Developing a multiscale, multi-resolution agent-based brain tumor model by graphics processing units

Theoretical Biology and Medical Modelling

Volumn 8, Issue 1, 2011, Pages

  Zhang, Le ^a,b   Jiang, Beini ^a   Wu, Yukun ^c   Strouthos, Costas ^d   Sun, Phillip Zhe ^e   Su, Jing ^f   Zhou, Xiaobo ^f  

^a MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

^b SOUTHWEST UNIVERSITY   (China)

^c University of Maryland School of Medicine Center for Vaccine Development   (United States)

^d CYPRUS INSTITUTE   (Cyprus)

^e MASSACHUSETTS GENERAL HOSPITAL   (United States)

^f HOUSTON METHODIST HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR;

ALGORITHM; ARTICLE; BRAIN TUMOR; COMPUTER GRAPHICS; DISEASE COURSE; GLIOBLASTOMA; HUMAN; PATHOLOGY; PHYSIOLOGY; SIGNAL TRANSDUCTION; THEORETICAL MODEL;

ALGORITHMS; BRAIN NEOPLASMS; COMPUTER GRAPHICS; DISEASE PROGRESSION; GLIOBLASTOMA; HUMANS; MODELS, THEORETICAL; RECEPTOR, EPIDERMAL GROWTH FACTOR; SIGNAL TRANSDUCTION;

EID: 83455238005     PISSN: None     EISSN: 17424682     Source Type: Journal    
DOI: 10.1186/1742-4682-8-46     Document Type: Article

References (47)

