Articles | Synapse Documentation

Articles

An index of articles available about Synapse.

Onboarding

Get a brief overview of some of the main components of Synapse.



Governance

Synapse enables responsible resource sharing with features that allow data contributors to control who views data and how. Sharing Settings can be defined on any File, Folder or Project to keep data private or grant access to any number of Users, including all Synapse users, or Teams.



Managing Data in Synapse

Synapse features provide novel functionality to help you organize your collections of data. In addition to uploading and downloading data, learn how to upload new versions of existing files, download previous file versions, create Tables to visualize data and create Views to surface file metadata.

  • Files and Versioning: Upload and manage file versions in Synapse.
  • Forms: Embedding Synapse Forms to Collect Data into Tables
  • Links: Creating, and modifying links on Synapse.
  • Tables: Create, modify, and query data in Synapse Tables.
  • Upload and Download Data in Bulk: Learn how to upload and download data in bulk using a manifest file and the Synapse programmatic clients.
  • Using Tabular Data in Wikis: Use Tables in wikis to augment team communication in projects.
  • Views: Use project and file views to query across multiple projects and folders.
  • Get Started with Downloading Data: Start here to learn the syntax and first steps to download data using the Synapse programmatic clients.


Collaboration and Communication

Synapse is a collaborative platform. Learn about tools that allow this, such as Discussion threads and Wikis.

  • Discussion Forums: Communicate with collaborators and other community members with the Synapse Discussion Forum.
  • Editing Wiki Page Order: Organize wiki pages into a sensible hierarchy
  • Managing Teams for Groups and Projects: Using Synapse teams for group permissions in projects.
  • Teams: Form teams to easily manage groups of users for purposes of project access, communication, and challenges.
  • Wikis: Create Wikis to provide narrative content for your research.


Administration and Settings

These topics will help you learn about useful settings in Synapse.



Metadata and Annotations

Annotations are a feature to systematically group and describe things in Synapse. Add Annotations to Files, Folders and Projects to surface search terms across datasets, helping users to find and query data.



API Clients

Unify data and code with Synapse programmatic clients. Programmatic clients provide an interface to Synapse to link computationally-intensive processing with relevant data stored on Synapse.



Reproducible Research

Cite data directly using a DOI to fully integrate publications and relevant evidence into your Synapse Project. You can set Provenance to explicitly link GitHub code and other resources to data files. Tracking these steps directly can increase trust in the reliability of your data and analyses.

  • Synapse Docker Registry: The Synapse Docker registry provides a space for Synapse users to store and distribute their Docker images per Synapse project.
  • Digital Object Identifiers (DOIs) in Synapse: Mint DOIs in Synapse to cite your research.
  • Evaluation Queues: A Synapse Queue contains user submitted models or files to execute for challenges and benchmarking.
  • Genome Browser: How to Configure the Genome Browser Widget
  • Provenance: Learn about how Synapse visualizes and tracks the relationships of files and projects for reproducibility.


Challenges

Synapse is being used to run Scientific Computing Challenges. Use these articles to find out more!



In Practice

Synapse In Practice guides show you how to solve a specific problem.