Implementation of informatics for integrating biology and the bedside (i2b2) platform as Docker containers.

BackgroundInformatics for Integrating Biology and the Bedside (i2b2) is an open source clinical data analytics platform used at over 200 healthcare institutions for querying patient data. The i2b2 platform has several components with numerous dependencies and configuration parameters, which renders the task of installing or upgrading i2b2 a challenging one. Even with the availability of extensive documentation and tutorials, new users often require several weeks to correctly install a functional i2b2 platform. The goal of this work is to simplify the installation and upgrade process for i2b2. Specifically, we have containerized the core components of the platform, and evaluated the containers for ease of installation.ResultsWe developed three Docker container images: WildFly, database, and web, to encapsulate the three major deployment components of i2b2. These containers isolate the core functionalities of the i2b2 platform, and work in unison to provide its functionalities. Our evaluations indicate that i2b2 containers function successfully on the Linux platform. Our results demonstrate that the containerized components work out-of-the-box, with minimal configuration.ConclusionsContainerization offers the potential to package the i2b2 platform components into standalone executable packages that are agnostic to the underlying host operating system. By releasing i2b2 as a Docker container, we anticipate that users will be able to create a working i2b2 hive installation without the need to download, compile, and configure individual components that constitute the i2b2 cells, thus making this platform accessible to a greater number of institutions

Implementation of informatics for integrating biology and the bedside (i2b2) platform as Docker containers

Abstract Background Informatics for Integrating Biology and the Bedside (i2b2) is an open source clinical data analytics platform used at over 200 healthcare institutions for querying patient data. The i2b2 platform has several components with numerous dependencies and configuration parameters, which renders the task of installing or upgrading i2b2 a challenging one. Even with the availability of extensive documentation and tutorials, new users often require several weeks to correctly install a functional i2b2 platform. The goal of this work is to simplify the installation and upgrade process for i2b2. Specifically, we have containerized the core components of the platform, and evaluated the containers for ease of installation. Results We developed three Docker container images: WildFly, database, and web, to encapsulate the three major deployment components of i2b2. These containers isolate the core functionalities of the i2b2 platform, and work in unison to provide its functionalities. Our evaluations indicate that i2b2 containers function successfully on the Linux platform. Our results demonstrate that the containerized components work out-of-the-box, with minimal configuration. Conclusions Containerization offers the potential to package the i2b2 platform components into standalone executable packages that are agnostic to the underlying host operating system. By releasing i2b2 as a Docker container, we anticipate that users will be able to create a working i2b2 hive installation without the need to download, compile, and configure individual components that constitute the i2b2 cells, thus making this platform accessible to a greater number of institutions

Automating Installation of the Integrating Biology and the Bedside (i2b2) Platform.

Informatics for Integrating Biology and the Bedside (i2b2) is an open source clinical data analytics platform used at more than 150 institutions for querying patient data. An i2b2 installation (called hive) comprises several i2b2 cells that provide different functionalities. Given the complex architecture of i2b2 installation, creating a working installation of the platform is challenging for new users. This is despite the availability of extensive documentation for i2b2 and access to a large and active mailing list community of i2b2 users. To address this problem, we have created an automated installation package, called i2b2-quickstart, which automatically downloads the latest i2b2 source code and dependencies, and compiles and configures the i2b2 cells to create a functional i2b2 hive installation. This package will serve as a convenient starting point and reference implementation that will facilitate researchers in the installation and exploration of the i2b2 platform

Automating Installation of the Integrating Biology and the Bedside (i2b2) Platform

Informatics for Integrating Biology and the Bedside (i2b2) is an open source clinical data analytics platform used at more than 150 institutions for querying patient data. An i2b2 installation (called hive) comprises several i2b2 cells that provide different functionalities. Given the complex architecture of i2b2 installation, creating a working installation of the platform is challenging for new users. This is despite the availability of extensive documentation for i2b2 and access to a large and active mailing list community of i2b2 users. To address this problem, we have created an automated installation package, called i2b2-quickstart, which automatically downloads the latest i2b2 source code and dependencies, and compiles and configures the i2b2 cells to create a functional i2b2 hive installation. This package will serve as a convenient starting point and reference implementation that will facilitate researchers in the installation and exploration of the i2b2 platform