Upload Data

Uploading and Organizing Data

Need to upload data to Synapse? This section will cover how to do so in an organized and efficient manner so that your data can be easily accessed, downloaded, and/or reused by you and your own team, as well as by community members (if applicable).

To upload files to Synapse, you need to be a certified user. Because Synapse stores data from human subjects research, Sage Bionetworks requires that you demonstrate understanding of and compliance with privacy and security issues. You can complete your certification by taking a short certification quiz on Synapse.

Synapse can be used to store files of all types. Files must be stored within a project. All files that you upload to a project will appear in the Files tab of that project, which is the root directory. You can also create nested folders within a Synapse project to manage files and keep them organized.

Learn all about uploading data (via the Synapse UI or programmatically), as well as organizing data in Synapse, including how to create projects, folders, table, and more, at Uploading and Organizing Data Into Projects, Files, and Folders.

Quick Overview: Uploading a File (via the Synapse UI)

To upload a file:

Within a project, navigate to the Files tab.
Click the File Tools menu to select Upload or Link to a File
Use the Browse button to select the file, or drag and drop it to upload, and click Save

To create a folder and upload a file:

Navigate to the Files tab.
Use the Files Tools menu to select Add New Folder (or the Folder Tools menu if adding a folder within a folder)
Decide on a folder name and click Save
Navigate into your new folder by clicking on the name, then use the Folder Tools menu to select Upload or Link to a File
Use the Browse button to select the file, or drag and drop it to upload, and click Save.

Uploading Large Data

Large data files can be uploaded programmatically using the Synapse Client at either the command line interface or within Python or R. Additional information about these methods is provided in the next section.

Data Transfer Methods

Upload Data Using the Command Line

REQUIREMENTS

You are a certified user on Synapse
Synapse Client 3.0.0+

This option is most suitable for upload of files on a cloud or your local machine. Click here for more information

Upload Data Using Synapse Python Client

REQUIREMENTS

You are a certified user on Synapse
Python v3.9+
Python Synapse Client 3.2.0+
This option is most suitable for upload of files on a cloud or your local machine. Click here for more information

Upload Data Using Synapse R Client

REQUIREMENTS

You are a certified user on Synapse
R version 4.1.3 or higher; Python version 3.8 or higher; or Reticulate version 1.28 or lower
Click here for a step-by-step upload guide

Upload Data Using the Synapse Web Interface

REQUIREMENTS

You are a certified user on Synapse
This option is useful for uploading files residing on your local machine to a Synapse cloud storage location. Click here for a step-by-step upload guide