ENISI MSM: A novel multi-scale modeling platform for computational immunology

Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014

Volumn , Issue , 2014, Pages 391-396

  Mei, Yongguo ^a   Carbo, Adria ^a   Hontecillas, Raquel ^a   Hoops, Stefan ^a   Liles, Nathan ^a   Lu, Pinyi ^a   Philipson, Casandra ^a   Bassaganya Riera, Josep ^a  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84922795145     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBM.2014.6999190     Document Type: Conference Paper

References (27)

1. J. M. Bower and H. Bolouri. Computational modeling of genetic and biochemical networks. MIT press, 2001.
2. A. Carbo, J. Bassaganya-Riera, M. Pedragosa, M. Viladomiu, M. Marathe, S. Eubank, K. Wendelsdorf, K. Bisset, S. Hoops, X. Deng, et al. Predictive computational modeling of the mucosal immune responses during helicobacter pylori infection. PloS one, 8(9):e73365, 2013.
3. A. Carbo, R. Hontecillas, B. Kronsteiner, M. Viladomiu, M. Pedragosa, P. Lu, C. W. Philipson, S. Hoops, M. Marathe, S. Eubank, et al. Systems modeling of molecular mechanisms controlling cytokine-driven cd4+ t cell differentiation and phenotype plasticity. PLoS computational biology, 9(4):e1003027, 2013.
4. A. K. Chakraborty, M. L. Dustin, and A. S. Shaw. In silico models for cellular and molecular immunology: successes, promises and challenges. Nature immunology, 4(10):933-936, 2003.
5. G. Dwivedi, L. Fitz, M. Hegen, S. Martin, J. Harrold, A. Heatherington, and C. Li. A multiscale model of interleukin-6-mediated immune regulation in crohns disease and its application in drug discovery and development. CPT: pharmacometrics & systems pharmacology, 3(1):e89, 2014.
6. S. Forrest and C. Beauchemin. Computer Immunology. Immunological Reviews, 216:176-197, 2007.
7. V. Grimm, E. Revilla, U. Berger, F. Jeltsch, W. M. Mooij, S. F. Railsback, H.-H. Thulke, J. Weiner, T. Wiegand, and D. L. DeAngelis. Pattern-oriented modeling of agent-based complex systems: lessons from ecology. science, 310(5750):987-991, 2005.
8. H. N. Hayenga, B. C. Thorne, P. Yen, J. A. Papin, S. M. Peirce, and J. D. Humphrey. Multiscale computational modeling in vascular biology: From molecular mechanisms to tissuelevel structure and function. In Multiscale Computer Modeling in Biomechanics and Biomedical Engineering, pages 209-240. Springer, 2013.
9. J. Hegewald, M. Krafczyk, J. Tölke, A. Hoekstra, and B. Chopard. An agent-based coupling platform for complex automata. In Computational Science-ICCS 2008, pages 227-233. Springer, 2008.
10. S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle, N. Simus, M. Singhal, L. Xu, P. Mendes, and U. Kummer. COPASI-a COmplex PAthway SImulator. Bioinformatics, 22(24):3067-3074, Dec 2006.
11. M. Hucka, A. Finney, H. M. Sauro, H. Bolouri, J. C. Doyle, H. Kitano, A. P. Arkin, B. J. Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, S. Dronov, E. D. Gilles, M. Ginkel, V. Gor, I. I. Goryanin, W. J. Hedley, T. C. Hodgman, J. H. Hofmeyr, P. J. Hunter, N. S. Juty, J. L. Kasberger, A. Kremling, U. Kummer, N. Le Novere, L. M. Loew, D. Lucio, P. Mendes, E. Minch, E. D. Mjolsness, Y. Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, J. C. Schaff, B. E. Shapiro, T. S. Shimizu, H. D. Spence, J. Stelling, K. Takahashi, M. Tomita, J. Wagner, and J. Wang. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics, 19(4):524-531, Mar 2003.
12. H. Kitano. Computational systems biology. Nature, 420(6912):206-210, Nov 2002.
13. A. Krinner, I. Roeder, M. Loeffler, and M. Scholz. Merging concepts-coupling an agent-based model of hematopoietic stem cells with an ode model of granulopoiesis. BMC systems biology, 7(1):117, 2013.
14. L. M. Loew and J. C. Schaff. The virtual cell: a software environment for computational cell biology. TRENDS in Biotechnology, 19(10):401-406, 2001.
15. C. M. Macal and M. J. North. Tutorial on agent-based modelling and simulation. Journal of Simulation, 8(2):177-183, Feb 2010.
16. W. Materi and D. S. Wishart. Computational systems biology in drug discovery and development: methods and applications. Drug discovery today, 12(7):295-303, 2007.
17. Y. Mei, A. Carbo, R. Hontecillas, and J. Bassaganya-Riera. Enisi sde: A novel web-based stochastic modeling tool for computational biology. In Bioinformatics and Biomedicine (BIBM), 2013 IEEE International Conference on, pages 392-397, Dec 2013.
18. Y. Mei, R. Hontecillas, X. Zhang, K. Bisset, S. Eubank, S. Hoops, M. Marathe, and J. Bassaganya-Riera. Enisi visual, an agentbased simulator for modeling gut immunity. In Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference on, pages 1-5, Oct 2012.
19. M. Meier-Schellersheim, I. D. Fraser, and F. Klauschen. Multiscale modeling for biologists. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 1(1):4-14, 2009.
20. M. J. North, T. R. Howe, N. T. Collier, and J. R. Vos. A Declarative Model Assembly Infrastructure for Verification and Validation. In Advancing Social Simulation: The First World Congress, Heidelberg, FRG, 2007. Springer.
21. H. V. D. Parunak, R. Savit, and R. L. Riolo. Agent-based modeling vs. equation-based modeling: A case study and users guide. In Multi-agent systems and agent-based simulation, pages 10-25. Springer, 1998.
22. A. S. Perelson and P. W. Nelson. Mathematical analysis of hiv-1 dynamics in vivo. SIAM review, 41(1):3-44, 1999.
23. Repast. http://repast. sourceforge. net/.
24. S. Schnell, R. Grima, and P. K. Maini. Multiscale modeling in biology. American Scientist, 95(2):134, 2007.
25. P. M. Sloot and A. G. Hoekstra. Multi-scale modelling in computational biomedicine. Briefings in bioinformatics, 11(1):142-152, 2010.
26. M. S. Waterman. Introduction to computational biology: maps, sequences and genomes. CRC Press, 1995.
27. K. V. Wendeldorf, J. Bassaganya-Riera, K. Bisset, S. Eubank, R. Hontecillas, and M. Marathe. Enteric Immunity Simulator: A Tool for in silica study of Gut Immunopathologies. In IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2011.