Connecting models to data in multiscale multicellular tissue simulations

Procedia Computer Science

Volumn 18, Issue , 2013, Pages 712-721

  Cooper, Jonathan ^a   Osborne, James ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Chaste; Functional curation; SED ML

Indexed keywords

EID: 84896917119     PISSN: 18770509     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1016/j.procs.2013.05.235     Document Type: Conference Paper

References (20)

1. National Research Council, Assessing the Reliability of Complex Models: Mathematical and Statistical Foundations of Verification, Validation, and Uncertainty Quantification, The National Academies Press, 2012.
2. J. Pitt-Francis, P. Pathmanathan, M. Bernabeu, R. Bordas, J. Cooper, A. Fletcher, G. Mirams, P. Murray, J. Osborne, A. Walter, S. Chapman, A. Garny, I. van Leeuwen, P. Maini, B. Rodríguez, S. Waters, J. Whiteley, H. Byrne, D. Gavaghan, Chaste: A test-driven approach to software development for biological modelling, Comput Phys Commun 180 (12) (2009) 2452-2471.
3. J. Cooper, A. Corrias, D. Gavaghan, D. Noble, Considerations for the use of cellular electrophysiology models within cardiac tissue simulations, Prog Biophys Mol Biol 107 (1) (2011) 74-80. doi:10.1016/j.pbiomolbio.2011.06.002.
4. J. Cooper, G. Mirams, S. Niederer, High throughput functional curation of cellular models, Prog Biophys Mol Biol 107 (1) (2011) 11-20. doi:10.1016/j.pbiomolbio.2011.06.003.
5. A. Garny, D. Nickerson, J. Cooper, R. W. dos Santos, S. McKeever, P. Nielsen, P. Hunter, CellML and associated tools and techniques, Phil Trans Roy Soc A 366 (1878) (2008) 3017-3043. doi:10.1098/rsta.2008.0094.
6. M. Hucka, A. Finney, B. Bornstein, S. Keating, B. Shapiro, J. Matthews, B. Kovitz, M. Schilstra, A. Funahashi, J. Doyle, H. Kitano, Evolving a lingua franca . . . : The Systems Biology Markup Language (SBML) project, Systems Biology 1 (1) (2004) 41-53.
7. W3C RDF Working Group, Resource Description Framework, http://www.w3.org/RDF/(2004).
8. J. R. Terkildsen, S. Niederer, E. J. Crampin, P. Hunter, N. P. Smith, Using Physiome standards to couple cellular functions for rat cardiac excitation-contraction, Exp Physiol 93 (7) (2008) 919-929. doi:10.1113/ expphysiol.2007.041871.
9. J. Cooper, S. McKeever, A model-driven approach to automatic conversion of physical units, Softw Pract Exper 38 (4) (2008) 337-359. doi:10.1002/spe.828.
10. VPH-FET Consortium, VPH-FET Research Roadmap, Ch. 4 https://www. biomedtown.org/VPHFET/reception/(Nov2011).
11. D. Köhn, N. Le Novère, SED-ML - An XML format for the implementation of the MIASE guidelines, in: Computational Methods in Systems Biology, Vol. 5307 of LNCS, Springer Berlin/Heidelberg, 2008, pp. 176-190. doi:10.1007/978-3-540-88562-7 15.
12. S. J. Dunn, P. Appleton, S. N. Nelson, I. Näthke, D. Gavaghan, J. Osborne, A two-dimensional model of the colonic crypt accounting for the role of the basement membrane and pericryptal fibroblast sheath, PLoS Comp. Biol. 8 (2012) e1002515. doi:10.1371/journal.pcbi.1002515.
13. G. T. Eisenhoffer, P. D. Loftus, M. Yoshigi, H. Otsuna, C.-B. Chien, P. A. Morcos, J. Rosenblatt, Crowding induces live cell extrusion to maintain homeostatic cell numbers in epithelia, Nature 484 (2012) 546 - 549.
14. G. De Matteis, A. Graudenzi, M. Antoniotti, A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development, Journal of mathematical biology (2012) 1-54.
15. J. M. Osborne, A.Walter, S. K. Kershaw, G. R. Mirams, A. G. Fletcher, P. Pathmanathan, D. Gavaghan, O. E. Jensen, P. K. Maini, H. M. Byrne, A hybrid approach to multi-scale modelling of cancer, Phil. Trans. (2010) 5013-5028.
16. I. M. M. Van Leeuwen, G. R. Mirams, A. Walter, A. Fletcher, P. Murray, J. Osborne, S. Varma, S. J. Young, J. Cooper, J. Pitt-Francis, L. Momtahan, P. Pathmanathan, J. P. Whiteley, S. J. Chapman, D. J. Gavaghan, O. E. Jensen, J. R. King, P. K. Maini, S. L.Waters, H. M. Byrne, An integrative computational model for intestinal tissue renewal, Cell Prolif. 42 (2009) 617 - 636.
17. G. Mirams, A. Fletcher, P. Maini, H. Byrne, A theoretical investigation of the effect of proliferation and adhesion on monoclonal conversion in the colonic crypt, Journal of Theoretical Biology 312 (7) (2012) 143-156. doi:10.1016/j.jtbi.2012.08.002.
18. W.Wong, N. Mandir, R. Goodlad, B.Wong, S. Garcia, S. Lam, N. Wright, Histogenesis of human colorectal adenomas and hyperplastic polyps: The role of cell proliferation and crypt fission, Gut 50 (2) (2002) 212-217.
19. The HDF Group, Hierarchical data format version 5, http://www.hdfgroup. org/HDF5(2000).
20. G. Wilson, Software carpentry: Getting scientists to write better code by making them more productive, Comput Sci Eng 8 (6) (2006) 66-69. URL http://www.software-carpentry.org/.