FAQ

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.

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

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.

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 email at SynapseInfo@sagebase.org.

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.

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: Custom Storage Locations).

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.