Faculty of Computer and Information Sciences, Ain Shams University, Cairo, 11566, Egypt

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Abstract—This paper describes a web-based interactive framework for the analysis and visualization of gene expressions and protein structures. The formulation of the proposed framework was encountered by many challenges due to the wide range of relevant analysis and visualization techniques, in addition to the existence of a diversity of biological data types, on which these techniques operate. The main challenges that guided the formulation of the present framework are: (a) the integration of data from heterogeneous resources, such as expert-driven data from text, public domain databases and diverse large scale experimental data sets, and (b) difficulty in integrating the most recent analysis and visualization tools due to the lack of standard I/O. Therefore, the fundamental innovation in the proposed framework is the integration of the state-ofthe- art techniques of both analysis and visualization for gene expressions and protein structures through a unified workflow. In addition, it supports a wide range of input data types and exports three dimensional interactive outputs using Virtual Reality Modeling Language (VRML) to be ready for exploration via off-the-shelf monitors as well as immersive, 3D, stereo display environments.

Index Terms—computer visualization, bioinformatics, gene expressions, protein structures

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Cite: Ashraf S. Hussein, " computer visualization, bioinformatics, gene expressions, protein structures," Journal of Software vol. 3, no. 7, pp. 2-11, 2008.