This guide is for new users who are interested in learning about Synapsetutorial will guide you through fundamental Synapse features for creating a project via the Synapse UI. You will learn fundamental Synapse features by performing some common taskshow to:
Create your own
Projectand add content to SynapseProvide a Project description alongside your materials via the SynapseWikitoolsown projectExplore the project dashboard
Add a description to your project in the wiki
Share your work with other Synapse users,
Teamsof users teams, or the public
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Prerequisites
Anyone can browse public content on the Synapse web site. To download and website, but to create content using this tutorial, you will need to register for an account using an your email address. You will receive an email message for verification to complete the registration process.
Getting Certified
Synapse is a data sharing platform approved for storing data 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. This requires special care and thought. To upload files, Sage Bionetworks requires that you demonstrate awareness understanding of privacy and security issues. You can complete this your certification by taking a Certification Quiz.
Making and Managing Projects in Synapse
Synapse Projects a short certification quiz on Synapse.
Creating a Project
Projects are the main “containers” where information is stored and organized in Synapse. They are online workspaces where researchers you can collaborate and organize their share your work . Synapse supports all kinds of working groups: with teammates. Projects can be shared with individuals, small teams, and or large consortia. Projects can be private so only you and your team can see what’s inside, or they can be shared publicly for anyone to browse.
To create a new Projectproject:
Navigate to the User Menu and click on Projects.
Click the Create a New Project button.
Decide on Click the Projects icon in the Synapse toolbar
Click the plus sign (+) next to Projects
Enter a unique name for your Project project and click Save.
Your Projects dashboard stores your collection of Projects.
Read about Projects in the User Guide.
Synapse IDs
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click Save
Synapse will automatically open your new project so you can view your project dashboard.
Exploring the Project Dashboard
Your project dashboard allows you to see the different elements of your project at once. At the top of the project page, you can click the star next to your project name to add it to a list of favorites.
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Below the project name, the Synapse ID (synID) is a unique number used to reference this project, and it is a powerful tool to identify and manage content. Projects, folders, files, tables, views, datasets, 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 webpage.
Organizing Content in Files and Folders
Projects 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:
Navigate to the Files tab.
Use the Files Tools menu to select Add New Folder.
Decide on a Folder name and click Save.
Navigate into your new Folder and 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.
To explore other features available for Files and Folders, read about annotating Files, assigning DOIs, versioning, Provenance, and sharing settings.
Adding a Wiki to your Project
A Wiki is a 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: A wiki is like a virtual notebook where you can describe your research so others can understand your goals, methods, or anything else you want to communicate about your project.
To learn more, see /wiki/spaces/DOCS/pages/1975746682.
Files: This tab contains a directory of all of your files and folders within this project. Use this tab to see the hierarchy or structure of information as you add it.
To learn more, see /wiki/spaces/DOCS/pages/2048327716.
Datasets: This tab contains any datasets that you have created. A dataset is a collection of files that already exist in Synapse that may be hosted in one or more Synapse projects or folders.
To learn more, see /wiki/spaces/DOCS/pages/2611281979.
Tables: This tab contains tabular data. You can upload data tables or create them directly from the Synapse interface. You can also use this tab to create views, which are tables of other data in Synapse.
To learn more about tables, see /wiki/spaces/DOCS/pages/2011038095.
To learn more about views, see /wiki/spaces/DOCS/pages/2011070739.
Discussion: Use this tab to communicate with teammates in a discussion forum.
To learn more, see /wiki/spaces/DOCS/pages/1985904796.
Docker: Docker is a platform for creating virtual containers to bundle code and other dependancies. You can add a Docker container to a project and share it with your teammates.
To learn more, see /wiki/spaces/DOCS/pages/2011037752.
Adding a Project Wiki
A wiki is a virtual document that can be edited by multiple people on the web. Synapse uses Wikis Wikis are powerful tools to add information about your project, and Synapse offers over a dozen widgets to customize your wiki pages. Use wikis to provide descriptions of your Project project goals, methods, and data.
Wiki pages can be written using text, Markdown 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 FilesTo add wiki content:
Click on the Wiki tab and use the Tools button and choose Edit Wiki.
During editing, you have the option to “Preview” your edits.
Add relevant text, and click Save.
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Wiki Tools menu.
Choose Edit Wiki to add or edit wiki content.
From the editing window, click Preview to check your work. Click Save when you are finished.
For more information on how to organize and customize your wiki content, see Creating and Managing Wikis.
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 ProjectBy 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.
For more information on how Synapse can help you control access to your data, see /wiki/spaces/DOCS/pages/2024276030.
To share a project:
Click on the Project Settings menu and select Project Sharing Settings.
Enter the usernames or team names to add collaborators.
To make the project publicly viewable, click Make public and then adjust the access levels for registered users and anyone on the web.
Groups of users can form Teams Synapse teams for collaboration. Teams can be used for managing permissions and for communicationcommunicating with your collaborators. Sharing things something with teams a single team instead of many individual users can provide simiplicity for administratorshelp administrators manage large, complex projects.
For more details, visit the Sharing Settings and Teams User Guide.
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 Learn more about teams /wiki/spaces/DOCS/pages/1985446029
And learn about using teams to manage group communication and project permissions at Managing Data Access With Teams.
Anything inside your project will automatically inherit the same sharing settings as the project itself. In other words, if your project is public, then all of the contents within the project will also be public. If needed, you can change these settings so that certain files or folders are only shared with specific groups of users.