1. Glioblastoma multiforme: a rare manifestation of extensive liver and bone metastases. Robert MC, Wastie ML, Biomed Imaging Interv J 2008 4 1
2. Genetic modulation of hypoxia induced gene expression and angiogenesis: relevance to brain tumors. Brat DJ, Kaur B, Van Meir EG, Frontiers in Bioscience 2003 8
3. Glioblastoma multiforme: clinical findings, magnetic resonance imaging, and pathology in five dogs. Lipsitz D, Higgins RJ, Kortz GD, Dickinson PJ, Bollen AW, Naydan DK, LeCouteur RA, Vet Pathol 2003 40 659 669 10.1354/vp.40-6-659 14608019 (Pubitemid 38393539)
4. Replication-competent retrovirus vectors for cancer gene therapy. Tai CK, Kasahara N, Front Biosci 2008 13 3083 3095 10.2741/2910 17981778 (Pubitemid 351589220)
5. Brain work and brain imaging. Raichle ME, Mintun MA, Annu Rev Neurosci 2006 29 449 476 10.1146/annurev.neuro.29.051605.112819 16776593 (Pubitemid 44476853)
6. Searching for a baseline: functional imaging and the resting human brain. Gusnard DA, Raichle ME, Raichle ME, Nat Rev Neurosci 2001 2 685 694 10.1038/35094500 11584306 (Pubitemid 33674814)
7. In silico cancer modeling: is it ready for prime time? Deisboeck TS, Zhang L, Yoon J, Costa J, Nat Clin Pract Oncol 2009 6 34 42 10.1038/ncponc1237 18852721
8. Computational modeling of brain tumors: discrete, continuum or hybrid? Wang Z, Deisboeck TS, Sci Model Simul 2009 68 381 393
9. Multiscale agent-based cancer modeling. Zhang L, Wang Z, Sagotsky JA, Deisboeck TS, J Math Biol 2009 58 545 559 10.1007/s00285-008-0211-1 18787828
10. Pattern of self-organization in tumour systems: complex growth dynamics in a novel brain tumour spheroid model. Deisboeck TS, Berens ME, Kansal AR, Torquato S, Stemmer-Rachamimov AO, Chiocca EA, Cell Prolif 2001 34 115 134 10.1046/j.1365-2184.2001.00202.x 11348426 (Pubitemid 32374712)
11. Simulating the impact of a molecular 'decision-process' on cellular phenotype and multicellular patterns in brain tumors. Athale C, Mansury Y, Deisboeck TS, J Theor Biol 2005 233 469 481 10.1016/j.jtbi.2004.10.019 15748909 (Pubitemid 40320594)
12. The effects of EGF-receptor density on multiscale tumor growth patterns. Athale CA, Deisboeck TS, J Theor Biol 2006 238 771 779 10.1016/j.jtbi.2005.06. 029 16126230 (Pubitemid 43175828)
13. The impact of "search precision" in an agent-based tumor model. Mansury Y, Deisboeck TS, J Theor Biol 2003 224 325 337 10.1016/S0022-5193(03) 00169-3 12941591 (Pubitemid 37297429)
14. Emerging patterns in tumor systems: simulating the dynamics of multicellular clusters with an agent-based spatial agglomeration model. Mansury Y, Kimura M, Lobo J, Deisboeck TS, J Theor Biol 2002 219 343 370 10.1006/jtbi.2002.3131 12419662 (Pubitemid 35341073)
15. Development of a three-dimensional multiscale agent-based tumor model: simulating gene-protein interaction profiles, cell phenotypes and multicellular patterns in brain cancer. Zhang L, Athale CA, Deisboeck TS, J Theor Biol 2007 244 96 107 10.1016/j.jtbi.2006.06.034 16949103 (Pubitemid 44751755)
16. Multi-scale, multi-resolution brain cancer modeling. Zhang L, Chen LL, Deisboeck TS, Math Comput Simul 2009 79 2021 2035 10.1016/j.matcom.2008.09.007 20161556
17. Simulating brain tumor heterogeneity with a multiscale agent-based model: Linking molecular signatures, phenotypes and expansion rate. Zhang L, Strouthos C, Wang Z, Deisboeck TS, Mathematical and Computer Modelling 2009 49 307 319 10.1016/j.mcm.2008.05.011 20047002
18. Employing graphics processing unit technology, alternating direction implicit method and domain decomposition to speed up the numerical diffusion solver for the biomedical engineering research. Jiang B, Struthers A, Zhang L, Sun Z, Feng Z, Zhao X, Dai W, Zhao K, Zhou X, Berens M, International Journal for Numerical Methods in Biomedical Engineering 2010
19. Dichotomy of astrocytoma migration and proliferation. Giese A, Loo MA, Tran N, Haskett D, Coons SW, Berens ME, Int J Cancer 1996 67 275 282 10.1002/(SICI)1097-0215(19960717)67:2<275::AID-IJC20>3.0.CO;2-9 8760599 (Pubitemid 26274161)
20. Induction of cancer cell migration by epidermal growth factor is initiated by specific phosphorylation of tyrosine 1248 of c-erbB-2 receptor via EGFR. Dittmar T, Husemann A, Schewe Y, Nofer JR, Niggemann B, Zanker KS, Brandt BH, Faseb J 2002 16 1823 1825 12354693
