User Guide


Getting Started with Synapse

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

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Making a Project

An overview of Synapse Projects.

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Downloading Data

Learn the best practices of finding and downloading files.

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What is Synapse?

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Annotations and Queries

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

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Participating in a Challenge

Learn how to participate in challenges.

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Client Configuration

How to fine-tune your config file.

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Custom Storage Locations

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

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

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Docker Registry

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

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Digital Object Identifiers (DOIs) in Synapse

Mint DOIs in Synapse to cite your research.

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Files and Versioning

Uploading files and file versioning in Synapse.

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Genome Browser

How to Configure the Genome Browser Widget

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

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The basics of creating, modifying, and querying tabular data on Synapse.

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

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Batch Processing

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

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

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Create wikis to provide narrative content for your research.

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Governance and Security

Governance Overview

A look at the Synapse governance process.

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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.

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User Types including Certified Users

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

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Contribute and Access Controlled Data

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

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Running a Challenge

Learn how to administer and start a challenge

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Got Questions?

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