Copyright 2007 Feagan et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
This paper presents the Bioinformatics Computational Journal (BCJ), a framework for conducting and managing computational experiments in bioinformatics and computational biology. These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment. Systems to manage computational experiments exist, ranging from libraries with standard data models to elaborate schemes to chain together input and output between applications. Yet, although such frameworks are available, their use is not widespread–ad hoc scripts are often required to bind applications together. The BCJ explores another solution to this problem through a computer based environment suitable for on-site use, which builds on the traditional laboratory notebook paradigm. It provides an intuitive, extensible paradigm designed for expressive composition of applications. Extensive features facilitate sharing data, computational methods, and entire experiments. By focusing on the bioinformatics and computational biology domain, the scope of the computational framework was narrowed, permitting us to implement a capable set of features for this domain. This report discusses the features determined critical by our system and other projects, along with design issues. We illustrate the use of our implementation of the BCJ on two domain-specific examples.
Feagan, Lance, Justin Rohrer, Alexander Garrett, Heather Amthauer, Ed Komp, David Johnson, Adam Hock, Terry Clark, Gerald Lushington, Gary Minden, and Victor Frost. "Bioinformatics Process Management: Information Flow via a Computational Journal." Source Code Biol Med Source Code for Biology and Medicine 2.1 (2007): 9. http://dx.doi.org/10.1186/1751-0473-2-9
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Except where otherwise noted, this item's license is described as: Copyright 2007 Feagan et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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