FAQ

Synapse allows researchers to share and describe data, analyses, and other content. Data and analyses can be stored in many types of locations, including private servers, local hard drives, or cloud storage. Synapse provides a common interface to describe these data or analyses, where they come from, and how to use them. Synapse also provides mechanisms for adding and retrieving data, analyses, and their respective descriptions.

Sage Bionetworks provides Synapse services free of charge to the scientific community through generous support from the National Cancer Institute (NCI), the National Heart, Lung, and Blood Institute (NIH NHLBI), the Children’s Tumor Foundation (CTF), the Neurofibromatosis Therapeutic Acceleration Program, the Alfred P. Sloan Foundation, the National Insitute on Aging (NIA), and the National Institute of Mental Health (NIMH).

Not directly. Synapse helps you manage data, analysis and results. However, using the programmatic interfaces built into Synapse makes it easy to set up analytical pipelines and ad hoc analysis that interacts with Synapse. By default Synapse uses Amazon’s cloud infrastructure (S3) for storage, making it simple to allocate large compute resources and collocate them next to data storage.

Anyone age 13 or older may use Synapse. We have highlighted a series of research communities that are currently using Synapse for their collaborative work and some open resources hosted in Synapse.

Our Discussion Forum is a great place to reach out to the broader Synapse community to find others that may be interested in a collaboration. You can also reach us directly via our virtual help desk.

The Terms and Conditions of Use fully describes the governance terms and conditions of Synapse. In order to register on Synapse, you must review and agree to the terms of the Synapse Awareness and Ethics Pledge. For more information, see /wiki/spaces/DOCS/pages/2004255211.

Yes, Synapse is released under the Apache 2.0 License The source code is available on GitHub. Synapse is also offered free of charge as a hosted Software as a Service (SaaS) at https://www.synapse.org/.

Yes, Synapse is built on top of a RESTful service that is automatically documented. In addition, we have purpose built APIs for Python, R, Java and a command line interface.

Synapse was developed with the philosophy to encourage collaboration across institutional boundaries and is therefore provided as “Software As A Service” with a single instance used by all users. This makes it easy both to discover new content and share with new collaborators. We do support private project spaces where content sharing is controlled by the individual user. In addition, Synapse has the ability to reference resources that are stored elsewhere. This allows Synapse to store metadata about the content such as annotations, descriptive wiki pages and provenance but not the actual data. Currently Synapse has specific support for files stored at URLs, on SFTP servers, on AWS S3 and arbitrary file servers (see: /wiki/spaces/DOCS/pages/2048327803).

You may browse open issues or file a bug through our Jira tracker system. To file a bug, use the blue “Create” button in the top center of the page. Please be sure to include your email address in your submission so we may follow up with you.

See /wiki/spaces/DOCS/pages/2055471150 for a breakdown of what you need to get started and how to make the most of Synapse.

Whether you are looking to access content or use Synapse to track your own work, start by registering for a Synapse user account. Before uploading files, you will need to take a short certification quiz that demonstrates your understanding of the ethical considerations in sharing data and the manner in which data is managed and shared in Synapse.

This will depend if the content is public or private. If private, you will need to make sure your colleague has shared this content with you. Shared content is visible from your “Dashboard page” under the tab “Shared directly with me”. If you favorite the content (using the star) it will appear under your list of favorites visible from the /wiki/spaces/DOCS/pages/2048557182 or on your /wiki/spaces/DOCS/pages/2055405596.

All public data is queryable. For more information see /wiki/spaces/DOCS/pages/2667642897 or from the “Search” box in the top right corner of any Synapse page.

Multiple research communities use Synapse to generate data that is released to the public. A description of some of these communities can be found on the Synapse Research Communities Page and public resources page.

You can browse public content in Synapse without registering. However, without an account you cannot add new content to Synapse, nor can you upload or download files or tables. With an account you can create projects and wikis, download open data and request access to controlled data. Further, an account lets you collaborate with other Synapse users and create user teams. For more information see the /wiki/spaces/DOCS/pages/2007072795 page.

