User Guide | Synapse Documentation
New to Synapse? Learn the basics with our introductory topics.
Browse short "How To" articles on leveraging specific features in Synapse.
Learn about how Governance and Ethics policies and tools make Synapse safe.
Synapse in Practice
Get ideas for how to use Synapse in your own research with a series of case studies.
Getting Started with Synapse
: A getting started guide for new users who are interested in learning about Synapse.
: Learn the best practices of finding and downloading files.
: What is Synapse?
How To Articles
Annotations and Queries
: Learn about using custom metadata, how to assign and modify annotations, and how to query them for analysis.
: Learn how to set-up the wireframe of a challenge.
Participating in a Challenge
: Learn how to participate in challenges.
Custom Storage Locations
: Follow these steps to set up custom storage locations and access them with Synapse.
: Explore the features of the discussion forum and how to use it to help your collaborations.
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.
Editing Wiki Page Order
: Organize wiki pages into a sensible hierarchy
: An queue accepts submission of Synapse entities for evaluation.
Files and Versioning
: Uploading and managing files and versions in Synapse.
: Embedding Synapse Forms to Collect Data into Tables
: How to Configure the Genome Browser Widget
: Creating, and modifying links on Synapse.
: Learn about how Synapse visualizes and tracks the relationships of files and projects for reproducibility.
: Creating, modifying, and querying tabular data on Synapse.
: Form teams to easily manage groups of users for purposes of project access, communication, and challenges.
Uploading and Downloading Data in Bulk
: Learn about bulk processes with files, annotations and provenance.
: Create your 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.
: Use project and file views to query across multiple projects and folders.
: Create wikis to provide narrative content for your research.
Making a Project
: An overview of Synapse Projects.
Governance and Security
: A look at the Synapse governance process.
Conditions for Use
: Conditions for Use determine how data in Synapse may be used by those who have been granted access.
: Sharing settings determine who can access content in Synapse.
User Types including Certified Users
: Find out about the three levels of Synapse users and the privileges and responsibilities associated with each level.
Contribute and Access Controlled Data
: Learn how to contribute and access different types of Controlled Data.
Getting Started with the Synapse API Clients
: Use Synapse programmatically.
: How to store login credentials and fine-tune your config file.
Integrating Synapse in your RNA-Seq workflow
: Using Synapse in an RNA-Seq workflow to manage files and track processing steps.
Managing Custom Metadata at Scale
: Update metadata in bulk using file views and programmatic clients.
Managing Teams for Groups and Projects
: Using Synapse teams for group permissions in projects.
Using Tabular Data in Wikis
: Use Tables in wikis to augment team communication in projects.
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