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Visualization in Medicine and Life Sciences II pp 265–283Cite as

Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data

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Part of the book series: Mathematics and Visualization ((MATHVISUAL))

Abstract

Three-dimensional gene expression PointCloud data generated by the Berkeley Drosophila TranscriptionNetwork Project (BDTNP) provides quantitative information about the spatial and temporal expression of genes in early Drosophila embryos at cellular resolution. The BDTNP team visualizes and analyzes Point- Cloud data using the software application PointCloudXplore (PCX). To maximize the impact of novel, complex data sets, such as PointClouds, the data needs to be accessible to biologists and comprehensible to developers of analysis functions.We address this challenge by linking PCX and Matlab® via a dedicated interface, thereby providing biologists seamless access to advanced data analysis functions and giving bioinformatics researchers the opportunity to integrate their analysis directly into the visualization application. To demonstrate the usefulness of this approach, we computationally model parts of the expression pattern of the gene even skipped using a genetic algorithm implemented in Matlab and integrated into PCX via our Matlab interface.

MATLAB is a registered trademark of The MathWorks Inc., 3 Apple Hill Drive Natick, MA 01760-2098, USA. Online at: http://www.mathworks.com/

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Author information

Authors and Affiliations

  1. Computational Research Division, Lawrence Berkeley National Laboratory (LBNL), One Cyclotron Road, Berkeley, CA, 94720, USA

    Oliver Rübel, Bernd Hamann & E. Wes Bethel

  2. Institute for Data Analysis and Visualization (IDAV), Department of Computer Science, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA

    Oliver Rübel & Bernd Hamann

  3. International Research Training Group 1131, Technische Universität Kaiserslautern, Erwin Schrödinger-Straße, 67653, Kaiserslautern, Germany

    Oliver Rübel, Hans Hagen & Bernd Hamann

  4. Genomics Division, LBNL, One Cyclotron Road, Berkeley, CA, 94720, USA

    Soile V. E. Keränen & Mark Biggin

  5. Life Sciences Division, LBNL, One Cyclotron Road, Berkeley, CA, 94720, USA

    David W. Knowles

  6. Computational Research Division, LBNL, One cyclotron Road, Berkeley, CA, 94720, USA

    Gunther H. Weber

Authors
  1. Oliver Rübel
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  2. Soile V. E. Keränen
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  3. Mark Biggin
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  4. David W. Knowles
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  5. Gunther H. Weber
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  6. Hans Hagen
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  7. Bernd Hamann
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  8. E. Wes Bethel
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Corresponding author

Correspondence to Oliver Rübel .

Editor information

Editors and Affiliations

  1. Bremen School of Engineering and Science, Jacobs University, 75 05 61, 28725, Bremen, Germany

    Lars Linsen

  2. FB Informatik, Universität Kaiserslautern, 30 49, 67653, Kaiserslautern, Germany

    Hans Hagen

  3. Institute for Data Analysis and Visualization Department of Computer Science, University of California, Davis, One Shields Avenue, Davis, CA, 95616-8562, USA

    Bernd Hamann

  4. Visualization and Data Analysis, Zuse Institute Berlin (ZIB), Takustr. 7, 14195, Berlin, Germany

    Hans-Christian Hege

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© 2012 Springer-Verlag Berlin Heidelberg

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Rübel, O. et al. (2012). Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data. In: Linsen, L., Hagen, H., Hamann, B., Hege, HC. (eds) Visualization in Medicine and Life Sciences II. Mathematics and Visualization. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21608-4_15

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