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| Arena3D |
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Motivation |
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The analysis and interpretation of relationships between biological molecules, networks and concepts is becoming a major bottleneck in systems biology. Very often the pure amount of data and their heterogeneity provides a challenge for the visualization of the data. There exist a wide variety of graph representations, which most often map the data on 2D graphs. These methods are applicable to a wide range of problems, nevertheless many of them reach a limit in terms of user friendliness and visualization when a large number of nodes and connections have to be analyzed and visualized. |
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Results |
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Here we present a new visualization tool called
Arena3D which introduces a new, staggered multi layer concept that
allows the analysis of big networks in a three dimensional space
representation. The different layers in the representation
correspond to different data types respective concepts like
sequences, structures, chemicals diseases, pathways etc. The data
entries for one specific data type, like sequences, can be ordered
or clustered on their respective layer by applying a data focused
similarity measurement like sequence similarity. Several clustering
methods are also supported to cluster several data types in
different layers. The different nodes of the layers can be connected
according to known or predicted relationships between the nodes. The
relationships are typically extracted from available databases and
available text minimg machineries and are predicted by various data
mining methods or originate from experimentally generated data.
Indirect connections that may hide some additional information can
also be explored. |
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Publications |
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Georgios A. Pavlopoulos, Sean I. O’Donoghue, Venkata P. Satagopam, Theodoros Soldatos, Evangelos Pafilis, and Reinhard Schneider, Arena3D: Visualization of Biological Networks in 3D, BMC Systems Biology 2008, 2:104. |