Sage Congress Demo Video

Thanks to everyone who joined Sage at the 2013 Congress.   It was great to get so much energy and feedback from everyone in attendance.  Our Congress Demo showing use of the newest features is now posted if you weren’t able to attend.

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Announcing Synapse DOIs and other features

Synapse software engineers have been hard at work churning out features leading up to the 2013 Sage Bionetworks Commons Congress. A new version of Synapse services will be released on Tuesday April 16th.

We allow users to create a DOI to reference Synapse content from external systems or scientific publications.  DOIs are a scientific publishing standard used to create robust links across many different websites to content, and provide users a short and easy way to share and reference their work (e.g. doi:10.7303/syn1234.5).  DOIs for Synapse Files, Folders, and Projects can be created on the Synapse webpage for each of these objects, and can reference either the current version, or a specific version of a file.  Also, any DOIs included in markdown will be converted into links automatically.

Other new features include:

  • external URLs in provenance views
  • ability to reference a Synapse File in markdown
  • ability to scale images imbedded into markdown
  • ability to wrap text around left-or-right-floated images

Announcing Wikis and other new features

We’ve just released a new version of Synapse with the following major updates.  Upgrading R and Python clients is recommended.:

Wiki pages for Projects and Folders: Synapse now allows users much more flexibility to create custom content in Synapse through dedicated areas for wiki content on Project and Folder pages in the Synapse web site.  Additionally, users may nest an arbitrary number of additional wiki pages below the top level page of a project or folder.  Previously we allowed wiki markdown in a Description field, which had a much more constrained area of the page for display.  Content previously present in the Description has now been migrated to the wiki section of pages.  The description field remains as a short plain-text summary of a project or folder.  Descriptions will be displayed throughout the site, e.g. on search results page or on tool-tips on lists of projects so it is useful to create both a short description for your Synapse projects as well as richer content using the wiki capabilities.

New Entity List widget replaces Summary Entities: Previous versions of Synapse allowed users to create a Summary, which was a page dedicated to a tabular view of other objects in the system.  We’ve now incorporated the same functionality into a component that can be embedded within Synapse wiki pages, giving users more flexibility to mix this visualization in with other content on the same page.  You can no longer create the old stand-alone Summary pages, but existing Summary pages will continue to be supported for at least 6 months.  To use the new Entity List visualization, edit a wiki page and choose Insert > Entity List from the main menu.

Project-centric search: The default search has been optimized to search for projects over other types of objects in the system.  We believe this change will more often help new users find the content they are looking for in Synapse.  We are now using the text of both the project Description and Wiki pages in our search index, so our search now has more content to work with.  This should also improve search results, especially as increasing numbers of projects are built out.  All the old functionality to search for other types of objects in the system is still available by removing the filter to narrow search results to only show projects.