An integration platform for heterogeneous bioinformatics software components

Siepel, A. C., Tolopko, A. N., Farmer, A. D., Steadman, P. A., Schilkey, F. D., Perry, B. D., Beavis, W. D. (2001) An integration platform for heterogeneous bioinformatics software components. IBM Systems Journal, 40 (2). pp. 570-591.

URL: http://domino.research.ibm.com/tchjr/journalindex....

Abstract

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 JavaTM language, that we call ISYSTM. 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.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > computers > computer software
CSHL Authors:
Communities: CSHL labs > Siepel lab
Depositing User: Matt Covey
Date Deposited: 12 Jan 2015 21:38
Last Modified: 12 Jan 2015 21:38
URI: http://repository.cshl.edu/id/eprint/31107

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