Getting Started with Synapse

Get Started with Synapse

This getting started guide is for new users who are interested in learning about Synapse. By following this guide, you will learn fundamental Synapse features by performing some simple tasks. You’ll learn how to:

  • Create your own project and add content to Synapse
  • Provide a project narrative which lives along side the scientific artifacts of your work, via the Synapse Wiki tools
  • Share your work with other Synapse users, teams of users, or make your work public

What is Synapse?

Synapse is an open source platform that can be used to carry out, track, and communicate research. Synapse enables co-location of scientific content (data, code, results) and narrative descriptions of that work. Synapse hosts a growing number of living research projects and resources including Sage/DREAM Challenges.

Sage Bionetworks provides Synapse services free of charge to the scientific community through generous support from various funding sources. Synapse hosts many living research projects and resources including Sage/DREAM Challenges.

Synapse operates under a complete governance process that includes Terms and Conditions of Use, guidelines and operating procedures, privacy enhancing technologies, as well as the right of audit and external reviews.

Register for a Synapse Account

Anyone can browse public content on the Synapse web site, but in order to download and create content you will need to register for an account using an email address. You will receive an email message for verification to complete the registration process.

Register

Since Synapse can store human subject data that has sharing and use restrictions, before you can upload files you will need to take a quiz about what kinds of items can be shared in Synapse. To start this process:

Become a Certified User

Explore our accounts, certification and profile validation page to find out more information on the different levels of users.

Project and Data Management on Synapse

Once you have a Synapse account you can start adding content. All Synapse content is organized in Projects where you can collaboratively access and share Wikis (narratives) and Files. Each Project also contains a Discussion Forum.

As an exercise we are going to create an example Project. Decide on a unique name for your Project. Go to your profile Page and click the Create Project button.

By default, your newly created Project is private; you are the only person who can access it and any content you include in it. Later on we will share your created Project with other users.

Objects like Files, Folders, Projects created in Synapse are assigned unique identifiers which are used for unique reference (a Synapse ID) with the format syn12345678.

If you want to find your project at a later time you can see your projects on your profile page.

Organizing Data: creating Files and Folders

You can use the Files tab to share your project’s data, code, results, and any other information. Synapse Files and Folders are identified by a unique identifier. Synapse Folders are used to organize content and can contain other Folders and Files.

To add a Folder, click on the Files tab, then use the Tools menu and select Add New Folder.

Pick a file to upload in the Folder you just created. Use the Tools menu and select Upload or Link to File. Use the Browse button to select the file, or drag and drop it to upload, and click Save.

To explore other features available for Files and Folders, read about annotating files, assigning DOIs, versioning, provenance,and sharing settings.

Adding a Wiki to your Project

The Wiki tab in a Project provides a space for you to write narrative content to describe your project. This Wiki can be organized with subpages and a table of contents.

Folders and Files in your Project can also have a Wiki. You can use this Wiki to document the contents of the Folder or File, similar to a README.

Wiki pages are written with Markdown, a lightweight syntax for styling text on the web. In addition to standard Markdown, Wiki pages can contain customized content, including images, tables, code blocks, LaTeX formatted equations, and scholarly references. Synapse-specific widgets also allow users to embed dynamic content based on other resources stored in Synapse.

See the Wiki user guide for more information and examples.

Here we will create a Wiki for our project. From the project page, click the Tools button and choose Edit Project Wiki. Add some text describing your Project, and then click Save.

To add a Wiki to a Folder or File, click on the Files tab and navigate to the Folder or File, then use the Tools menu and select Edit Folder Wiki or Edit File Wiki.

Local Folder and File Sharing Settings

By default, access to Folders and Files is controlled by the sharing settings that the project has. You may also set individual sharing settings for specific Folders nd Files within a Project.

To share a Project with specific people or make it public, click on the Project Settings menu and select Project Sharing Settings. For more details, read the How to Share Projects section of the Sharing Settings and Conditions for Use instructions.

For instructions on changing sharing settings for Folders and Files, read the Sharing Other Content section of the Sharing Settings and Conditions for Use instructions.

Find additional information and tutorials through our User Guide.

For information on using Synapse programmatically, see the documentation for the Python client, command line client, and R client

Need More Help?

Try posting a question to our Forum.

Let us know what was unclear or what has not been covered. Reader feedback is key to making the documentation better, so please let us know or open an issue in our Github repository (Sage-Bionetworks/synapseDocs).