COBRA Toolbox

COBRA Toolbox: The COnstraint-Based Reconstruction and Analysis Toolbox is a MATLAB software suite for quantitative prediction of cellular and multicellular biochemical networks with constraint-based modelling. It implements a comprehensive collection of basic and advanced modelling methods, including reconstruction and model generation as well as biased and unbiased model-driven analysis methods. It is widely used for modelling, analysing and predicting a variety of metabolic phenotypes using genome-scale biochemical networks.

References in zbMATH (referenced in 13 articles )

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  1. Krzysztof Ciomek, Miłosz Kadziński: Polyrun: A Java library for sampling from the bounded convex polytopes (2021) not zbMATH
  2. Frioux, Clémence; Schaub, Torsten; Schellhorn, Sebastian; Siegel, Anne; Wanko, Philipp: Hybrid metabolic network completion (2019)
  3. Hala, D.; Cullen, J. A.; Hernout, B.; Ivanov, I.: \textitInsilico predicted transcriptional regulatory control of steroidogenesis in spawning female fathead minnows (\textitPimephalespromelas) (2018)
  4. Latif, Majid jun.; May, Elebeoba E.: A multiscale agent-based model for the investigation of E. coli K12 metabolic response during biofilm formation (2018)
  5. Xu, Zixiang; Guo, Jing; Yue, Yunxia; Meng, Jing; Sun, Xiao: \textitInsilico genome-scale reconstruction and analysis of the \textitShewanellaloihica PV-4 metabolic network (2018)
  6. Fleming, Ronan M. T.; Vlassis, Nikos; Thiele, Ines; Saunders, Michael A.: Conditions for duality between fluxes and concentrations in biochemical networks (2016)
  7. Lule, Ivan; D’Huys, Pieter-Jan; Van Mellaert, Lieve; Anné, Jozef; Bernaerts, Kristel; Van Impe, Jan: Metabolic impact assessment for heterologous protein production in \textitStreptomyceslividans based on genome-scale metabolic network modeling (2013)
  8. Fleming, R. M. T.; Maes, C. M.; Saunders, M. A.; Ye, Y.; Palsson, B.Ø.: A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks (2012)
  9. 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
  10. Boghigian, Brett A.; Lee, Kyongbum; Pfeifer, Blaine A.: Computational analysis of phenotypic space in heterologous polyketide biosynthesis -- applications to \textitEscherichiacoli, \textitBacillussubtilis, and \textitSaccharomycescerevisiae (2010)
  11. Breitling, Rainer; Donaldson, Robin A.; Gilbert, David R.; Heiner, Monika: Biomodel engineering -- from structure to behavior (2010)
  12. Koschützki, Dirk; Junker, Björn H.; Schwender, Jörg; Schreiber, Falk: Structural analysis of metabolic networks based on flux centrality (2010)
  13. Xu, Zixiang; Sun, Xiao; Yu, Shihai: Genome-scale analysis to the impact of gene deletion on the metabolism of \textitE. Coli: constraint-based simulation approach (2009) ioport