display a table of the team member names, Institutions, and Synapse email addresses. |
User | Tag a user by entering their Synapse username. You can also do this by typing ‘@’ while editing a Wiki |
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and enter the Synapse username or part of their full name in the dialog that appears |
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Video | Video, Vimeo Video, and YouTube Video insert a video from various sources. |
Widgets in Experimental Mode
Some widgets are available only in Experimental Mode, or alpha mode. These widgets are still under development but are available for public use. To access these widgets, navigate to the lower right hand corner of your screen in Synapse, and click Experimental Mode Off. Read the Experimental Mode statement and click OK. Navigate back to a wiki page, where a new @ Insert menu option will appear at the top of the Wiki editing window with a list of widgets in development. Use these widgets with caution, as they may change in the future and data created using them could be lost during upgrade.
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Important: Wiki pages do not have specific Conditions for Use. Do not put any protected human data (Controlled Data) in Synapse Wikis. |
See the Synapse Data Use Procedure document for details. |
See Also
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