21. Multi-scale, multi-resolution brain cancer modeling. Zhang L, Chen LL, Deisboeck TS, Math Comput Simul 2009
22. Monitoring cell growth. Strober W, Current Protocols in Immunology 2001 5
23. NVIDIA CUDA Programming Guide. NVIDIA, NVIDIA 2008
24. Morton kQ, Mayers DF, Numerical solution of partial differential equations New York: Cambridge University Press 2 2008
25. A Parallel Algorithm for Direct Solution of Large Scale Five-Diagonal Linear Systems. Dai W, Proceedings of the Seventh SIAM Conference on Parallel Processing for Scientific Computing; 1995 San Francisco, CA, Bailey DH, 1995 875 SIAM
26. Smith B, Biqrstad P, Gropp W, Domain Decomposition: Parallel multilevel methods for elliptic partial differential equation New York: Cambridge University Press 1 2004
27. Optimized Restricted Additive Schwarz Methods. St-Cyr A, Gander MJ, Thomas SJ, 16th International Conference on Domain Decomposition Methods; Jan 11, 2005; New York 2005
28. NVIDIA CUDA Programming Guide. NVIDIA, NVIDIA 2009
29. On the Robust Mapping of Dynamic Programming onto a Graphics Processing Unit. Xiao SC, Aji AM, Feng WC, International Conference on Parallel and Distributed Systems Shenzhen, China 2009
30. Automated Dynamic Analysis of CUDA Programs. Boyer M, Sarkis M, Weimer W, Third Workshop on Software Tools for MultiCore Systems in conjunction with the IEEE/ACM International Symposium on Code Generation and Optimization (CGO) Boston, MA 2008
31. Inter-Block GPU Communication via Fast Barrier Synchronization. Xiao SC, Feng WC, In Proc of the IEEE International Parallel and Distributed Processing Symposium Atlanta, GA 2010
32. A restricted additive Schwarz preconditioner for general sparse linear systems. Cai XC, Sarkis M, Siam Journal on Scientific Computing 1999 21 792 797 10.1137/S106482759732678X
33. Zhu JP, Solving Partial Differential Equations On Parallel Computers London: World Scientific Publishing Co. Pte. Ltd 1994
34. Kernighan BW, Ritchie DM, The C Programming Language Englewood Cliffs, New Jersey: Prentice Hall 2 1988
35. Kochan SG, Programming in C Indianapolis, Indiana: Sams 3 2004
36. The CUDA Compiler Driver NVCC. NVIDIA, NVIDIA 2007
37. Tuning CUDA Applications for Fermi. NVIDIA, NVIDIA 2010
38. NVIDIA's Fermi: The First Complete GPU Computing Architecture. Glaskowsky PN, 2009
39. Looking Beyond Graphics. Halfhill TR, 2009
40. The collection of the motile population of cells from a living tumor. Wyckoff JB, Segall JE, Condeelis JS, Cancer Res 2000 60 5401 5404 11034079
41. Description and characterization of a chamber for viewing and quantifying cancer cell chemotaxis. Soon L, Mouneimne G, Segall J, Wyckoff J, Condeelis J, Cell Motil Cytoskeleton 2005 62 27 34 10.1002/cm.20082 16025469 (Pubitemid 41254608)
42. Epidermal growth factor receptor distribution during chemotactic responses. Bailly M, Wyckoff J, Bouzahzah B, Hammerman R, Sylvestre V, Cammer M, Pestell R, Segall JE, Mol Biol Cell 2000 11 3873 3883 11071913
43. Mitogenic signaling from the egf receptor is attenuated by a phospholipase C-gamma/protein kinase C feedback mechanism. Chen P, Xie H, Wells A, Mol Biol Cell 1996 7 871 881 8816994 (Pubitemid 26181723)
44. Epidermal growth factor receptor-mediated cell motility: phospholipase C activity is required, but mitogen-activated protein kinase activity is not sufficient for induced cell movement. Chen P, Xie H, Sekar MC, Gupta K, Wells A, J Cell Biol 1994 127 847 857 10.1083/jcb.127.3.847 7962064 (Pubitemid 24332978)
45. A molecular 'switch' between cell migration and proliferation in human gliomas: Characterizing the role of Phospholipase-C- and its MKK3 signaling effector. Demuth T, Nakada M, Reavie LB, Nakada S, Henrichs A, Anderson E, Hoelzinger DB, Beaudry C, Zhang L, Wang Z, et al. submitted
46. Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Schoeberl B, Eichler-Jonsson C, Gilles ED, Muller G, Nat Biotechnol 2002 20 370 375 10.1038/nbt0402-370 11923843 (Pubitemid 34286330)
47. A mathematical model of combination therapy using the EGFR signaling network. Araujo RP, Petricoin EF, Liotta LA, Biosystems 2005 80 57 69 10.1016/j.biosystems.2004.10.002 15740835 (Pubitemid 40312407)