Skip to main content

An Approach to the Engineering of Cellular Models Based on P Systems

  • Conference paper
Mathematical Theory and Computational Practice (CiE 2009)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5635))

Included in the following conference series:

  • 860 Accesses

Abstract

Living cells assembled into colonies or tissues communicate using complex systems. These systems consist in the interaction between many molecular species distributed over many compartments. Among the different cellular processes used by cells to monitor their environment and respond accordingly, gene regulatory networks, rather than individual genes, are responsible for the information processing and orchestration of the appropriate response [16].

In this respect, synthetic biology has emerged recently as a novel discipline aiming at unravelling the design principles in gene regulatory systems by synthetically engineering transcriptional networks which perform a specific and prefixed task [2]. Formal modelling and analysis are key methodologies used in the field to engineer, assess and compare different genetic designs or devices.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Alon, U.: Network motifs: theory and experimental approaches. Nature Reviews Genetics 8, 450–461 (2007)

    Article  Google Scholar 

  2. Andrianantoandro, E., Basu, S., Karig, D., Weiss, R.: Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems biology 2, 2006.0028 (2006)

    Google Scholar 

  3. Bernardini, F., Gheorghe, M., Romero-Campero, F.J., Walkinshaw, N.: A Hybrid Approach to Modeling Biological Systems. In: Eleftherakis, G., Kefalas, P., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2007. LNCS, vol. 4860, pp. 138–159. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  4. Bernardini, F., Gheorghe, M., Krasnogor, N.: Quorum Sensing P Systems. Theoretical Computer Science 371(1-2), 20–33 (2007)

    Article  MathSciNet  MATH  Google Scholar 

  5. Bernardini, F., Manca, V.: Dynamical aspects of P systems. BioSystems 70(2), 85–93 (2003)

    Article  MATH  Google Scholar 

  6. Besozzi, D., Cazzaniga, P., Pescini, D., Mauri, G., Colombo, S., Martegani, E.: Modeling and stochastic simulation of the Ras/cAMP/PKA pathway in the yeast Saccharomyces cerevisiae evidences a key regulatory function for intracellular guanine nucleotides pools. Journal of Biotechnology 133(3), 377–385 (2008)

    Article  Google Scholar 

  7. Bianco, L., Fontana, F., Manca, V.: P systems with reaction maps. International Journal of Foundations of Computer Science 17(1), 27–48 (2006)

    Article  MathSciNet  MATH  Google Scholar 

  8. Gillespie, D.T.: Stochastic Simulation of Chemical Kinetics. Annu. Rev. Phys. Chem. 58, 35–55 (2007)

    Article  Google Scholar 

  9. Kaern, M., Elston, T.C., Blake, W.J., Collins, J.J.: Stochasticity in gene expression: from theories to phenotypes. Nature Reviews Genetics 6, 451–464 (2005)

    Article  Google Scholar 

  10. Krasnogor, N., Gheorghe, M., Terrazas, G., Diggle, S., Williams, P., Camara, M.: An appealing computational mechanism drawn from bacterial quorum sensing. Bulletin of the EATCS 85, 135–148 (2005)

    MathSciNet  MATH  Google Scholar 

  11. Păun, G.: Computing with Membranes. Journal of Computer and System Sciences 61(1), 108–143 (2000)

    Article  MathSciNet  MATH  Google Scholar 

  12. Păun, G.: Membrane Computing: An Introduction. Springer, Heidelberg (2002)

    Book  MATH  Google Scholar 

  13. Păun, A., Pérez-Jiménez, M.J., Romero-Campero, F.J.: Modeling signal transduction using P systems. In: Hoogeboom, H.J., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2006. LNCS, vol. 4361, pp. 100–122. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  14. Pérez-Jiménez, M.J., Romero-Campero, F.J.: P Systems, a new computational modelling tool for systems biology. In: Priami, C., Plotkin, G. (eds.) Transactions on Computational Systems Biology VI. LNCS (LNBI), vol. 4220, pp. 176–197. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  15. Pescini, D., Besozzi, D., Mauri, G., Zandron, C.: Dynamical probabilistic P systems. International Journal of Foundations of Computer Science 17(1), 183–204 (2006)

    Article  MathSciNet  MATH  Google Scholar 

  16. Ptashne, M., Gann, A.: Genes and Signals. Cold Spring Harbor Laboratory Press (2002)

    Google Scholar 

  17. Romero-Campero, F.J., Pérez-Jiménez, M.J.: Modelling gene expression control using P systems: the Lac Operon, a case study. BioSystems 91(3), 438–457 (2008)

    Article  Google Scholar 

  18. Romero-Campero, F.J., Pérez-Jiménez, M.J.: A model of the quorum sensing system in Vibrio fischeri using P systems. Artificial Life 14(1), 1–15 (2008)

    Article  Google Scholar 

  19. Păun, G., Romero-Campero, F.J.: Membrane Computing as a Modeling Framework. Cellular Systems Case Studies. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol. 5016, pp. 168–214. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  20. Romero-Campero, F.J., Gheorghe, M., Ciobanu, G., Auld, J.M., Pérez-Jiménez, M.J.: Cellular modelling using P systems and process algebra. Progress in Natural Science 17(4), 375–383 (2007)

    Article  MathSciNet  MATH  Google Scholar 

  21. Romero-Campero, F.J., Cao, H., Cámara, M., Krasnogor, N.: Structure and Parameter Estimation for Cell Systems Biology Models. In: Proc. of the Genetic and Evolutionary Computation Conference, Atlanta, USA, July 12 - 16, pp. 331–338 (2008)

    Google Scholar 

  22. Romero-Campero, F.J., Twycross, J., Cámara, M., Bennett, M., Gheorghe, M., Krasnogor, N.: Modular Assembly of Cell Systems Biology Models Using P Systems. International Journal of Foundations of Computer Science (2008) (in press)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Romero-Campero, F.J., Krasnogor, N. (2009). An Approach to the Engineering of Cellular Models Based on P Systems. In: Ambos-Spies, K., Löwe, B., Merkle, W. (eds) Mathematical Theory and Computational Practice. CiE 2009. Lecture Notes in Computer Science, vol 5635. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-03073-4_44

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-03073-4_44

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-03072-7

  • Online ISBN: 978-3-642-03073-4

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics