Bioinfo-Kit: A Sharing Software Tool for Bioinformatics

Abstract:

In bioinformatics research, for the lacks of an effective algorithm-integrating mechanism and a friendly graphical user interface of the toolkits in the field of biological data processing and analyzing, the authors designed and implemented a sharing software system Bioinfo-Kit based on the Java 2 Platform Enterprise Edition (J2EE), which provides 1) a general application development interface to integrate or bridge other programs and 2) a workflow mechanism to operate them and make them talk easily. In addition, a module for biological data (multiple electrodes data, biomedical data and etc.) analysis was implemented in the software system, which provided a workflow mechanism to integrate a series of algorithms and visualization tools. Because the interface developed is very general and flexible, new analysis tools can be integrated effectively as required. Bioinfo-Kit implies an ideal environment for integrative bioinformatics research.

• Periodical: Applied Mechanics and Materials (Volume 472)
• Pages: 466-469
• DOI: https://doi.org/10.4028/www.scientific.net/AMM.472.466
• Online since: January 2014
• Authors: Yu Huang, Jian Yong Wang, Xiao Mei Wei, Bin Hu*
• Keywords: Bioinformatics, Integrative, Workflow

References

[1] Egert U, Knott Th, Schwarz C, Nawrot M, Brandt A, Rotter S, et al. MEA-Tools: an open source toolbox for the analysis of multi-electrode data with Matlab, J Neurosci Meth, vol. 117, Apr. 2002, pp.33-42, doi: 10. 1016/S0165-0270(02)00045-6.

DOI: 10.1016/s0165-0270(02)00045-6

[2] Mar´ıa P. Bonomini, Jos´e M. Ferrandez, Jose Angel Bolea, Eduardo Fernandez, DATA-MEAns: An open source tool for the classification and management of neural ensemble recordings, J Neurosci Meth, vol. 148, June. 2005, pp.137-146.

DOI: 10.1016/j.jneumeth.2005.04.008

[3] ZHAO Ming-Chang, TIAN Jie1, XUE Jian, ZHU Xun, HE Hui-Guang, LÜ Ke. Design and Implementation of MITK for 3D Medical Image Processing and Analyzing. Journal of Software, 2005, 16(4): 485-495.

DOI: 10.1360/jos160485

[4] Schroeder W, Martin K, Lorensen B. The Visualization toolkit: An Object Oriented Approach to 3D Graphics. 3rd Edition. New York: Kitware, Inc. Publisher, (2003).

DOI: 10.1016/b978-012387582-2/50003-4

[5] Schroeder WJ, Avila LS, Hoffman W. Visualizing with VTK: A tutorial. IEEE Trans. on Computer Graphics and Applications, 2000, 20(5): 20−27.

DOI: 10.1109/38.865875

[6] Schroeder WJ, Martin KM, Lorensen WE. The design and implementation of an object-oriented toolkit for 3D graphics and visualization. In: Nielson GM, Yagel R. eds. Proc. of the IEEE Visualization'96. IEEE Computer Society Press, 1996. 93−100.

DOI: 10.1109/visual.1996.567752