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An integration platform for heterogeneous bioinformatics software components

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7 Author(s)
A. C. Siepel ; National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, New Mexico 87505, USA ; A. N. Tolopko ; A. D. Farmer ; P. A. Steadman
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Although computer programs and database resources for bioinformatics applications are becoming more widely available, these resources are unstandardized and frequently incompatible. The problem of integrating heterogeneous software is of immense importance to the field, especially because a rapid pace of change and a general scarcity of development resources discourage re-engineering and compel developers to find ways to use legacy resources. In this paper, we describe an approach to the problem of integration of heterogeneous bioinformatics resources that relies on a generalized software platform, written in the Java™ language, that we call ISYS™. The ISYS platform employs techniques for interoperation among loosely coupled components, such as brokered service exchange and mediated event exchange, that are increasingly common in software engineering but still not used widely in bioinformatics. In addition, it further promotes loose coupling of independent components through a flexible, semistructured data model that supports run-time association of attributes with objects, and allows different components to maintain different “views” of the same object. We describe our general approach, the architecture of the system, the mechanics of event and service exchange, and the implementation of the data model. The platform is not restricted in its utility to bioinformatics, and could be useful for any rapidly changing field in which the integration of heterogeneous legacy components is important.

Note: The Institute of Electrical and Electronics Engineers, Incorporated is distributing this Article with permission of the International Business Machines Corporation (IBM) who is the exclusive owner. The recipient of this Article may not assign, sublicense, lease, rent or otherwise transfer, reproduce, prepare derivative works, publicly display or perform, or distribute the Article.  

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IBM Systems Journal  (Volume:40 ,  Issue: 2 )