Wikis provide a space to write narrative content to describe a project or content within a project. Wikis are available in Synapse on projects, folders, and 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 plain text, basic HTML, or Markdown. If you choose Markdown to write your wiki, a formatting guide is available within the wiki editing window (it is also available as a wiki here). Useful shortcuts are also available in the wiki editor tool bar, including: heading, bold, italic, strike-through, code block, subscript and superscript.

A wiki inherits 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.

Create, Edit, and Delete a Wiki

You can create, edit, or delete a wiki using the web client or the Python and R clients. Like files, folders, and other objects in Synapse, wikis have a unique Synapse ID (synID) associated with them, and you can use this synID to reference them elsewhere.

Web

Create a new project, then select the Wiki tab. Navigate to the Wiki Tools menu and select the Edit Project Wiki. Content in this project wiki becomes your project’s home page. You can add subpages to your project wiki that will become links on the left side of your home page (jump to the subpages section below to read more).

To add a wiki to a folder or file, navigate to the folder or file and select Edit Wiki from the Tools menu. Content added to a wiki can be previewed before saving. To delete a wiki select Delete Wiki Page under the Wiki Tools menu.

Command line

The command line client does not support the creation of wiki content. We suggest using the web client to create wiki content.

Python

import synapseclient
syn = synapseclient.login()

projWiki = Wiki(title='Data Summary', owner = myProj)
markdownText = '''This is an example sentence.'''
projWiki['markdown'] = markdownText
projWiki = syn.store(myWiki)
PY

R

library(synapser)
synLogin()

markdownText <- "This is example sentence."
wiki <- Wiki(owner="myProj", title="Data summary", markdown=markdownText)
wiki <- synStore(myWiki)
R

Create Page Hierarchy with Subpages

A project wiki can have subpages, which will appear nested below the main wiki page. Creating subpages will also create a navigation bar on the left side of the screen 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 Wiki Tools menu and then click Add Wiki Subpage. You can edit this sub-page like any other wiki page through the Wiki Tools menu and Edit Project Wiki.

Modify Page Order

By default, wiki pages are created at a single level, or without a page hierarchy. As your wiki evolves over time, you may want to change the order and hierarchy of pages. To do this, click the Edit Order button below the wiki page navigation bar to change both the order and hierarchy 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 nest subpages deeper or promote them higher in a page hierarchy. When you are finished, click Done to save your work. Note that only users with the ability to edit the wiki content have the ability to edit the wiki order. Changing the wiki order does not change the synID of the wiki page.

Wiki Widgets

Widgets are Synapse features that can be added to supplement any Markdown text and customize your wiki. These include inserting images, tagging individuals, querying tables, and more. Use the Insert menu at the top of the wiki editor 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, 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

Description

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 '&highlight=true' to the end of the widget markdown

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 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.

Link

Insert a URL or Synapse ID linked to text.

Provenance Graph

Embeds the provenance graph created for a file.

Reference

Create a reference list by linking to papers using the References widget

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 Synapse 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 Table/View

Provides a query for any Synapse table or view and displays the information in the wiki.

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 and enter the Synapse username or part of their full name in the dialog that appears.

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.

Important: Wiki pages do not have specific conditions for use. Do not put any protected human data in Synapse Wikis.

Discussion Forums


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