Uploading Resources to your Synapse Project

Once you are a Certified Synapse user and you have been provided access to your grant’s Synapse Project, you are ready to begin uploading resources.

Before you begin

It is recommended that you review Synapse documentation on Data Access Types and Sharing Settings, Permissions, and Conditions for Use prior to uploading files to Synapse. If you have any questions or are unsure if your resources can be openly shared, please contact the MC² Center for assistance.

Please note: your Synapse Project is configured to mark uploaded resources as “Private” until changed by you or another user with access to your Synapse Project. 

Resource upload steps

1. Within your Synapse Project, access the Files tab to display the folders currently available for uploading data. You can learn more about the Synapse Project Files tab here. 

   1. For datasets that do not currently have a specific metadata schema available, you may use the pre-existing top-level Datasets Folder in your Synapse Project Files explorer.

   2. If you previously submitted resource information using an MC² Center Resource Sharing Plan, top-level folders for the resources you intend to upload should be available.

   3. If the Folder you are looking for does not already exist, please Request a Meeting through the MC² Center Help Desk. A representative from the MC² Center will contact you regarding an introductory meeting, to guide you through preparing a resource sharing strategy.

2. Navigate to the Folder that matches the resource type you will be uploading and select the “Upload Link or File” icon. You can learn more about uploading resources using the Synapse UI here. 

   1. If you would prefer to upload files programmatically, you can learn more about programmatic options here. Documentation on available Synapse clients can be found here. 

3. From the “Upload or Link to File” window that opens, you can:

   1. Drag and drop files to upload your resources.

   2. Select “Browse” to upload from your local file system.

   3. From the “Link to URL” tab, you can provide a URL, which will create a record of the file in the selected Synapse Folder. This is helpful if the resource is stored in another repository (e.g., GEO, SRA, etc.).

      1. Note: When linking resources, please use the top level Datasets Folder in your Synapse project. If you are interested in using an alternative folder, please contact the MC2 Center.

4. The files you uploaded should now be visible in the target folder. You can now move to the Validate and Submit your Metadata step. Resources without annotations cannot be listed on the Cancer Complexity Knowledge Portal.

5. Here are some things that can done with resources stored in Synapse:

   1. You can create a Digital Object Identifier (DOI) for the file or its containing folder.

   2. You can create a table from a stored CSV or TSV file