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BioTapestry: A Tool to Visualize the Dynamic Properties of Gene Regulatory Networks

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Gene Regulatory Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 786))

Abstract

BioTapestry is an open source, freely available software tool that has been developed to handle the ­challenges of modeling genetic regulatory networks (GRNs). Using BioTapestry, a researcher can ­construct a network model and use it to visualize and understand the dynamic behavior of a complex, spatially and temporally distributed GRN. Here we provide a step-by-step example of a way to use BioTapestry to build a GRN model and discuss some common issues that can arise during this process.

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Acknowledgments

BioTapestry development is a collaboration between the Institute for Systems Biology and the Davidson Lab at the California Institute of Technology; many thanks are due to Dr. Eric Davidson for his vision, leadership, and support. Also, thanks to Dr. Hamid Bolouri for his excellent comments and suggestions on this manuscript. BioTapestry is supported by NIGMS grant GM061005.

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Authors and Affiliations

  1. Institute for Systems Biology, Seattle, WA, USA

    William J. R. Longabaugh

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  1. William J. R. Longabaugh
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Correspondence to William J. R. Longabaugh .

Editor information

Editors and Affiliations

  1. Inst. Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland

    Bart Deplancke

  2. Faculté de Biologie det Médecine, Centre Intégratif de Génomique, Université de Lausanne, Bâtiment Génopode, Lausanne, 1015, Switzerland

    Nele Gheldof

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Longabaugh, W.J.R. (2012). BioTapestry: A Tool to Visualize the Dynamic Properties of Gene Regulatory Networks. In: Deplancke, B., Gheldof, N. (eds) Gene Regulatory Networks. Methods in Molecular Biology, vol 786. Humana Press. https://doi.org/10.1007/978-1-61779-292-2_21

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  • DOI: https://doi.org/10.1007/978-1-61779-292-2_21

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-291-5

  • Online ISBN: 978-1-61779-292-2

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