Paper Info
Title
KDE Bioscience: platform for bioinformatics analysis workflows.
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. Nucleotide and protein sequences from local flat 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.
Year
DOI
Venue
2006
10.1016/j.jbi.2005.09.001
Journal of Biomedical Informatics
Keywords
DocType
Volume
ideal integrated informatics environment,generic workflow mechanism,integration,bioinformatics analysis workflows,future bioinformatics,integrated algorithm,integrative bioinformatics platform,kde bioscience,web browser,bioinformatics tool,platform,systems biology research,bioinformatics,dynamic research area,system biology,relational database,protein sequence,web pages,sequence analysis,nucleotides,client server
Journal
39
Issue
ISSN
Citations 
4
1532-0480
9
PageRank 
References 
Authors
0.67
8
8
Name
Order
Citations
PageRank
Qiang Lu1531.95
Pei Hao2361.75
Vasa Curcin311127.79
Weizhong He4382.73
Yuanyuan Li520630.10
Qingming Luo614315.71
Yike Guo71319165.32
Yixue Li878960.24