This getting started guide is for new users who are interested in learning about Synapse. By following this guide, you will learn fundamental Synapse features by performing some simple tasks. You’ll learn how to:
Synapse is an open source platform that can be used to carry out, track, and communicate research. Synapse enables co-location of scientific content (data, code, results) and narrative descriptions of that work. Synapse hosts a growing number of living research projects and resources including Sage/DREAM Challenges.
Sage Bionetworks provides Synapse services free of charge to the scientific community through generous support from various funding sources. Synapse hosts many living research projects and resources including Sage/DREAM Challenges.
Synapse operates under a complete governance process that includes Terms and Conditions of Use, guidelines and operating procedures, privacy enhancing technologies, as well as the right of audit and external reviews.
Anyone can browse public content on the Synapse web site, but in order to download and create content you will need to register for an account using an email address. You will receive an email message for verification to complete the registration process.
Since Synapse can store human subject data that has sharing and use restrictions, before you can upload files you will need to take a quiz about what kinds of items can be shared in Synapse. To start this process:
Explore our accounts, certification and profile validation page to find out more information on the different levels of users.
Once you have a Synapse account you can start adding content. All Synapse content is organized in
Projects where you can collaboratively access and share
Wikis (narratives) and
Project also contains a
As an exercise we are going to create an example
Project. Decide on a unique name for your
Project. Go to your profile Page and click the Create Project button.
By default, your newly created
Project is private; you are the only person who can access it and any content you include in it. Later on we will share your created
Project with other users.
Projects created in Synapse are assigned unique identifiers which are used for unique reference (a Synapse ID) with the format
If you want to find your project at a later time you can see your projects on your profile page.
You can use the
Files tab to share your project’s data, code, results, and any other information. Synapse
Folders are identified by a unique identifier. Synapse
Folders are used to organize content and can contain other
To add a
Folder, click on the
Files tab, then use the Tools menu and select Add New Folder.
Pick a file to upload in the
Folder you just created. Use the Tools menu and select Upload or Link to File. Use the Browse button to select the file, or drag and drop it to upload, and click Save.
Wiki tab in a
Project provides a space for you to write narrative content to describe your project. This
Wiki can be organized with subpages and a table of contents.
Files in your
Project can also have a
Wiki. You can use this
Wiki to document the contents of the
File, similar to a README.
Wiki pages are written with Markdown, a lightweight syntax for styling text on the web. In addition to standard Markdown,
Wiki pages can contain customized content, including images, tables, code blocks, LaTeX formatted equations, and scholarly references. Synapse-specific widgets also allow users to embed dynamic content based on other resources stored in Synapse.
See the Wiki user guide for more information and examples.
Here we will create a
Wiki for our project. From the project page, click the Tools button and choose Edit Project Wiki. Add some text describing your
Project, and then click Save.
To add a
Wiki to a
File, click on the
Files tab and navigate to the
File, then use the Tools menu and select Edit Folder Wiki or Edit File Wiki.
By default, access to
Files is controlled by the sharing settings that the project has. You may also set individual sharing settings for specific
Files within a
To share a
Project with specific people or make it public, click on the Project Settings menu and select Project Sharing Settings. For more details, read the How to Share Projects section of the Sharing Settings and Conditions for Use instructions.
For instructions on changing sharing settings for
Files, read the Sharing Other Content section of the Sharing Settings and Conditions for Use instructions.
Find additional information and tutorials through our User Guide.
Try posting a question to our Forum.
Let us know what was unclear or what has not been covered. Reader feedback is key to making the documentation better, so please let us know or open an issue in our Github repository (Sage-Bionetworks/synapseDocs).