Skip to main content
SpringerLink
Log in

Extending the Metabolic Network of Ectocarpus Siliculosus Using Answer Set Programming

  • Conference paper
Logic Programming and Nonmonotonic Reasoning (LPNMR 2013)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 8148))

Abstract

Metabolic network reconstruction is of great biological relevance because it offers a way to investigate the metabolic behavior of organisms. However, reconstruction remains a difficult task at both the biological and computational level. Building on previous work establishing an ASP-based approach to this problem, we present a report from the field resulting in the discovery of new biological knowledge. In fact, for the first time ever, we automatically reconstructed a metabolic network for a macroalgae. We accomplished this by taking advantage of ASP’s combined optimization and enumeration capacities. Both computational tasks build on an improved ASP problem representation, incorporating the concept of reversible reactions. Interestingly, optimization greatly benefits from the usage of unsatisfiable cores available in the ASP solver unclasp. Applied to Ectocarpus siliculosus, only the combination of unclasp and clasp allowed us to obtain a metabolic network able to produce all recoverable metabolites among the experimentally measured ones. Moreover, 70% of the identified reactions are supported by an homologous enzyme in Ectocarpus siliculosus, confirming the quality of the reconstructed network from a biological viewpoint.

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

Access this chapter

Log in via an institution
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. Barabási, A., Oltvai, Z.: Network biology: Understanding the cell’s functional organization. Nature Reviews Genetics 5(2), 101–113 (2004)

    Article  Google Scholar 

  2. Joyce, A., Palsson, B.: The model organism as a system: Integrating ’omics’ data sets. Nature Reviews Molecular Cell Biology 7(3), 198–210 (2006)

    Article  Google Scholar 

  3. Yamada, T., Bork, P.: Evolution of biomolecular networks: Lessons from metabolic and protein interactions. Nature Reviews Molecular Cell Biology 10(11), 791–803 (2009)

    Article  Google Scholar 

  4. Orth, J., Conrad, T., Na, J., Lerman, J., Nam, H., Feist, A., Palsson, B.: A comprehensive genome-scale reconstruction of Escherichia coli metabolism. Molecular Systems Biology 7, Article 535 (2011)

    Google Scholar 

  5. de Oliveira Dal’Molin, C., Quek, L., Palfreyman, R., Brumbley, S., Nielsen, L.: AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis. Plant Physiology 152(2), 579–589 (2009)

    Article  Google Scholar 

  6. Zengler, K., Palsson, B.: A road map for the development of community systems (CoSy) biology. Nature Reviews Microbiology 10(5), 366–372 (2012)

    Google Scholar 

  7. Swainston, N., Smallbone, K., Mendes, P., Kell, D., Paton, N.: The subliminal toolbox: automating steps in the reconstruction of metabolic networks. Journal of Integrative Bioinformatics 8, Article 186 (2011)

    Google Scholar 

  8. Handorf, T., Ebenhöh, O., Heinrich, R.: Expanding metabolic networks: Scopes of compounds, robustness, and evolution. Journal of Molecular Evolution 61(4), 498–512 (2005)

    Article  Google Scholar 

  9. Satish Kumar, V., Dasika, M., Maranas, C.: Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 8, Article 212 (2007)

    Google Scholar 

  10. Christian, N., May, P., Kempa, S., Handorf, T., Ebenhöh, O.: An integrative approach towards completing genome-scale metabolic networks. Molecular BioSystems 5(12), 1889–1903 (2009)

    Article  Google Scholar 

  11. Schaub, T., Thiele, S.: Metabolic network expansion with answer set programming. In: Hill, P.M., Warren, D.S. (eds.) ICLP 2009. LNCS, vol. 5649, pp. 312–326. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  12. Baral, C.: Knowledge Representation, Reasoning and Declarative Problem Solving. Cambridge University Press (2003)

    Google Scholar 

  13. Andres, B., Kaufmann, B., Matheis, O., Schaub, T.: Unsatisfiability-based optimization in clasp. In: Dovier, A., Santos Costa, V. (eds.) Technical Communications of the Twenty-Eighth International Conference on Logic Programming, ICLP 2012. Leibniz International Proceedings in Informatics, vol. 17, pp. 212–221. Dagstuhl Publishing (2012)

    Google Scholar 

  14. Gebser, M., Kaufmann, B., Schaub, T.: Conflict-driven answer set solving: From theory to practice. Artificial Intelligence 187-188, 52–89 (2012)

