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

BMC Medical Informatics and Decision Making

Kavishwar B. Wagholikar¹  Shawn N. Murphy¹  Michael E. Mendis²  Pralav Dessai³  Javier Sanz³  Douglas S. Bell³ 

[1] Massachusetts General Hospital;Partners Healthcare;University of California Los Angeles;

关键词: I2B2;    Docker;    Containerization;    Docker;    High performance computing;    Biomedical research;   

DOI  :  10.1186/s12911-018-0646-2

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown