User Guide | Synapse Documentation

Introduction

Getting Started with Synapse

A getting started guide for new users who are interested in learning about Synapse.

Learn More
Downloading Data

Learn the best practices of finding and downloading files.

Learn More
FAQ

What is Synapse?

Learn More

How-To's

Annotations and Queries

Learn about using custom metadata, how to assign and modify annotations, and how to query them for analysis.

Learn More
Challenge Infrastructure

Learn how to set-up the wireframe of a challenge.

Learn More
Participating in a Challenge

Learn how to participate in challenges.

Learn More
Client Configuration

How to fine-tune your config file.

Learn More
Custom Storage Locations

Follow these steps to set up custom storage locations and access them with Synapse.

Learn More
Discussion

Explore the features of the discussion forum and how to use it to help your collaborations.

Learn More
Docker Registry

The Synapse Docker registry provides a space for Synapse users to store and distribute their Docker images per Synapse project.

Learn More
Digital Object Identifiers (DOIs) in Synapse

Mint DOIs in Synapse to cite your research.

Learn More
Files and Versioning

Uploading and managing files and versions in Synapse.

Learn More
Forms

Embedding Synapse Forms to Collect Data into Tables

Learn More
Genome Browser

How to Configure the Genome Browser Widget

Learn More
Links

Creating, and modifying links on Synapse.

Learn More
Making a Project

An overview of Synapse Projects.

Learn More
Provenance

Learn about how Synapse visualizes and tracks the relationships of files and projects for reproducibility.

Learn More
Tables

Creating, modifying, and querying tabular data on Synapse.

Learn More
Teams

Form teams to easily manage groups of users for purposes of project access, communication, and challenges.

Learn More
Batch Processing

Learn about uploading files and associated annotations and provenance in bulk.

Learn More
User Profiles

Create your user account and manage your profile

Learn More
Views

Use project and file views to query across multiple projects and folders.

Learn More
Wikis

Create wikis to provide narrative content for your research.

Learn More

Governance and Security

Governance Overview

A look at the Synapse governance process.

Learn More
Sharing Settings and Conditions for Use

Synapse has two content controls -- the Sharing setting and Conditions for Use. Learn how to set Sharing settings and Conditions for Use.

Learn More
User Types including Certified Users

Find out about the three levels of Synapse users and the privileges and responsibilities associated with each level

Learn More
Contribute and Access Controlled Data

Learn how to contribute and access different types of Controlled Data.

Learn More

In Practice

Integrating Synapse in your RNA-Seq workflow

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

Learn More
Managing Custom Metadata at Scale

Update metadata in bulk using file views and programmatic clients.

Learn More
Using Tabular Data in Wikis

Use Tables in wikis to augment team communication in projects.

Learn More

Got Questions?

Can't find what you're looking for? Try posting a question to our forum.

Forum