This tutorial will guide you through fundamental Synapse features by performing some common tasks:
Create your own project
Upload and annotate content
Download a file
Add a description to your work
Share your work with other Synapse users, teams, or the public
Prerequisites
Anyone can browse public content on the Synapse web site, but to download and create content using this tutorial, you will need to register for an account using your email address. You will receive an email message for verification to complete the registration process.
To upload files to Synapse, you will need to perform the additional step of becoming a Certified User. Synapse stores data from human subjects research, which requires special handling and awareness. To upload files, Sage Bionetworks requires that you demonstrate understanding of privacy and security issues. You can complete your certification by taking a short Certification Quiz on Synapse.
Creating a Project
Synapse Projects are the main “containers” where information is stored and organized in Synapse. They are online workspaces where researchers can collaborate and share their work with teammates. Synapse Projects can be shared with individuals, small teams, or large consortia. Projects can be private so only you can see what’s inside, or they can be shared publicly for anyone to browse.
To create a new Project:
Navigate to your Synapse Dashboard. The Projects tab should already be selected.
Click the Create a New Project button.
Decide on a unique name for your Project and click Save.
Synapse will automatically open your new project so you can view your project dashboard.
At the top of the page, find your project name. You can click the green star next to the project name to add it to a list of your favorites. The Synapse ID is below the project name. The Synapse ID is a unique number used as a reference in Synapse, and it is a powerful tool to identify and manage content. Often abbreviated to “synID”, these identifiers are assigned to many things in Synapse; projects, folders, files, tables, views, and wikis all have unique synIDs that can be used to navigate to and reference these specific items. The synID never changes and is always accessible in the URL and visible on the web. If you use one of the programmatic clients to interact with Synapse, you can use synIDs to create scripts that will work universally for anyone and without the need for specifying file paths.
The project dashboard also has tabs for different sections of your project:
Wiki -
Files -
Tables -
Discussion -
Docker -
Organizing Content
You can create folders within a project to organize your files. Files and folders also have their own unique Synapse IDs and can be moved within or between Projects. Uploaded files are stored within Synapse storage.
Adding a Project Wiki
A Wiki is a document that can be edited by multiple people on the web. Synapse uses Wikis to provide descriptions of your Project and data.
Wiki pages can be written using text, Markdown, or basic HTML. Content can include images, tables, code blocks, LaTeX formatted equations, scholarly references, and references to other things in Synapse.
Use the Tools menu to see available Wiki options on Projects, Folders and Files:
Click the Tools button and choose Edit Wiki.
During editing, you have the option to “Preview” your edits.
Add relevant text, and click Save.
See the Wiki User Guide for more information and examples.
Sharing and Teams
The default setting for new Projects in Synapse is private. As a project owner, you choose who to share with, and how. You can find Project sharing settings under the Project Settings menu. Permissions or sharing settings at the Project level are automatically inherited by all Files and Folders within the Project. If needed, you can Create Local Sharing Settings to make certain Files or Folders have permissions that differ from the parent Project.
Groups of users can form Teams for collaboration. Teams can be used for permissions and for communication. Sharing things with teams instead of individual users can provide simiplicity for administrators.
For more details, visit the Sharing Settings and Teams User Guide.
Sharing a Project
By default, your Project and anything inside it are private, so only you can see it. However, you can share an entire project with specific users, teams, or make it public so anyone can browse your content. If you’d like to share your Project with others, see our article on sharing and accessing data to understand how to use Synapse to control access to your data. Then, learn more about how to share an entire Project or just parts of it by reading Sharing Settings and Permissions.
More Guides
Find additional information in our User Guide.
Read about Synapse governance and Terms and Conditions of Use.
For information on using Synapse programmatically, see the documentation for the Python client, command line client, and R client