Getting Started with Synapse | Synapse Documentation

Get Started with Synapse

This guide is for new users who are interested in learning about Synapse. You will learn fundamental Synapse features by performing some common tasks:

  • Create your own project and add content to Synapse
  • Provide a project description alongside your materials via the Synapse Wiki tools
  • Share your work with other Synapse users, teams of users, or the public

What is Synapse?

Synapse is an open source collaborative platform. It can store data, code, results, and descriptions research work. Synapse hosts many research projects and resources. It also hosts crowdsourced competitions, including DREAM Challenges. Sage Bionetworks provides Synapse services free of charge to the scientific community through generous support from various funding sources.

Synapse operates under a thorough governance process. This includes Terms and Conditions of Use, guidelines, and operating procedures.

Register for a Synapse Account

Anyone can browse public content on the Synapse web site, but 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

Synapse can store human subject data with sharing and use restrictions. Before you can upload files, you must demonstrate you understand what you can share in Synape. To start this process:

Become a Certified User

Read the accounts, certification, and profile validation page to learn more about the different levels of users.

Project and Data Management on Synapse

Synapse content is organized in Projects. In a project you can upload files and write descriptions (Wikis). Each Project also contains a discussion forum.

To create a Project:

  1. Go to your projects list on your dashboard.
  2. Click the Create Project button.
  3. Decide on a unique name for your Project and click Save.

By default, your newly created Project is private. You are the only person who can access it, including any content in it. In another tutorial you will learn how to share your project with other users.

Synapse projects are assigned a Synapse ID, unique identifiers used for reference with the format syn12345678.

To find your project at any time, you can see your projects on your dashboard.

Organizing Data: creating Files and Folders

You can use the Files tab to upload data, code, results, and other information to your project. Synapse Folders are used to organize content and can contain other Folders and Files. Synapse Folders and Files are also assigned a unique identifier (Synapse ID).

To add a Folder:

  1. Click on the Files tab.
  2. Use the Tools menu and select Add New Folder.
  3. Decide on a Folder name and click ‘Save’.

To upload a file into that folder:

  1. Use the Tools menu and select Upload or Link to File.
  2. 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

A Wiki is a document that can be edited by multiple people on the web. The Wiki tab in a project provides a space to write a description. 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 the 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 Wiki widgets also allow you to embed content based on other resources stored in Synapse.

See the Wiki user guide for more information and examples.

Create a Project wiki:

  1. From the project page, click the Tools button and choose Edit Project Wiki.
  2. Add some text describing your project, and then click Save.

To add a wiki to a folder or file:

  1. Click on the Files tab and navigate to the Folder or File.
  2. Use the Tools menu and select Edit Folder Wiki or Edit File Wiki.
  3. Add some text describing the folder or file, and then click Save.

Local Folder and File Sharing Settings

By default, access to folders and files is controlled by the same sharing settings as the project. You may set different sharing settings for specific folders and files in a project.

You may share a Project with specific people or make it public.

  1. Click on the Project Settings menu and select Project Sharing Settings.
  2. Add individuals or teams with different permissions.

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 in 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).