E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria

  • Matej Troják
  • David Šafránek
  • Jakub Hrabec
  • Jakub Šalagovič
  • Františka Romanovská
  • Jan Červený
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9859)


E-cyanobacterium.org is an online platform providing tools for public sharing, annotation, analysis, and visualization of dynamical models and wet-lab experiments related to cyanobacteria. The platform is unique in integrating abstract mathematical models with a precise consortium-agreed biochemical description provided in a rule-based formalism. The general aim is to stimulate collaboration between experimental and computational systems biologists to achieve better understanding of cyanobacteria.


  1. 1.
    Ashburner, M., et al.: Gene ontology: tool for the unification of biology. Gene Ontology Consortium, Nat. Genet. 25(1), 25–29 (2000)Google Scholar
  2. 2.
    Bateman, A., et al.: Uniprot: a hub for protein information. Nucleic Acids Res. 43(D1), D204–D212 (2015)MathSciNetCrossRefGoogle Scholar
  3. 3.
    Beard, D.A., et al.: CellML metadata standards, associated tools and repositories. Philos. Trans. R. Soc. Lond. A Math. Phys. Eng. Sci. 367(1895), 1845–1867 (2009)CrossRefGoogle Scholar
  4. 4.
    Croft, D., et al.: The reactome pathway knowledgebase. Nucleic Acids Res. 42(D1), D472–D477 (2014)CrossRefGoogle Scholar
  5. 5.
    Dada, J.O., et al.: SBRML: a markup language for associating systems biology data with models. Bioinformatics 26(7), 932–938 (2010)CrossRefGoogle Scholar
  6. 6.
    Eaton, J.W., et al.: GNU Octave version 3.0.1 manual: a high-level interactive language for numerical computations. CreateSpace Independent Publishing Platform, Seattle (2009)Google Scholar
  7. 7.
    Harris, T.W., et al.: Wormbase: a comprehensive resource for nematode research. Nucleic Acids Res. 38(suppl 1), D463–D467 (2010)CrossRefGoogle Scholar
  8. 8.
    Hertel, S., et al.: Revealing a two-loop transcriptional feedback mechanism in the cyanobacterial circadian clock. PLoS Comput. Biol. 9(3), 1–16 (2013)MathSciNetCrossRefGoogle Scholar
  9. 9.
    Hoops, S., et al.: COPASI - a complex pathway simulator. Bioinformatics 22(24), 3067–3074 (2006)CrossRefGoogle Scholar
  10. 10.
    Hucka, M., et al.: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4), 524–531 (2003)CrossRefGoogle Scholar
  11. 11.
    Jablonsky, J., et al.: Multi-level kinetic model explaining diverse roles of isozymes in prokaryotes. PLoS ONE 9(8), 1–8 (2014)MathSciNetCrossRefGoogle Scholar
  12. 12.
    Kanehisa, M., et al.: KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44(D1), D457–D462 (2016)CrossRefGoogle Scholar
  13. 13.
    Kent, E., et al.: Condor-COPASI: high-throughput computing for biochemical networks. BMC Syst. Biol. 6(1), 1–13 (2012)CrossRefGoogle Scholar
  14. 14.
    Keseler, I.M., et al.: EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res. 41(D1), D605–D612 (2013)CrossRefGoogle Scholar
  15. 15.
    Klement, M., et al.: A comprehensive web-based platform for domain-specific biological models. Electron. Notes Theoret. Comput. Sci. 299, 61–67 (2013)CrossRefGoogle Scholar
  16. 16.
    Klement, M., et al.: Biochemical space: a framework for systemic annotation of biological models. In: Proceedings of the 5th International Workshop on Interactions Between Computer Science and Biology (CS2Bio-14). Electronic Notes in Theoretical Computer Science, vol. 306, pp. 31–44 (2014)Google Scholar
  17. 17.
    Le Novère, N., et al.: Biomodels database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 34, D689–D691 (2006)CrossRefGoogle Scholar
  18. 18.
    Miyoshi, F., et al.: A mathematical model for the kai-protein-based chemical oscillator and clock gene expression rhythms in cyanobacteria. J. Biol. Rhythms 22(1), 69–80 (2007)CrossRefGoogle Scholar
  19. 19.
    Olivier, B.G., et al.: Web-based kinetic modelling using jws online. Bioinformatics 20(13), 2143–2144 (2004)CrossRefGoogle Scholar
  20. 20.
    Rizk, A., et al.: A general computational method for robustness analysis with applications to synthetic gene networks. Bioinformatics 25(12), i169–i178 (2009)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG 2016

Authors and Affiliations

  • Matej Troják
    • 1
  • David Šafránek
    • 1
  • Jakub Hrabec
    • 1
  • Jakub Šalagovič
    • 1
  • Františka Romanovská
    • 1
  • Jan Červený
    • 2
  1. 1.Faculty of InformaticsMasaryk UniversityBrnoCzech Republic
  2. 2.Global Change Research Centre AS CR, v. v. i.BrnoCzech Republic

Personalised recommendations