Validating your profile is a process where your identity is established through a combination of your profile information, your ORCID, a signed Synapse Pledge, and an external credential. Validation increases transparency between researchers and data donors. A validated profile is needed for access to specific datasets, and is currently required for access to data collected through Sage Bionetworks’ research apps. Profile validation instructions can be found in the Settings tab of your Synapse profile page. Click on the ‘Request Profile Validation’ link to see the required steps.

Synapse makes it easy to share files of any sort, with whomever you choose whether a small group of collaborators or the general public. You may share raw data, summarized data, analysis results, or anything in between. See /wiki/spaces/DOCS/pages/2002846338 for information and instructions on sharing your data.

User certification ensures that you understand your responsibilities for sharing data through Synapse, especially data derived from human participants. These responsibilities include making sure that data derived from human participants is de-identified and that all applicable privacy laws and regulations are observed.

To become a certified user, you will need to pass a brief quiz.

No. Use sharing settings to control who can see the content you create. By default, projects and their content are visible only to the user who created it. By using the Synapse sharing settings, you have the ability to grant other Synapse users, Synapse teams, or the public access to your Project content. You can learn more here: /wiki/spaces/DOCS/pages/2024276030.

Yes. Synapse has an IRB-approved data governance procedure that employs Conditions for Use to allow for the sharing of sensitive data in a controlled manner. You can learn more by reading /wiki/spaces/DOCS/pages/2024276030 and /wiki/spaces/DOCS/pages/2004255211. If you have questions or would like assistance in applying Conditions of Use to your data, please contact the Synapse Access and Compliance Team at act@sagebase.org.

Synapse stores content in Amazon Web Services, which provides a layer of security measures designed and implemented by Amazon. While Synapse is an open access site, each user has control over who may access their content by using sharing settings.

By default, Synapse stores files in Amazon Simple Storage Services (S3). However it is possible to set up Synapse to store files in different locations such as your local SFTP server. For files stored outside of S3, Synapse can be used to organize, manage, and access files through the use of Synapse annotations to store file-specific metadata. (see: /wiki/spaces/DOCS/pages/2048327803)

Sage can help you prepare materials for your data management and sharing plan and budget. We will provide a quote for services for use in your budget as well as standardized text for your plan.

Sage will help you setup your project and storage through self-service and easy-to-follow documentation.  For data coordination projects we provide customized support and storage

No, accounts and projects are grandfathered with their current agreement with Sage.

You can mint DOIs for projects and files uploaded to Synapse, extremely useful for citing data.  Learn More

Sage provides consulting to help you upload your data and make it F.A.I.R.  For the Managed Plan, this includes 2 hours of consulting with our governance team to ensure you set the appropriate sharing policies as well as a 3 hours of solutions architect time to assist you creating your project and uploading data.  These consulting hours can be customized in your quote to better meet your needs.

You and your data downloaders can use the Sage help desk to ask questions and receive support within our SLAs.  With the Data Coordination plan, a point of contact is assigned to you for support. 

These are the general storage limitations for each plan. These can be customized for the Managed and Data Coordination plans.  There are no data limits if you use your own cloud bucket and, depending on the dataset uploaded, may be sponsored by an existing project.  Contact us to learn more.

By default, data is stored in AWS US-EAST-1.  You can customize the location in the Standard and Managed Plans by providing your own cloud bucket.  This can be customized for you in the Data Coordination Plan.  Learn More

Sage offers controlled access data hosting in the Managed and Data Coordination plans only.

Sage offers integrations with multiple cloud compute environments for customized Data Coordination Plans.

In the Standard Plan you can manually add or remove Synapse users to your project spaces.  If you contact us, we can setup additional data use limitations and require accessors to record their agreement to comply with the terms through a “clickwrap” before accessing content (There is a nominal fee in the Standard Plan. This is included in the Managed and Data Coordination plans).  

For the Data Coordination Plan we offer a complete data access committee service, either managed by you or by Sage to review/administer requests to controlled-access data.

The content will revert to the Standard Plan, the content will not be deleted.

Sage offers bespoke portals for customized Data Coordination Plan.  For the Standard and Managed Plans, you can create your own lightweight portal directly in Synapse.