DNA
            <i>in Virtuo</i>
            visualization and exploration of 3D genomic structures

Hérisson, Joan; Gros, Pierre-Emmanuel; Férey, Nicolas; Magneau, Olivier; Gherbi, Rachid

doi:10.1145/1029949.1029955

Cited by 11 publications

(9 citation statements)

References 2 publications

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“…The entire gene sequence can be visualized in a double-helix form representing the connections between the nitrogenous base pairs (A-T and C-G). This representation can be performed along with the connections backbones [12]. Each of the nucleotides, A, C, G and T, is distinguished by a distinct color.…”

Section: ) Gene Scalementioning

confidence: 99%

“…The atomic scale visualizes gene sequences (or part of them) to show the atomic structure of the nitrogenous bases and their connections [12]. There are two standard representations for the atomic scale: the 'wire-frame' (the connections are visualized as cylinders) and the 'ball-andstick' (the nucleotides are visualized as spheres and the connections between them as cylinders).…”

Section: ) Atomic Scalementioning

confidence: 99%

“…Desktop applications like RasMol [7], PyMOL [9] and IBM Protein Viewer [10] render several representations of the protein structures [10]. Also, ADN-Viewer is specialized in visualizing the DNA sequences using various methods [12].…”

Section: Introductionmentioning

confidence: 99%

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Analysis and Visualization of Gene Expressions and Protein Structures

Hussein

2008

JSW

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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-of-the-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.

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Section: ) Gene Scalementioning

confidence: 99%

Section: ) Atomic Scalementioning

confidence: 99%

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Analysis and Visualization of Gene Expressions and Protein Structures

Hussein

2008

JSW

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“…Multimedia is becoming an important tool for faculty in the biological sciences due to some conceptual and functional of educational complexity that in fact cannot or very hard to be conveyed appropriately by using traditional teaching methods [8]. The 3D structure of such complex conformation is very crucial in many vital biological mechanisms, like replication, transcription or regulating [5].…”

Section: Interactive 3d Virtual Multimedia Application Helps In Biolomentioning

confidence: 99%

Integrated 3D Multimedia Web Based Application in Biology: A Prototype

Kamsin

2007

Computer Graphics, Imaging and Visualisation (CGIV 2007)

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Since the middle of 1990s, Malaysia has already showed its commitment and emphasis on the idea of Information and Communication Technology (ICT). Malaysia's Multimedia Super Corridor (MSC) is being developed in order to satisfy the country's ambition to achieve the fully developed status by the year 2020. Recent studies showed that online learning for secondary students had become more established and accepted as a standard way of learning nowadays. Educators are always being encouraged to incorporate technology into their classroom teaching. 3D interactions with multimedia elements relatively allow the learners to learn and grasp the lessons being taught much faster than in a normal classroom. The use of computer training tools where the student can interact with a computer model can give good feedbacks. 3D analytical approach is especially useful in determining the fundamental molecular events using a web-based, visually-oriented system that allows efficient querying of gene expression. The implementation of VRML is perceivably efficient and effective method for conveying molecular models over the net. In molecular science, 3D impressions and conceptions are elementary in order to transfer and understand further complex structural information. A prototype of an Interactive 3D Multimedia Learning Tool in Biology was created in order to provide users with a 3D element multimedia study environment in Biology subject. The prototype contains three main divisions which are the 3DiC, animations and tutorials. It allows users to learn and study about the biological cells and animations in an interactive and interesting 3D environment.

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“…As in ADN-Viewer (Hérisson, Gros, Férey, Magneau & Gherbi, 2004) and SequenceWord (Rojdestvenski, Pettersson & Modjeska, 2000) our objective is to elaborate new solution in order to explore in virtual environment various kinds of genomic data. These data come from the many databases, such as GenBank (DDBJ/EMBL/Genbank n.d.), SwissProt (SIB/EBI n.d.), or Decrypthon (AFM, GENOMINING, IBM, 2000).…”

Section: Introductionmentioning

confidence: 99%