Synapse is a collaborative research platform where that helps you and your team can share, organize, and discuss your projects. You can access Synapse through a web browser. We also provide access to Synapse features and services for programmers through a REST API, Python client, command line client, and R client.
Synapse is a technology platform that allows researchers to aggregate, organize, analyze, and share scientific data, code and insights. Synapse is designed to integrate seamlessly with your analytical workflow. Therefore, options to download data are available in the R client, command line client and Python client.
Synapse hosts many research projects and resources. It also hosts crowdsourced competitions, including DREAM Challenges. Sage Bionetworks provides Synapse services free of charge to the scientific community through generous support from various funding sources.
Synapse is a collaborative research platform dedicated to supporting large-scale pooling of data, knowledge, and expertise across institutional boundaries to solve research problems. Synapse helps scientists solve a series of problems:
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Finding and using relevant data - It can be difficult for scientists to find and access data and resources generated by others, even within the same organization. Synapse provides a central registry for scientific data and results, where data can be annotated and queried even if components of a study reside in different systems.
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Understanding analysis workflows - Synapse is built with the understanding that most analytical research is experimental and ad hoc, with hardened analysis methods only emerging over time. Tracking who has run what version of code on what version of the data immediately helps projects run more smoothly, and ultimately enables reproducible workflows that allow others to build off of prior work.
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Supporting genome-scale analysis - Analyzing large datasets is currently limited to those with access to significant computational resources and IT support. Synapse facilitates a computational model where code and users can move to the data, wherever it is stored.
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scientific research. Whether you are part of a small private team or global consortia, Synapse offers tools to help you make connections across datasets, code, and other insights.
Who manages Synapse?
Synapse was created and is managed by Sage Bionetworks (that’s us!)
Sage is a nonprofit health research organization based in Seattle, Washington. We were founded in 2009 on the basis of open science and patient advocacy. We aim to promote reproducible research and responsible data sharing throughout the biomedical community. That’s why we created Synapse.
Ethical use of data is of the utmost importance to Sage, and we employ robust governance policies and procedures to monitor compliance and ensure data privacy.
In addition to, and in conjunction with Synapse, Sage operates multiple platforms and data portals that serve the current and future needs of our communities.
Platforms | Community Portals |
|---|---|
A collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate. | dHealth (Digital Health) Knowledge Portal Designed to enable the discovery and download of digital and mobile health data, tools, and benchmarked outcomes and digital biomarkers. |
An open-science, collaborative competition framework for evaluating and comparing computational algorithms. | Cancer Complexity Knowledge Portal The NCI Division of Cancer Biology supports multiple research programs composed of interdisciplinary communities of scientists who aim to integrate approaches, data, and tools to address important questions in basic and translational cancer research. |
An interactive platform for visually exploring curated genomic analyses of Alzheimer’s disease (AD), including a list of early AD candidate target nominations. | A platform for accessing data, analyses, and tools that the National Institute on Aging’s Alzheimer’s Disease Translational Research Program generates. |
Designed to help openly explore and share NF datasets, analysis tools, resources, and publications related to neurofibromatosis. | |
| PsychENCODE (PEC) Knowledge Portal A platform designed to promote a community for sharing data from neuropsychiatric disease research. |
How does Synapse help scientific research?
Synapse is helping scientists in several ways:
Building community around data sharing: Synapse hosts many research communities and open scientific resources. It is a central place where researchers can come together to share data and collaborate. Data can be annotated and queried in one place, even if it is physically stored in different locations.
Making research more reproducible: Most research projects are complex and change over time. Synapse helps you track who performed what parts of an analysis. It also tracks when data was added or changed within a project, and it helps you understand how a dataset or an analysis evolved. These tools help you to publish reproducible work that can be used more easily by others.
Benchmarking and challenges: Tackling a complex problem alone can be difficult. Synapse hosts crowdsourced competitions, including DREAM Challenges, where many people come together to solve important computational problems or to compare analytical approaches.
Protecting sensitive data: Synapse is designed to keep sensitive data safe while still being shared responsibly. The platform offers built-in features to control who can access data and how that data can be used. Synapse is also backed by a governance team who routinely monitor data use and who set policies and procedures to govern data access.
Accessing data programmatically: If you are a programmer, you can also access Synapse through a REST API, Python client, R client, or command line client. Accessing Synapse programmatically allows you to seamlessly integrate Synapse with your scientific computing and analytical workflows.