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 email

One way Synapse protects your privacy is by not exposing the email address you used to register with the system. However now you may contact other users via email by using the address, <username>@synapse.org, where <username> is the name shown on an individual’s dashboard (and elsewhere in the system). You may also broadcast messages to a Synapse Team on which you are a member by emailing <team>@synapse.org, where <team> is the name of the team (leaving out spaces and other email-address-illegal characters). For security (and to block spam), you must send all Synapse emails from an address which you registered with Synapse. You can turn off email notifications at any time from your dashboard settings page. We hope that this new feature will allow you to contact other users directly with questions about their work, strike up new collaborations, and communicate with DREAM Challenge participants or organizers. As always, we welcome your feedback.

-The Synapse Team

Synapse provenance editor

Provenance is a great way to both record what has been done to generate a result and also to get credit for the work you are doing.

Previously, Synapse provenance services have only been exposed via our REST API and our analytical clients (R, python, and command line). We have recently build a web interface to enable both creation and editing of provenance associated with any File stored in Synapse.

The Synapse provenance system allows users to specify how a File was generated – by providing a name, description, as well as any resources (either a Synapse-specific or external URL reference) which were ‘Used’ or ‘Executed’ in order to generate that File.

Currently, the provenance editor can be accessed by using the Tools menu on any File page – and selecting ‘Edit Provenance’.

-The Synapse Team

Synapse Tables in Wikis

Users are now able to embed a specific query from a Synapse Table in any Synapse Wiki page. This provides the powerful ability to include a single query in a Wiki representing underlying data stored in a Table which can be updated without actually changing the Wiki text.

Here is an example:

Screen Shot 2015-06-12 at 4.01.44 PM

Users should note that only individuals who are logged in and have access to the Table data will be able to see the Table query in the Wiki.

Happy researching!

-The Synapse Team

New releases of R and Python clients

There are new releases of both the R and python clients available for installation.

The updated version (1.9-0) of the R client includes updated functions to interact with Synapse Tables, the ability to upload to a user-owned S3 bucket, as well as added robustness to file uploads. As always, see the R client Getting Started Guide for instructions on installing and using the client.

The updated version (1.3) of the python client is available via pypi and includes added robustness to file uploads, the ability to download filehandle(s) from a Synapse Table, and a variety of bug fixes.

Upgrade your clients today!

-The Synapse Team

R Client release 1.7-1

There is a new release of the R synapseClient available for installation. This updated version (version 1.7-1) includes functionality to interact with Synapse Tables and specifically download fileHandles from TableColumns (syntax: synDownloadTableFile). As always, see the R client Getting Started Guide for instructions on installing and using the client.

-The Synapse Team

Synapse User Dashboard

The Synapse Team is happy to announce a new Synapse User Dashboard where users can find all of their Synapse content in one convenient place. You can now access the Projects that you have recently worked on, filter by how Projects were shared with you, and track your ‘Favorite’ Synapse objects. You can also manage the Teams you are a member of as well as build up your Synapse profile.

Happy researching!

-The Synapse Team

Introducing Synapse Tables (beta)

The Synapse Team is proud to announce a new beta feature called Tables. Synapse Tables have been designed to provide users the ability to create web-accessible, sharable, and queryable data. Columns in Synapse Tables have a user-specified structured schema which provides many of the benefits of a database, but without the overhead of maintaining one.

Table functionality is available with the most release of both of our analytical clients as well (R Client version 1.5-4 and Python Client version 1.2). For an overview of the Tables feature, see our Getting Started Guide.

Please try Tables and feel free to give feedback either via our issue tracking system or at synapseinfo@sagebase.org.

-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

DREAM’s First Ever Hackathon! AML Challenge Organizers Run Hackathon to Foster Collaboration

Although the DREAM Challenges do an excellent job bringing together researchers from several different areas of science and several different institutions to work on the same problem, the competitive setting provides little incentive for these great minds to work together. While the cornerstone of crowdsourcing is in fact the application of several different approaches to the same issue, the organizers of the Amyloid Myeloid Leukemia (AML) Outcome Prediction DREAM Challenge would still like to see participants working on similar or complementary approaches collaborating and possibly even joining teams. To encourage these partnerships we decided to hold the first ever DREAM Hackathon! The Hackathon took place on July 26-27 at Rice University and was simultaneously broadcast over the web. The Hackathon was designed to catalyze conversations about the AML Challenge in two ways:

First, we wanted to use the Hackathon to encourage Challenge participants to share a little about their general approach to model building. While we wanted participants to present their ideas, we were also mindful that the AML Outcome Prediction DREAM Challenge is a competition, and we didn’t want participants to present their approach at a level of detail that could make their methodology available to others. Considering this fine line, we encouraged participants to present only as much as they were comfortable with: no details about the approach or efficacy of their methods had to be presented.

For this part of the Hackathon, two Challenge teams signed up and presented an overview of their model-building methodologies via live webinar to other Challenge participants around the world. Both teams had excellent presentations and received some valuable feedback from Hackathon-Challenge participants! While both presenters had very good approaches, it was clear that Hackathon spectators with different expertise and “fresh eyes” had numerous good ideas on how these two teams could improve even further. In the end, while the turnout for this section of the Hackathon was low, the exercise was very constructive and the main goal was achieved for those who participated.

The second goal we had for the Hackathon was to invite a few “experts in the field” — for both model building methodology as well as approaches to predict AML outcome — to present during the Hackathon in order to get participants discussing new ideas that could help their model building efforts.   These talks along with their Q&A sessions were very constructive, particularly the one by Dr. Kenneth Hess from MD Anderson Cancer Center, who presented on general statistical analysis of survival time data tailored to the DREAM 9 dataset. Given the diverse nature of these talks, we believe participants of the AML Outcome Prediction DREAM Challenge were able to get an insight on different approaches that could be incorporated into their methods. These talks could also give them different perspectives on the Challenge, opening new horizons not considered before. These presentation were recorded and are available in the Synapse website (https://www.synapse.org/#!Synapse:syn2455683/wiki/64687).

Overall I believe this was a really successful first DREAM Hackathon! We will continue to follow up with the participants about what they liked or didn’t like about this event, and we are open to ideas on how we can improve. With your help we hope to make this event more and more successful in subsequent editions of the DREAM Challenges.

Thank you,
André Schultz: member of the AML DREAM Challenge Organizing Team

 

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