KDE bioscience: platform for bioinformatics analysis workflows

Authors:
Qiang Lu;Pei Hao;Vasa Curcin;Weizhong He;Yuan-Yuan Li;Qing-Ming Luo;Yi-Ke Guo;Yi-Xue Li
Affiliations:
School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China and Department of Computing, Imperial College London, Queen's Gate, London, UK;Shanghai Center for Bioinformation Technology, Shanghai, China;Department of Computing, Imperial College London, Queen's Gate, London, UK;Shanghai Center for Bioinformation Technology, Shanghai, China;Shanghai Center for Bioinformation Technology, Shanghai, China;School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China;Department of Computing, Imperial College London, Queen's Gate, London, UK;Shanghai Center for Bioinformation Technology, Shanghai, China
Venue:
Journal of Biomedical Informatics
Year:
2006

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Abstract

Bioinformatics is a dynamic research area in which a large number of algorithms and programs have been developed rapidly and independently without much consideration so far of the need for standardization. The lack of such common standards combined with unfriendly interfaces make it difficult for biologists to learn how to use these tools and to translate the data formats from one to another. Consequently, the construction of an integrative bioinformatics platform to facilitate biologists' research is an urgent and challenging task. KDE Bioscience is a java-based software platform that collects a variety of bioinformatics tools and provides a workflow mechanism to integrate them. Nudeotide and protein sequences from local fiat files, web sites, and relational databases can be entered, annotated, and aligned. Several home-made or 3rd-party viewers are built-in to provide visualization of annotations or alignments. KDE Bioscience can also be deployed in client-server mode where simultaneous execution of the same workflow is supported for multiple users. Moreover, workflows can be published as web pages that can be executed from a web browser. The power of KDE Bioscience comes from the integrated algorithms and data sources. With its generic workflow mechanism other novel calculations and simulations can be integrated to augment the current sequence analysis functions. Because of this flexible and extensible architecture, KDE Bioscience makes an ideal integrated informatics environment for future bioinformatics or systems biology research.