Metatool 5.0: fast and flexible elementary modes analysis. Summary: Elementary modes analysis is a powerful tool in the constraint-based modeling of metabolic networks. In recent years, new approaches to calculating elementary modes in biochemical reaction networks have been developed. As a consequence, the program Metatool, which is one of the first programs dedicated to this purpose, has been reimplemented in order to make use of these new approaches. The performance of Metatool has been significantly increased and the new version 5.0 can now be run inside the GNU octave or Matlab environments to allow more flexible usage and integration with other tools.

References in zbMATH (referenced in 23 articles )

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  1. Röhl, Annika; Bockmayr, Alexander: Finding MEMo: minimum sets of elementary flux modes (2019)
  2. Gainer-Dewar, Andrew; Vera-Licona, Paola: The minimal hitting set generation problem: algorithms and computation (2017)
  3. Gawthrop, Peter J.; Crampin, Edmund J.: Energy-based analysis of biomolecular pathways (2017)
  4. Nabli, Faten; Martinez, Thierry; Fages, François; Soliman, Sylvain: On enumerating minimal siphons in Petri nets using CLP and SAT solvers: theoretical and practical complexity (2016)
  5. Oddsdóttir, Hildur Æsa; Hagrot, Erika; Chotteau, Véronique; Forsgren, Anders: Robustness analysis of elementary flux modes generated by column generation (2016)
  6. Oddsdóttir, Hildur Æsa; Hagrot, Erika; Chotteau, Véronique; Forsgren, Anders: On dynamically generating relevant elementary flux modes in a metabolic network using optimization (2015)
  7. Reimers, Arne C.; Goldstein, Yaron; Bockmayr, Alexander: Generic flux coupling analysis (2015)
  8. Klamt, Steffen; Hädicke, Oliver; von Kamp, Axel: Stoichiometric and constraint-based analysis of biochemical reaction networks (2014)
  9. Müller, Arne C.; Bockmayr, Alexander: Flux modules in metabolic networks (2014)
  10. Marashi, Sayed-Amir; David, Laszlo; Bockmayr, Alexander: On flux coupling analysis of metabolic subsystems (2012)
  11. Sajitz-Hermstein, Max; Nikoloski, Zoran: Restricted cooperative games on metabolic networks reveal functionally important reactions (2012)
  12. Samal, Satya Swarup; Errami, Hassan; Weber, Andreas: PoCaB: a software infrastructure to explore algebraic methods for bio-chemical reaction networks (2012)
  13. Hoppe, Andreas; Hoffmann, Sabrina; Gerasch, Andreas; Gille, Christoph; Holzhütter, Hermann-Georg: FASIMU: flexible software for flux-balance computation series in large metabolic networks (2011) ioport
  14. Jevremović, Dimitrije; Trinh, Cong T.; Srienc, Friedrich; Sosa, Carlos P.; Boley, Daniel: Parallelization of nullspace algorithm for the computation of metabolic pathways (2011)
  15. Srienc, Friedrich; Unrean, Pornkamol: A statistical thermodynamical interpretation of metabolism (2010)
  16. Kielbassa, J.; Bortfeldt, R.; Schuster, S.; Koch, I.: Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets (2009)
  17. Larhlimi, Abdelhalim; Bockmayr, Alexander: A new constraint-based description of the steady-state flux cone of metabolic networks (2009)
  18. Behre, Jörn; Wilhelm, Thomas; von Kamp, Axel; Ruppin, Eytan; Schuster, Stefan: Structural robustness of metabolic networks with respect to multiple knockouts (2008)
  19. Montero, Francisco; Nuño, Juan Carlos; Meléndez-Hevia, Enrique; Olasagasti, Felix; Vázquez, Sara; Morán, Federico: Stoichiometric analysis of self-maintaining metabolisms (2008)
  20. Nazaret, Christine; Mazat, Jean-Pierre: An old paper revisited: “A mathematical model of carbohydrate energy metabolism. interaction between glycolysis, the krebs cycle and the H-transporting shuttles at varying atpases load” by V. V. Dynnik et al. (2008)

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