This tutorial will guide you through fundamental Synapse features by performing some common tasks:
Create your own project
Explore the project dashboard
Add a description to your project in the wiki
Share your work with other Synapse users, teams, or the public
Prerequisites
Anyone can browse public content on the Synapse website, but to create content using this tutorial, you will need to register for an account using your email address. You will receive an email message for verification to complete the registration process.
To upload files to Synapse, you will need to perform the additional step of becoming a Certified User. Synapse stores data from human subjects research, which requires special handling and awareness. To upload files, 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.
Creating a Project
Synapse Projects are the main “containers” where information is stored and organized in Synapse. They are online workspaces where researchers can collaborate and share their work with teammates. Synapse Projects can be shared with individuals, small teams, or large consortia. Projects can be private so only you can see what’s inside, or they can be shared publicly for anyone to browse.
To create a new Project:
Navigate to your Synapse Dashboard. The Projects tab should already be selected.
Click the Create a New Project button.
Decide on a unique name for your Project and 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 green star next to the project name to add it to a list of your favorites. Below the project name, the Synapse ID for this project is visible. The Synapse ID is a unique number used as a reference in Synapse, and it is a powerful tool to identify and manage content. Often abbreviated to “synID”, these identifiers are assigned to many things in Synapse; projects, folders, files, tables, views, 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 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.
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.
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.
Discussion - Use this tab to communicate with teammates in a discussion forum.
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.
Adding a Project Wiki
A Wiki is a virtual document that can be edited by multiple people on the web. Use Wikis to provide descriptions of your project goals, methods, 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.
To add wiki content:
Click on the Wiki tab and use the 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.
Wikis are powerful tools to add information about your project, and Synapse offers over a dozen widgets to customize your wiki pages. See the Wiki for more information on how to organize and customize your wiki.
Sharing and Teams
By 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. If you’d like to share your project with others, see our article on sharing and accessing data to understand how Synapse can help you control access to your data.
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 for collaboration. Teams can be used for permissions and for communication. Sharing things with teams instead of individual users can be a simple solution for administrators. Read more about using teams to manage /wiki/spaces/DOCS/pages/1985446029 and /wiki/spaces/DOCS/pages/2030502408.
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 shared with different groups of users. For more details, visit the Sharing Settings and /wiki/spaces/DOCS/pages/2030502408 User Guides.
Related Articles
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