ENISI multiscale modeling of mucosal immune responses driven by high performance computing

Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

Volumn , Issue , 2015, Pages 680-684

  Abedi, Vida ^a   Hontecillas, Raquel ^a   Hoops, Stefan ^a   Liles, Nathan ^a   Carbo, Adria ^b   Lu, Pinyi ^a   Philipson, Casandra ^b   Abassaganya Riera, Josep ^a  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^b BIOTHERAPEUTICS INC   (United States)

Author keywords

CD4+ T cell differentiation; ENISI; HPC; inflammatory bowel disease; multiscale modeling

Indexed keywords

BIOINFORMATICS; T-CELLS;

CELL DIFFERENTIATION; ENISI; HIGH PERFORMANCE COMPUTING; HIGH PERFORMANCE COMPUTING (HPC); INFLAMMATORY BOWEL DISEASE; LARGE-SCALE INFORMATION PROCESSING; MUCOSAL IMMUNE RESPONSE; MULTI-SCALE MODELING;

IMMUNE SYSTEM;

EID: 84962360268     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBM.2015.7359768     Document Type: Conference Paper

References (33)

1. B. Ramsundar, S. Keames, P. Riley, D. Webster, D. Konerding, and V. Pande, "Massively Multitask Networks for Drug Discovery, " arXiv preprint ar Xiv: 1502. 02072, 2015.
2. A. Masoudi-Nejad, G. Bidkhori, S. Hosseini Ashtiani, A. Najafi, J. H. Bozorgmehr, and E. Wang, "Cancer systems biology and modeling: Microscopic scale and multiscale approaches., " Seminars in cancer biology, vol. 30C, pp. 60-69, 2015.
3. C. Valero, E. Javierre, J. M. Garcia-Aznar, A. Menzel, and M. J. Gomez-Benito, "Challenges in the Modeling of Wound Healing Mechanisms in Soft Biological Tissues, " Ann Biomed Eng, Dec 2 2014.
4. F. Castiglione, F. Pappalardo, C. Bianca, G. Russo, and S. Motta, "Modeling biology spanning different scales: an open challenge., " BioMed research international, vol. 2014, p. 902545, 2014.
5. G. Dwivedi, L. Fitz, M. Hegen, S. W. Martin, J. Harrold, A. Heatherington, et al., "A multi scale model of interleukin-6-mediated immune regulation in Crohn's disease and its application in drug discovery and development, " CPT Pharmacometrics Syst Pharmacol, vol. 3, p. e89, 2014.
6. H. Hayenga, B. Thome, P. Yen, J. Papin, S. Peirce, and J. Humphrey, "Multiscale Computational Modeling in Vascular Biology: From Molecular Mechanisms to Tissue-Level Structure and Function, " in Multiscale Computer Modeling in Biomechanics and Biomedical Engineering. vol. 14, G. Amit, Ed., ed: Springer Berlin Heidelberg, 2013, pp. 209-240.
7. M. Meier-Schellersheim, I. D. Fraser, and F. Klauschen, "Multiscale modeling for biologists, " Wiley Interdiscip Rev Syst Bioi Med, vol. 1, pp. 4-14, Jul-Aug 2009.
8. S. Schnell, R. Grima, and P. K. Maini, "Multi scale modeling in biology - New insights into cancer illustrate how mathematical tools are enhancing the understanding of life from the smallest scale to the grandest, " American Scientist, vol. 95, pp. 134-142, Mar-Apr 2007.
9. T. Sutterlin, C. Kolb, H. Dickhaus, D. Jager, and N. Grabe, "Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI, " Bioinformatics, vol. 29, pp. 223-9, Jan 15 2013.
10. Y. Mei, A. Carbo, R. Hontecillas, S. Hoops, N. Liles, P. Lu, et al., "ENISI MSM: A Novel Multi-Scale Modeling Platform for Computational Immunology, " presented at the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014.
11. C. DeLisi, "Mathematical modeling in immunology, " Annu Rev Biophys Bioeng, vol. 12, pp. 117-38, 1983.
12. P. M. A. Sioot and A. G. Hoekstra, "Multi-scale modelling in computational biomedicine, " Briefings in Bioinformatics, vol. 11, pp. 142-152, Jan 2010.
13. M. Bernaschi and F. Castiglione, "Design and implementation of an immune system simulator, " Comput Biol Med, vol. 31, pp. 303-31, Sep 2001.
14. E. Sklar, "NetLogo, a multi-agent simulation environment, " Artif Life, vol. 13, pp. 303-11, Summer 2007.
