Articles Index | Synapse Documentation

Onboarding

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

Getting Started with Synapse: A getting started guide for new users who are interested in learning about Synapse.
User Accounts: Create your user account and manage your profile.
Governance Overview: A look at the Synapse governance process.
User Types including Certified Users: Find out about the three levels of Synapse users and the privileges and responsibilities associated with each level.
Making a Project: An overview of Synapse Projects.
Discussion Forums: Explore the features of the discussion forum and how to use it to help your collaborations.
Wikis: Create wikis to provide narrative content for your research.
Getting Started with the Synapse API Clients: Use Synapse programmatically.

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.

Governance Overview: Learn the values of the Synapse community and how to share data consistent with Synapse governance policies.
Conditions for Use: Conditions for Use determine how data in Synapse may be used by those who have been granted access.
Sharing Settings: Sharing settings determine who can access content in Synapse.
User Types including Certified Users: Learn about the privileges and responsibilities associated with each of the three levels of Synapse Users.
Contribute and Access Controlled Data: Learn how to contribute and access different types of Controlled Data.

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.
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.

Custom Storage Locations: Follow these steps to set up custom storage locations and access them with Synapse.
User Accounts: Create your Synapse user account and manage your profile.
Using Synapse as an OAuth 2.0 Server: Follow these steps to register an OAuth Client and authorize access to 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.

Annotations and Queries: Learn how to assign and modify Annotations as custom metadata and construct queries to find the files you need.
Managing Custom Metadata at Scale: Update Annotations in bulk using File Views and programmatic clients.

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.

API Documentation: Technical documentation for interacting with Synapse using R, Python, command line, and the REST API.
Getting Started with the Synapse API Clients: Use Synapse programmatically.
Client Configuration: How to store login credentials and fine-tune your config file.

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: An queue accepts submission of Synapse entities for evaluation.
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!

Challenge Infrastructure: Learn how to set-up the wireframe of a challenge.
Participating in a Challenge: Learn how to participate in challenges.

In Practice

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

Integrating Synapse in your RNA-Seq workflow: Using Synapse in an RNA-Seq workflow to manage files and track processing steps.