JSW 2008 Vol.3(7): 2-11 ISSN: 1796-217X
doi: 10.4304/jsw.3.7.2-11
doi: 10.4304/jsw.3.7.2-11
Analysis and Visualization of Gene Expressions and Protein Structures
Ashraf S. Hussein
Faculty of Computer and Information Sciences, Ain Shams University, Cairo, 11566, Egypt
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
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
Cite: Ashraf S. Hussein, " computer visualization, bioinformatics, gene expressions, protein structures," Journal of Software vol. 3, no. 7, pp. 2-11, 2008.
General Information
ISSN: 1796-217X (Online)
Frequency: Quarterly
Editor-in-Chief: Prof. Antanas Verikas
Executive Editor: Ms. Yoyo Y. Zhou
Abstracting/ Indexing: DBLP, EBSCO, CNKI, Google Scholar, ProQuest, INSPEC(IET), ULRICH's Periodicals Directory, WorldCat, etc
E-mail: jsw@iap.org
-
Apr 26, 2021 News!
Vol 14, No 4- Vol 14, No 12 has been indexed by IET-(Inspec) [Click]
-
Nov 18, 2021 News!
Papers published in JSW Vol 16, No 1- Vol 16, No 6 have been indexed by DBLP [Click]
-
Dec 24, 2021 News!
Vol 15, No 1- Vol 15, No 6 has been indexed by IET-(Inspec) [Click]
-
Nov 18, 2021 News!
[CFP] 2022 the annual meeting of JSW Editorial Board, ICCSM 2022, will be held in Rome, Italy, July 21-23, 2022 [Click]
-
Feb 09, 2023 News!
Vol 18, No 1 has been published with online version [Click]