Skip to main content
Have a personal or library account? Click to login
Building Mathematical Models of Biological Systems with modelbase Cover

Building Mathematical Models of Biological Systems with modelbase

Open Access
|Nov 2018

References

  1. Almquist, J, Cvijovic, M, Hatzimanikatis, V, Nielsen, J and Jirstrand, M 2014 Kinetic models in industrial biotechnology – Improving cell factory performance. Metabolic Engineering, 24: 3860. DOI: 10.1016/j.ymben.2014.03.007
  2. Oliphant, T E 2007 Python for scientific computing. Computing in Science and Engineering, 9(3): 1020. DOI: 10.1109/MCSE.2007.58
  3. Pettersson, G and Ryde-Pettersson, U 1988 A mathematical model of the Calvin photosynthesis cycle. Eur. J. Biochem, 175(3): 661672. DOI: 10.1111/j.1432-1033.1988.tb14242.x
  4. McIntyre, L M, Thorburn, D R, Bubb, W A and Kuchel, P W 1989 Comparison of computer simulations of the F-type and L-type non- oxidative hexose monophosphate shunts with 31P-NMR experimental data from human erythrocytes. Eur J Biochem, 180(2): 399420. DOI: 10.1111/j.1432-1033.1989.tb14662.x
  5. Poolman, M G 2006 ScrumPy: Metabolic modelling with Python. IEE Proc.-Syst. Biol, 153(5): 375378. DOI: 10.1049/ip-syb:20060010
  6. Olivier, B G, Rohwer, J M and Hofmeyr, J H S 2005 Modelling cellular systems with PySCeS. Bioinformatics, 21(4): 560561. DOI: 10.1093/bioinformatics/bti046
  7. Ebenhöh, O and Spelberg, S 2018 The importance of the photosynthetic Gibbs effect in the elucidation of the Calvin-Benson-Bassham cycle. Biochemical Society Transactions. DOI: 10.1042/BST20170245
  8. Kandler, O and Gibbs, M 1956 Asymmetric Distribution of C14 in the Glucose Phosphates Formed During Photosynthesis. Plant physiology, 31(5): 411. DOI: 10.1104/pp.31.5.411
  9. Gibbs, M and Kandler, O 1957 Asymmetric distribution of C14 in sugars formed during photosynthesis. Proc. Natl. Acd. Sci. U.S.A., 43: 446451. DOI: 10.1073/pnas.43.6.446
  10. Andersson, C, Claus, F and Akesson, J 2015 ScienceDirect Assimulo: A unified framework for ODE solvers. Mathematics and Computers in Simulation, 116: 2643. DOI: 10.1016/j.matcom.2015.04.007
  11. Hindmarsh, A C, Brown, P N, Grant, K E, Lee, S L, Serban, R, Shumaker, D E and Woodward, C S 2005 SUNDIALS: Suite of Nonlinear and Differential/Algebraic Equation Solvers. ACM Transactions on Mathematical Software, 31(3): 363396. DOI: 10.1145/1089014.1089020
  12. Jones, E, Oliphant, T, Peterson, P, et al. 2001 Scipy: Open source scientific tools for python.
  13. Hunter, J D 2007 Matplotlib: A 2D graphics environment. Computing In Science and Engineering, 9(3): 9095. DOI: 10.1109/MCSE.2007.55
  14. Ebrahim, A, Lerman, J A, Palsson, B O and Hyduke, D R 2013 COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Systems Biology, 7(1): 1. DOI: 10.1186/1752-0509-7-74
  15. Ebenhöh, O, Fucile, G, Finazzi, G G, Rochaix, J-D and Goldschmidt-Clermont, M 2014 Short-term acclimation of the photosynthetic electron transfer chain to changing light: A mathematical model. Philosophical Transactions B, 369(1640). DOI: 10.1098/rstb.2013.0223
  16. Poolman, M G, Fell, D A and Thomas, S 2000 Modelling photosynthesis and its control. Journal of Experimental Botany, 51(90001): 319328. DOI: 10.1093/jexbot/51.suppl_1.319
  17. Berthon, H A, Bubb, W A and Kuchel, P W 1993 13C n.m.r. isotopomer and computer-simulation studies of the non-oxidative pentose phosphate pathway of human erythrocytes. Biochem J, 296: 379387. DOI: 10.1042/bj2960379
  18. Ebenhöh, O, Houwaart, T, Lokstein, H, Schlede, S and Tirok, K 2011 A minimal mathematical model of nonphotochemical quenching of chlorophyll fluorescence. Biosystems, 103(2): 196204. DOI: 10.1016/j.biosystems.2010.10.011
  19. Matuszyńska, A B, Heidari, S, Jahns, P and Ebenhöh, O 2016 A mathematical model of non-photochemical quenching to study short-term light memory in plants. Biochimica et Biophysica Acta (BBA) – Bioenergetics, 1857(12): 17. DOI: 10.1016/j.bbabio.2016.09.003
  20. Crown, S B, Ahn, W and Antoniewicz, M R 2012 Rational design of 13C-labeling experiments for metabolic ux analysis in mammalian cells. BMC Systems Biology, 6(1): 43. DOI: 10.1186/1752-0509-6-43
  21. Kluyver, T, Ragan-Kelley, B, Perez, F, Granger, B, Bussonnier, M, Frederic, J, Kelley, K, Hamrick, J, Grout, J, Corlay, S, Ivanov, P, Avila, D, Abdalla, S and Willing, C 2016 Jupyter Notebooks — a publishing format for reproducible computational workows. In: Schmidt, B and Loizides, F (eds.), Positioning and Power in Academic Publishing: Players, Agents and Agendas 8790. IOS Press.
DOI: https://doi.org/10.5334/jors.236 | Journal eISSN: 2049-9647
Language: English
Submitted on: Jun 27, 2018
Accepted on: Oct 16, 2018
Published on: Nov 16, 2018
Published by: Ubiquity Press
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year

© 2018 Oliver Ebenhöh, Marvin van Aalst, Nima P. Saadat, Tim Nies, Anna Matuszyńska, published by Ubiquity Press
This work is licensed under the Creative Commons Attribution 4.0 License.