15. S. Tisue and U. Wilensky, "Netlogo: A simple environment for modeling complexity, " presented at the International Conference on Complex Systems, 2004.
16. N. Collier, T. R. Howe, and M. J. North, "Onward and upward: The transition to Repast 2.0, " in Proceedings of the first annual North American Association for Computational Social and Organizational Science conference Pittsburgh, 2003.
17. Swarm. Available: hup://www.swarm.org
18. S. Railsback, S. Lytinen, and S. Jackson, "Agent-based Simulation Platforms: Review and Development Recommendations, " Simulation, vol. 82, pp. 609-623, 2006.
19. K. Wendelsdorf, M. Alam, J. Bassaganya-Riera, K. Bisset, S. Eubank, R. Hontecillas, et al., "ENteric Immunity Simulator: A tool for in silico study of gastroenteric infections, " IEEE Transactions on NanoBioScience, vol. 11, pp. 273-288, 2012.
20. Y. Mei, R. Hontecillas, X. Zhang, K. Bisset, S. Eubank, S. Hoops, et al., "ENISI Visual, an agent-based simulator for modeling gut immunity, " IEEE International Conference of Bioinformatics and Biomedicine (BIBM), 2012.
21. A. Carbo, D. Olivares-Villagomez, R. Hontecillas, J. Bassaganya-Riera, R. Chaturvedi, M. B. Piazuelo, et al., "Systems modeling of the role of interleukin-21 in the maintenance of effector CD4+ T cell responses during chronic Helicobacter pylori infection, " MBio, vol. 5, pp. e01243-14, 2014.
22. A. Carbo, R. Hontecillas, T. Andrew, K. Eden, Y. Mei, S. Hoops, et al., "Computational modeling of heterogeneity and function of CD4+ T cells, " Front Cell Dev Biol, vol. 2, p. 31, 2014.
23. A. Carbo, R. Hontecillas, B. Kronsteiner, M. Viladomiu, M. Pedragosa, P. Lu, et al., "Systems modeling of molecular mechanisms controlling cytokine-driven CD4+ T cell differentiation and phenotype plasticity, " PLoS Comput Biol, vol. 9, p. el003027, Apr 2013.
24. M. J. North, N. T. Collier, J. Ozik, E. R. Tatara, C. M. Macal, M. Bragen, et al., "Complex adaptive systems modeling with Repast Simphony, " Complex Adaptive Systems Modeling, vol. I, p. 3, 2013.
25. N. Collier and M. North, "Repast HPC: A Platform for Large-Scale Agent-Based Modeling, " in Large-Scale Computing, ed: John Wiley & Sons, Inc., 2012, pp. 81-109.
26. H. Childs, E. Brugger, B. Whitlock, J. Meredith, S. Ahern, D. Pugmire, et al., "VisIt: An End-User Tool For Visualizing and Analyzing Very Large Data, " in High Performance Visualization-Enabling ExtremeScale Scientific insight, ed, 2012, pp. 357-372.
27. A. Leber, M. Viladomiu, R. Hontecillas, V. Abedi, C. Philipson, S. Hoops, et al., "Systems Modeling of Interactions between Mucosal Immunity and the Gut Microbiome during Clostridium difficile Infection, " PLoS One, vol. 10, p. e0134849, 2015.
28. L. V. K. a. G. Zheng, "Charm++ and AMPI: Adaptive Runtime Strategies via Migratable Objects, " in Advanced Computational infrastructures for Parallel and Distributed Adaptive Applications, ed: John Wiley & Sons, Inc., 2009.
29. S. Negara, K.-C. Pan, G. Zheng, N. Negara, R. E. Johnson, L. V. Kale, et al., "Automatic MPI to AMPI Program Transformation, " Parallel Programming Laboratory2010.
30. Parallel Science and Engineering Applications: The Charm + + Approach: Taylor & Francis Group, CRC Press, 2013.
31. P. Lu, V. Abedi, Y. Mei, R. Hontecillas, S. Hoops, A. Carbo, et al., "Suervised learning methods in modeling of CD4+ T cell heterogeneity, " BioData Mining, vol. In press, 2015.
32. P. Lu, V. Abedi, Y. Mei, R. Hontecillas, C. Philipson, S. Hoops, et al., "Supervised learning with artificial neural networks in modeling of cell differentiation processes, " in Emerging Trends in Computational Biology, Bioinformatics and Systems Biology, ed Burlignton, MA: Morgan Kaufmann, 2015.
33. Y. Mei, R. Hontecillas, X. Zhang, A. Carbo, and J. Bassaganya-Riera, "Neural network models for classifying immune cell subsets, " presented at the BIBM, Shangai, China, 2013.