    Google Scholar 

  15. Gebser, M., Kaminski, R., Kaufmann, B., Ostrowski, M., Schaub, T., Thiele, S.: A user’s guide to gringo, clasp, clingo, and iclingo, http://potassco.sourceforge.net

  16. Gebser, M., Kaminski, R., Kaufmann, B., Schaub, T.: Answer Set Solving in Practice. Morgan and Claypool Publishers (2012)

    Google Scholar 

  17. Nikoloski, Z., Grimbs, S., May, P., Selbig, J.: Metabolic networks are NP-hard to reconstruct. Journal of Theoretical Biology 254(4), 807–816 (2008)

    Article  MathSciNet  Google Scholar 

  18. Nikoloski, Z., Grimbs, S., Selbig, J., Ebenhöh, O.: Hardness and approximability of the inverse scope problem. In: Crandall, K.A., Lagergren, J. (eds.) WABI 2008. LNCS (LNBI), vol. 5251, pp. 99–112. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  19. Beard, D., Liang, S., Qian, H.: Energy balance for analysis of complex metabolic networks. Biophysical Journal 83(1), 79–86 (2002)

    Article  Google Scholar 

  20. Li, C., Manyà, F.: MaxSAT. In: Biere, A., Heule, M., van Maaren, H., Walsh, T. (eds.) Handbook of Satisfiability. Frontiers in Artificial Intelligence and Applications, vol. 185, pp. 613–631. IOS Press (2009)

    Google Scholar 

  21. Tonon, T., Eveillard, D., Prigent, S., Bourdon, J., Potin, P., Boyen, C., Siegel, A.: Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment. Omics: A Journal of Integrative Biology 15(12), 883–892 (2011)

    Article  Google Scholar 

  22. Karp, P., Paley, S., Romero, P.: The Pathway Tools software. Bioinformatics 18(suppl. 1), S225–S232 (2002)

    Google Scholar 

  23. Loira, N., Dulermo, T., Nicaud, J., Sherman, D.: A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. BMC Systems Biology 6, Article 35 (2012)

    Google Scholar 

  24. Gebser, M., Kaufmann, B., Otero, R., Romero, J., Schaub, T., Wanko, P.: Domain-specific heuristics in answer set programming. In: des Jardins, M., Littman, M. (eds.) Proceedings of the Twenty-Seventh National Conference on Artificial Intelligence, AAAI 2013. AAAI Press (to appear, 2013)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. CNRS, UMR 6074 IRISA, Campus de Beaulieu, 35042, Rennes, France

    Guillaume Collet, Anne Siegel & Sven Thiele

  2. UMR 6241 LINA, Université de Nantes, 2 rue de la Houssinière, 44300, Nantes, France

    Damien Eveillard

  3. Institut für Informatik, Universität Potsdam, August-Bebel-Str. 89, D-14482, Deutschland

    Martin Gebser & Torsten Schaub

  4. UMR 6074 IRISA, University of Rennes 1, Campus de Beaulieu, 35042, Rennes, France

    Sylvain Prigent

  5. INRIA, Centre Rennes-Bretagne-Atlantique, Projet Dyliss, Campus de Beaulieu, 35042, Rennes cedex, France

    Guillaume Collet, Sylvain Prigent, Anne Siegel & Sven Thiele

  6. INRIA-CIRIC, Rosario Norte 555, Of. 703, Las Condes, Santiago de Chile, Chile

    Sven Thiele

Authors
  1. Guillaume Collet
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Damien Eveillard
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Martin Gebser
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sylvain Prigent
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Torsten Schaub
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Anne Siegel
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Sven Thiele
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Computer Science, University of Corunna, Campus de Elviña s/n, 15071, Corunna, Spain

    Pedro Cabalar

  2. Department of Computer Science, New Mexico State University, 1290 Frenger Mall, SH 123, MSC CS, P.O. Box 30001, 88003, Las Cruces, NM, USA

    Tran Cao Son

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Collet, G. et al. (2013). Extending the Metabolic Network of Ectocarpus Siliculosus Using Answer Set Programming. In: Cabalar, P., Son, T.C. (eds) Logic Programming and Nonmonotonic Reasoning. LPNMR 2013. Lecture Notes in Computer Science(), vol 8148. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-40564-8_25

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-40564-8_25

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-40563-1

  • Online ISBN: 978-3-642-40564-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation