sbtoolbox

Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology. We present a Systems Biology Toolbox for the widely used general purpose mathematical software MATLAB. The toolbox offers systems biologists an open and extensible environment, in which to explore ideas, prototype and share new algorithms, and build applications for the analysis and simulation of biological and biochemical systems. Additionally it is well suited for educational purposes. The toolbox supports the Systems Biology Markup Language (SBML) by providing an interface for import and export of SBML models. In this way the toolbox connects nicely to other SBML-enabled modelling packages. Models are represented in an internal model format and can be described either by entering ordinary differential equations or, more intuitively, by entering biochemical reaction equations. The toolbox contains a large number of analysis methods, such as deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis and bifurcation analysis.


References in zbMATH (referenced in 16 articles )

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  1. Stalidzans, Egils; Landmane, Katrina; Sulins, Jurijs; Sahle, Sven: Misinterpretation risks of global stochastic optimisation of kinetic models revealed by multiple optimisation runs (2019)
  2. Edwin Tye, Tom Finnie, Ian Hall, Steve Leach: PyGOM - A Python Package for Simplifying Modelling with Systems of Ordinary Differential Equations (2018) arXiv
  3. Laranjeira, Simão; Symmonds, Mkael; Palace, Jacqueline; Payne, Stephen J.; Orlowski, Piotr: A mathematical model of cellular swelling in neuromyelitis optica (2017)
  4. Justin Feigelman, Stefan Ganscha, Manfred Claassen: matLeap: A fast adaptive Matlab-ready tau-leaping implementation suitable for Bayesian inference (2016) arXiv
  5. Draelants, Delphine; Kłosiewicz, Przemysław; Broeckhove, Jan; Vanroose, Wim: Solving general auxin transport models with a numerical continuation toolbox in Python: PyNCT (2015)
  6. Khoshnaw, Sarbaz H. A.: Reduction of a kinetic model of active export of importins (2015)
  7. Liu, Weijiu: Store-operated calcium entry could prevent continuous spiking of membrane potential to sustain normal intracellular calcium oscillations and normal potential bursting in pancreatic (\beta)-cells (2013)
  8. Andasari, V.; Chaplain, M. A. J.: Intracellular modelling of cell-matrix adhesion during cancer cell invasion (2012)
  9. Rodriguez-Fernandez, Maria; Banga, Julio R.; Doyle, Francis J. III: Novel global sensitivity analysis methodology accounting for the crucial role of the distribution of input parameters: application to systems biology models (2012)
  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. Preedy, Katharine F.; Schofield, Pietà G.; Liu, Sijia; Matzavinos, Anastasios; Chaplain, Mark A. J.; Hubbard, Stephen F.: Modelling contact spread of infection in host-parasitoid systems: vertical transmission of pathogens can cause chaos (2010)
  12. Cloutier, Mathieu; Bolger, Fiachra B.; Lowry, John P.; Wellstead, Peter: An integrative dynamic model of brain energy metabolism using in vivo neurochemical measurements (2009) ioport
  13. Lai, Xin; Nikolov, Svetoslav; Wolkenhauer, Olaf; Vera, Julio: A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis (2009)
  14. Perumal, Thanneer M.; Wu, Yan; Gunawan, Rudiyanto: Dynamical analysis of cellular networks based on the Green’s function matrix (2009)
  15. Uhrmacher, Adelinde M.; Himmelspach, Jan; Jeschke, Matthias; John, Mathias; Leye, Stefan; Maus, Carsten; Röhl, Mathias; Ewald, Roland: One modelling formalism & simulator is not enough! A perspective for computational biology based on James II (2008) ioport
  16. Schmidt, Henning; Jirstrand, Mats: Systems biology toolbox for MATLAB: A computational platform for research in systems biology (2006) ioport