This tutorial will guide you through fundamental Synapse features for managing files and folders via with the web interface. You will learn how to:
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To upload files to Synapse, you will need to perform the additional step of becoming a certified user. Because Synapse stores data from human subjects research, 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.
Before you begin this tutorial, make sure you have already created a project (see Quick Start: Setting Up a Project).
Uploading a File
Synapse can be used to store files of all types. All files that you upload to a project will appear in the Files tab, which is the root directory. You can also create nested folders within a Synapse project to manage files and keep them organized.
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:
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Annotations help you find files and search for data, and they are an essential component of the FAIR principles for data management. In Synapse, annotations are stored as key-value pairs, where the key defines a particular aspect of your data (for example, species, assay, file format) and the value defines a variable that belongs to that category (mouse, RNAseq, .bam). You can add annotations to projects, files, folders, tables, and views in Synapse. In this example, you will annotate the file that you uploaded in the previous section of this tutorial:
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Before you can download a file from Synapse, you must determine whether you have access to it. Click on a file name and look for a green or yellow lock symbol. A green unlock symbol means that the file is available for you to download. A yellow locked symbol means that the file is not available to you. Contact the project owner or click Request Access. To learn more about data access, see Sharing and Accessing Data.
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To download a file from the web:
Navigate to the Files tab of your project and find a file to download. Note that you cannot download entire folders from the web interface, so you may need to expand a folder in the directory to see its contents.
Click the file name to navigate to the file details see a detail page.
Click Download Options button and then Download File.
From this menu, you can also choose to Add to Download listList, which will start a list of files that you can download all at once. Alternatively, you can view the Programmatic Options to see example code that you can use to download files with one of the programmatic clients.
See Getting Started with Synapse API Clients to install your preferred API client. For more instructions on how to download using the programmatic clientsdata from Synapse programmatically, visit the docs for Python, R, and or command line.
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