Welcome to the Pennsieve Documentation Hub. Within these pages, you will be able to find information about the functionality of the platform, information about our client tools, and in depth developer and API Documentation. This section introduces the platform and its various components. Other sections describe these components in more detail and explain use-cases and workflows for using the Pennsieve platform to collaborate in a meaningful way.

What is the Pennsieve Platform?

The Pennsieve platform is a cloud-based scientific data management platform focused on integrating complex datasets, fostering collaboration and publishing scientific data according to all FAIR principles of data sharing.

The platform is developed to enable individual labs, consortiums, or inter-institutional projects to manage, share and curate data in a secure cloud-based environment and to integrate complex metadata associated with scientific files into a high-quality interconnected data ecosystem. The platform is used as the backend for a number of public repositories including the NIH SPARC (https://sparc.science)) and Pennsieve discover (https://discover.pennsieve.io) repositories. It supports flexible metadata schemas and support a large number of scientific file-formats and modalities.

In addition, the platform provides fully integrated mechanisms to publish datasets to make them publicly available, version snapshots of dataset, and enable investigators to cite datasets in publications. Our publishing mechanisms include multiple steps to ensure the resulting published data is highly visible, has complete meta-data and adheres to all NIH and FAIR requirements for data sharing.

Components of the Pennsieve Data Platform

The Pennsieve Platform consists of the following components. The documentation hub provides detailed information about each of the components in different sections.

Platform Component	Description	Documentation link
Pennsieve Web Application	The Pennsieve web-application is the primary entry-point for users to interact with the platform in the web-browser. Users can log into the platform at: https://app.pennsieve.io	Pennsieve web application
Pennsieve Discover	Pennsieve Discover is a web-application that allows anybody to interact with public datasets that are published through the Pennsieve platform. Users can find the public datasets at: https://discover.pennsieve.io	Pennsieve Discover
Pennsieve Documentation Hub	The Pennsieve Documentation Hub provides documentation about the Pennsieve platform as well as the API reference.	Pennsieve Documentation Hub
Pennsieve API	The Pennsieve API provides full programmatic access to all functionality on the Pennsieve platform over a REST interface.	API Reference
Pennsieve Agent	The Pennsieve Agent is an installable application that runs in the background of the user's computer and manages large-scale uploads/downloads and other interactions with the Pennsieve platform	The Pennsieve Agent
Pennsieve Python Client	The Pennsieve Python client provides a simple way to interact with the Pennsieve Data Platform using Python. It interacts with the Pennsieve Agent to facilitate efficient data transfer and integration with the platform	The Python Client

Background

In 2015, The University of Pennsylvania spun of a company (Blackfynn Inc.) to develop a robust, scalable platform solution for scientific collaboration and data integration. Through a number of Grants, partnerships and private investments, we developed the Blackfynn Data Management Platform. In early 2021, Blackfynn decided to make the platform open source, and the development and management of the platform moved to the University of Pennsylvania where it is currently actively being maintained as part of the Institute of Biomedical Informatics and the Department of Biostatistics, Epidemiology and Informatics.

More information about Pennsieve's funding sources can be found here: Pennsieve Funding Sources