This guide is for new users who are interested in learning about Synapse. You will learn fundamental Synapse features by performing some common tasks:
Project and add content to SynapseWiki toolsTeams of users, or the publicSynapse is a collaborative research platform that allows individuals and teams to share, track, and discuss their data and analysis in projects. Synapse is built to work on the web. We provide access to Synapse features and services for programmers through a REST API, Python client, command line client, and R client.
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.
Anyone can browse public content on the Synapse web site. 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.
Synapse is a data sharing platform approved for storing data from human subjects research. This requires special care and thought. To upload files, Sage Bionetworks requires you demonstrate awareness of privacy and security issues.
You can complete this by taking a Certification Quiz.
Synapse Projects are online workspaces where researchers can collaborate and organize their work. Synapse supports all kinds of working groups: individuals, small teams, and large consortia.
To create a new Project:
Your Projects dashboard stores your collection of Projects.
Read about Projects in the User Guide.
Synapse Projects are assigned a Synapse ID, a globally unique identifier used for reference with the format syn12345678. Often abbreviated to “synID”, the ID of an object never changes, even if the name does. The Synapse ID is always accessible in the URL and visible on the webpage.
Files and FoldersProjects contain Files, which can be organized into Folders. Folders and Files also have their own unique Synapse IDs and can be moved within or between Projects. Uploaded files are stored within Synapse storage.
Use the Tools Menu to upload a file:
To explore other features available for Files and Folders, read about annotating Files, assigning DOIs, versioning, Provenance, and sharing settings.
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:
See the Wiki User Guide for more information and examples.
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.
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
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).