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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/wiki/spaces/DOCS/pages/2024276030 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.
You can create wikis using the Synapse UI or programatically. 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.
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Creating,
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Editing, and
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Deleting a Wiki via the Synapse UI
Within an existing project or a new one, click the Wiki tab. Navigate to the Wiki Tools menu and select the Click 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 read more in the subpages section below to read more).
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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.
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Creating a Wiki Programatically
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
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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) |
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library(synapser) synLogin() markdownText <- "This is example sentence." wiki <- Wiki(owner="myProj", title="Data summary", markdown=markdownText) wiki <- synStore(myWiki) |
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Creating 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.
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Modifying 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.
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Widget | Description |
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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 Genome Browser section below 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/wiki/spaces/DOCS/pages/1985446029. |
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. |
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Wiki table widgets allow you to embed tabular data into a wiki, enabling quick access to files or data. There are two ways to embed tabular data into a wiki: either paste the data directly, or select data from existing tables or file views in Synapse.
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Pasting Tabular Data
To embed tabular data in a wiki page, navigate to the wiki and select Wiki Tools, then Edit Wiki. From the Insert menu in the wiki editing window, select Table: Paste Tabular Data. In the next window, paste tab delimited data and click Save.
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Selecting Data from a Synapse Table or View
If you uploaded a table or created a view in Synapse, you can use the Table: Query on a Synapse Table/View widget to add the entire table or view to your wiki. You can also choose to add only a subset of your table or view using a SQL-like query.
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In the example below, a specific subset of data from a file view is embedded in a wiki. This file view contains both RNA-Seq and SNP genomic data, as depicted in the file view scope shown in the image below. The scope can be restricted to RNA-Seq data with additional queries on the embedded table. This example will demonstrate how to highlight .fastq and .bam RNA-Seq files in an embedded wiki table, so that team members have a clear path to access files for reproducible studies.
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Restricting a Query
A table query is required to embed table or file view data into your wiki. In this example, the parent file view is a combination of multiple assay types, and the query is restricted to isolate relevant RNA-Seq entries. Additionally, the columns can be limited to ensure only imperative information is visible in the wiki.
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SELECT id,currentVersion,fileFormat,assay,genomeBuild,modifiedOn FROM syn17097374 WHERE "assay" = 'rnaSeq' AND "fileFormat" = 'bam' OR "fileFormat" = 'fastq' |
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Embedding a Table
Navigate to Wiki Tools to Edit Project Wiki or to Folder Tools to Edit Folder Wiki. From the wiki editing window, select Insert and Table:Query on a Synapse Table/View to insert the intended file view query. The result is a direct link to relevant files from a wiki page. Add narrative text to provide additional information or context for this view.
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In order to use forms, you’ll need to create a table first. Read more
Learn about creating tables at /wiki/spaces/DOCS/pages/2011038095.
Activating and Deactivating Experimental Mode
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Entering data into a form is equivalent to editing the data in a table, so users who wish to add data using the form will need to have Edit permissions on the table. See Sharing settings
See /wiki/spaces/DOCS/pages/2024276030 for more information on controlling who can edit your table.
See also:
Tables, Wikis, Sharing Settings and Permissions
Genome Browser
Biodalliance Setup
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