Check out the New Synapse UI

The Synapse Engineering Team is proud to announce a new Synapse web interface! Major changes include:

  • stylistic changes across the site
  • new content on homepage to highlight interesting projects (e.g. communities, open resources, etc.)
  • implementation of a Twitter feed as primary news source (@SageSynapse)
  • improved project branding by moving the project title into the header
  • probably a bunch more stuff that we are forgetting – it’s pretty neat

As always, we appreciate any feedback.

-The Synapse Team


Synapse Support for SFTP Storage

Synapse supports a diverse set of scientific projects through a federated model for storing digital assets – files can be store in a variety of back-end services with aggregation of appropriate metadata and indexing done centrally. While the default Synapse storage location has been (and will continue to be) storing Files uploaded to Synapse in Amazon Simple Storage Service (S3), we have recently added support for another type of external storage solution: SFTP servers. Synapse will continue to handle authentication to access the metadata surrounding Files registered and stored on external SFTP servers, however users must have appropriate credentials to download or edit content stored on specific SFTP resources.

In order to support communication with external SFTP storage solutions, we have released new versions of both the R Client (version 1.4-6) on our LRAN as well as the Python Client (version 1.1) on PyPi. Upgrade your clients today in order to enable interactions with SFTP resources.

We are pleased to announce that the first external users to leverage SFTP storage are analysts working with The Cancer Genome Atlas (TCGA). As in the Pan Cancer Analysis Working Group (AWG) in 2013, TCGA will continue to leverage Synapse for many of their ongoing collaborative efforts.

We are excited to make SFTP storage available to our users, and envision expanding to other storage solutions in the future.

-The Synapse Team

Synapse Certified User Community

The benefit of sharing data and knowledge to accelerate biomedical research are well understood. As a Synapse user you are already contributing data and insight and benefitting from the broad dissemination of these digital assets from other Synapse members. In order to better support your collaborative research efforts while continuing to safeguard the integrity and appropriateness of the content in Synapse we have updated our governance policies and data protection measures.

Starting on October 15th, 2014 users wishing to contribute content into Synapse must pass a short certification quiz to demonstrate their understanding of the Synapse data stewardship approach and handling of potentially sensitive information. Even though most researchers are aware of data protection principles, the Synapse user community will be able to recognize those “certified” users who have pass the quiz and trust that these users understand how to appropriately handle data and content within Synapse. A brief tutorial is available to guide users before taking the quiz.

Ultimately, we believe these changes will strengthen the community of Synapse users who lead the way in making digital research assets more accessible – whether through individual projects, large collaborations or DREAM challenges – for the benefit of all researchers and patients. The Synapse development team is committed to working with the community to further enable open and transparent communication of science on the web.

Useful links:

Synapse is provided as a service to the biomedical research community by Sage Bionetworks, a non profit organization in Seattle, WA.

Focus on Pan-Cancer Analysis

The TCGA Pan-Cancer working group has published a set of papers in Nature Publishing Group (NPG) journals exploring the DNA, chromatin and RNA alterations across a diverse set of cancers.  Much of the analysis done by the working group leveraged Synapse services to share and evolve data, results and methodologies while performing integrative analysis, as described in this commentary. There is now a nice summarization of these studies with links to the full papers on the Nature website.

Kudos to the TCGA Pan-Cancer working group for their great research. The Synapse Team is excited to see researchers continue to benefit from their use of the platform. We hope the TCGA Pan-Cancer group can be used as a template for future large-scale collaborative research efforts.