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

  • William J. R. LongabaughEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 786)


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.

Key words

Genetic regulatory networks Network modeling Network visualization Systems biology software Drawing gene networks Layout of gene networks Modeling Computational biology 



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.


  1. 1.
    Longabaugh, W. J. R., Davidson, E. H., and Bolouri, H. (2005) Computational representation of developmental genetic regulatory networks, Developmental biology 283, 1–16.PubMedCrossRefGoogle Scholar
  2. 2.
    Longabaugh, W. J. R., Davidson, E. H., and Bolouri, H. (2009) Visualization, documentation, analysis, and communication of large-scale gene regulatory networks, Biochimica et biophysica acta 1789, 363–374.PubMedGoogle Scholar
  3. 3.
    Davidson, E. H., Rast, J. P., Oliveri, P., Ransick, A., Calestani, C., Yuh, C. H., Minokawa, T., Amore, G., Hinman, V., Arenas-Mena, C., Otim, O., Brown, C. T., Livi, C. B., Lee, P. Y., Revilla, R., Rust, A. G., Pan, Z., Schilstra, M. J., Clarke, P. J., Arnone, M. I., Rowen, L., Cameron, R. A., McClay, D. R., Hood, L., and Bolouri, H. (2002) A genomic regulatory ­network for development, Science 295, 1669–1678. URL: Google Scholar
  4. 4.
    Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome research 13, 2498–2504.PubMedCrossRefGoogle Scholar
  5. 5.
    Vokes, S. A., Ji, H., McCuine, S., Tenzen, T., Giles, S., Zhong, S., Longabaugh, W. J. R., Davidson, E. H., Wong, W. H., and McMahon, A. P. (2007) Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning, Development 134, 1977–1989. URL:
  6. 6.
    Bonneau, R., Facciotti, M. T., Reiss, D. J., Schmid, A. K., Pan, M., Kaur, A., Thorsson, V., Shannon, P., Johnson, M. H., Bare, J. C., Longabaugh, W., Vuthoori, M., Whitehead, K., Madar, A., Suzuki, L., Mori, T., Chang, D. E., Diruggiero, J., Johnson, C. H., Hood, L., and Baliga, N. S. (2007) A predictive model for transcriptional control of physiology in a free living cell, Cell 131, 1354–1365. URL: Google Scholar
  7. 7.
    Georgescu, C., Longabaugh, W. J. R., Scripture-Adams, D. D., David-Fung, E. S., Yui, M. A., Zarnegar, M. A., Bolouri, H., and Rothenberg, E. V. (2008) A gene regulatory network armature for T lymphocyte specification, Proceedings of the National Academy of Sciences of the United States of America 105, 20100–20105. URL:∼tcellgrn/TCellMap.html
  8. 8.
    Chan, T. M., Longabaugh, W., Bolouri, H., Chen, H. L., Tseng, W. F., Chao, C. H., Jang, T. H., Lin, Y. I., Hung, S. C., Wang, H. D., and Yuh, C. H. (2009) Developmental gene regulatory networks in the zebrafish embryo, Biochimica et biophysica acta 1789, 279–298. URL: Google Scholar
  9. 9.
    Levine, M., and Davidson, E. H. (2005) Gene regulatory networks for development, Proceedings of the National Academy of Sciences of the United States of America 102, 4936–4942.PubMedCrossRefGoogle Scholar
  10. 10.
    Stathopoulos, A., and Levine, M. (2005) Genomic regulatory networks and animal development, Developmental cell 9, 449–462.PubMedCrossRefGoogle Scholar
  11. 11.
    Wellmer, F., Alves-Ferreira, M., Dubois, A., Riechmann, J. L., and Meyerowitz, E. M. (2006) Genome-wide analysis of gene expression during early Arabidopsis flower development, PLoS genetics 2, e117.PubMedCrossRefGoogle Scholar
  12. 12.
    Mori, A. D., Zhu, Y., Vahora, I., Nieman, B., Koshiba-Takeuchi, K., Davidson, L., Pizard, A., Seidman, J. G., Seidman, C. E., Chen, X. J., Henkelman, R. M., and Bruneau, B. G. (2006) Tbx5-dependent rheostatic control of cardiac gene expression and morphogenesis, Developmental biology 297, 566–586.PubMedCrossRefGoogle Scholar
  13. 13.
    Hoffman, B. G., Zavaglia, B., Witzsche, J., Ruiz de Algara, T., Beach, M., Hoodless, P. A., Jones, S. J., Marra, M. A., and Helgason, C. D. (2008) Identification of transcripts with enriched expression in the developing and adult pancreas, Genome biology 9, R99.PubMedCrossRefGoogle Scholar
  14. 14.
    Kioussi, C., and Gross, M. K. (2008) How to build transcriptional network models of mammalian pattern formation, PloS one 3, e2179.PubMedCrossRefGoogle Scholar
  15. 15.
    Smith, J., and Davidson, E. H. (2008) Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo, Proceedings of the National Academy of Sciences of the United States of America 105, 20089–20094.PubMedCrossRefGoogle Scholar
  16. 16.
    Ririe, T. O., Fernandes, J. S., and Sternberg, P. W. (2008) The Caenorhabditis elegans vulva: a post-embryonic gene regulatory network controlling organogenesis, Proceedings of the National Academy of Sciences of the United States of America 105, 20095–20099.PubMedCrossRefGoogle Scholar
  17. 17.
    Materna, S. C., and Oliveri, P. (2008) A protocol for unraveling gene regulatory networks, Nature protocols 3, 1876–1887.PubMedCrossRefGoogle Scholar
  18. 18.
    Tamplin, O. J., Kinzel, D., Cox, B. J., Bell, C. E., Rossant, J., and Lickert, H. (2008) Microarray analysis of Foxa2 mutant mouse embryos reveals novel gene expression and inductive roles for the gastrula organizer and its derivatives, BMC genomics 9, 511.PubMedCrossRefGoogle Scholar
  19. 19.
    Bolouri, H. (2008) Computational Modeling of Gene Regulatory Networks: a Primer, Imperial College Press.Google Scholar
  20. 20.
    Morley, R. H., Lachani, K., Keefe, D., Gilchrist, M. J., Flicek, P., Smith, J. C., and Wardle, F. C. (2009) A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation, Proceedings of the National Academy of Sciences of the United States of America 106, 3829–3834.PubMedCrossRefGoogle Scholar
  21. 21.
    Su, Y. H., Li, E., Geiss, G. K., Longabaugh, W. J. R., Krämer, A., and Davidson, E. H. (2009) A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo, Developmental biology 329, 410–421.PubMedCrossRefGoogle Scholar
  22. 22.
    Sansom, S. N., Griffiths, D. S., Faedo, A., Kleinjan, D. J., Ruan, Y., Smith, J., van Heyningen, V., Rubenstein, J. L., and Livesey, F. J. (2009) The level of the transcription factor Pax6 is essential for controlling the balance between neural stem cell self-renewal and neurogenesis, PLoS genetics 5, e1000511.PubMedCrossRefGoogle Scholar
  23. 23.
    Davidson, E. H. (2006) The Regulatory Genome: Gene Regulatory Networks in Development and Evolution, Elsevier.Google Scholar
  24. 24.
    Shannon, P. T., Reiss, D. J., Bonneau, R., and Baliga, N. S. (2006) The Gaggle: an open-source software system for integrating bioinformatics software and data sources, BMC bioinformatics 7, 176.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Institute for Systems BiologySeattleUSA

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