FAQ

General

What is Synapse?

Synapse is a collaborative informatics platform dedicated to supporting large-scale pooling of data, knowledge, and expertise across institutional boundaries to solve research problems. Synapse helps scientists solve a series of problems:

  • Finding and using relevant data - It can be difficult for scientists to find and access data and resources generated by others, even within the confines of the same organization. Synapse provides a central registry for scientific data and results, in which data can be annotated and queried even while components of a study resides in different systems.
  • Understanding analysis workflows - Synapse is built with the understanding that most analytical research is experimental and ad hoc in nature, with hardened analysis methods only emerging over time. Tracking who has run what version of code on what version of the data immediately helps projects run more smoothly, and ultimately enables reproducible workflows that allow others to build off of prior work.
  • Supporting genome-scale analysis - Analyzing whole genome datasets is currently limited to those with access to large computational resources and significant IT support. Synapse facilitates a computational model where code and users can move to the data, wherever it is stored.
  • Forming and maintaining productive collaborations - Most scientists tend to start a research effort from scratch rather than elaborate on work in an unknown state. Synapse helps scientists track what work has already been done in a particular area and create and sustain active collaborations in which research results are published online as they are generated.

What does Synapse do?

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.

No, seriously what does Synapse do?

For a comprehensive introduction to Synapse see our Getting Started guide.

How much does it cost to use Synapse?

We allow groups to get started for free by subsidizing relatively moderate amounts of internal Synapse cloud storage (e.g. 10s of GB). If your needs will exceed this limit we suggest contacting SynapseInfo@sagebase.org for other solutions, including the ability for groups to host their own content either in cloud storage, proxied from local file servers or as external links.

How is Synapse funded?

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 Alfred P. Sloan Foundation, the National Insitute on Aging (NIA), and the National Institute of Mental Health (NIMH).

Is Synapse a data analysis platform?

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.

Who uses Synapse?

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.

Is there someone that can help me use Synapse in my collaboration?

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 email at SynapseInfo@sagebase.org.

What are the Synapse Terms of Use?

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 the complete Synapse Governance policies.

Is Synapse open source?

Yes, Synapse is published under The MIT Licence The source code is available on the Sage Bionetworks GitHub page. Synapse is also offered free of charge as a hosted Software as a Service (SaaS).

I am a developer - is there API documentation?

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.

How do I set up my own instance of Synapse?

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: Custom Storage Locations).

What do I do if I find a bug?

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.

How do I get started?

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. See the Getting Started guide for tips on how to access data, create your own project, and share content with others.

Accessing Content

My colleague put some content in Synapse. How do I find it?

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 yellow star) it will appear under your list of favorites visible from the top of any Synapse page or on your Profile.

All public data is queryable. For more information see help on querying or from the “Search” box in the top right corner of any Synapse page.

I have heard Synapse hosts several public datasets. How do I find them?

Synapse hosts multiple research communities that generate data which 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.

What does a Synapse account let me do than I can’t do without it?

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 User Credentials page.

What is a validated profile?

Validating your profile is a process where your identity is established through a combination of your profile information, your ORCID, a signed oath, 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 on your profile page. Click on the ‘Request Profile Validation’ link to see the required steps.

Adding Content

Why do I have to be a certified user to upload content?

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. See the How to contribute data for more information.

How do I get certified?

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

Is everything I share on Synapse public?

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: Sharing Settings and Conditions for Use.

Can I store sensitive information about human subjects in Synapse?

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 our Sharing Settings and Conditions for Use documentation and Governance documentation. 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.

How do I know the content I put in Synapse will be secure? What security measures does Synapse have?

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.

Where are my files stored?

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: Custom Storage Locations)

I have my research results - How can Synapse help me share them?

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. We recommend using Getting started with Synapse guide for more details on how to upload and manage content.

Need More Help!

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).

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