Java in Bioinformatics

In 2009 I attended the UCLA Clinical and Translational Science Institute (CTSI) Enterprise-Level Research Informatics in the Health Sciences Symposium at the California NanoSystems Institute (CNSI). There were many speakers there from institutions like Johns Hopkins University, Stanford University School of Medicine, as well as Harvard University School of Medicine. However, the presentation that caught my ear the most was that of Isaac S. (Zak) Kohane, MD - co-Director of the i2b2 (Informatics for Integrating Biology and the Bedside) project based at Partners HealthCare System in Boston, Massachusetts. The websites states: "The key challenge that i2b2 is designed to address is that of creating a comprehensive software and methodological framework to enable clinical researchers to accelerate the translation of genomic and “traditional” clinical findings into novel diagnostics, prognostics, and therapeutics. Conversely, it provides a collaborative organizational and software infrastructure to allow basic researchers to leverage insights arising from clinical studies." Written in Java, i2b2's Hive and associated Workbench are great examples of concepts like persistent storage and service wrappers. Described as a "hive" of interoperable cells, web services couple these cells and allow intercommunication (yes, via SOAP). Of course, all these functional cells can be separated from each other, yet use the same persi...

Date: March, 10 2010
Url: http://www.java.net/blog/christianabryant/archive/2010/03/10/java-bioinformatics

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