Page Comparison

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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 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 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).

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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

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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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 Organizing Data With Tables.

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 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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