Cloud computing and validation of expandable in silico livers

BMC Systems Biology

Volumn 4, Issue , 2010, Pages

  Ropella, Glen E P ^a   Hunt, C Anthony ^b  

^a TEMPUS DICTUM INC   (United States)

^b San Francisco   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

XENOBIOTIC AGENT;

ANIMAL; ARTICLE; BIOLOGY; CLUSTER ANALYSIS; COMPUTER; LIVER; METABOLISM; METHODOLOGY; RAT; VALIDATION STUDY;

ANIMALS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; COMPUTERS; LIVER; RATS; XENOBIOTICS;

EID: 78649574884     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-168     Document Type: Article

References (17)

1. Yan L, Ropella GE, Park S, Roberts MS, Hunt CA. Modeling and simulation of hepatic drug disposition using a physiologically based, multi-agent in silico liver. Pharm Res 2008, 25:1023-1036. 10.1007/s11095-007-9494-y, 18044012.
2. Yan L, Sheihk-Bahaei S, Park S, Ropella GE, Hunt CA. Predictions of hepatic disposition properties using a mechanistically realistic, physiologically based model. Drug Metab Dispos 2008, 36:759-768. 10.1124/dmd.107.019067, 18227144.
3. Park S, Ropella GE, Kim SH, Roberts MS, Hunt CA. Computational strategies unravel and trace how liver disease changes hepatic drug disposition. J Pharmacol Exp Ther 2009, 328:294-305. 10.1124/jpet.108.142497, 18948498.
4. Park S, Kim SH, Ropella GE, Roberts MS, Hunt CA. Tracing multiscale mechanisms of drug disposition in normal and diseased livers. J Pharmacol Exp Ther 2010, 334:124-136. 10.1124/jpet.110.168526, 20406856.
5. Hung DY, Chang P, Weiss M, Roberts MS. Structure-hepatic disposition relationships for cationic drugs in isolated physiological models. J Pharm Exp Therap 2001, 297:780-789.
6. Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, Legrand S, Beberg AL, Ensign DL, Bruns CM, Pande VS. Accelerating molecular dynamic simulation on graphics processing units. J Comput Chem 2009, 30:864-872. 10.1002/jcc.21209, 2724265, 19191337.
7. Ropella GE, Park S, Hunt CA. Evaluating an Hepatic Enzyme Induction Mechanism through Coarse- and Fine-Grained Measurements of an In Silico Liver. Complexity 2008, 14:28-34.
8. Noble D. The rise of computational biology. Nat Rev Mol Cell Biol 2002, 3:460-3.
9. Hunt CA, Ropella GEP, Lam TN, Tang J, Kim SHJ, Engelberg JA, Sheikh-Bahaei S. At the biological modeling and simulation frontier. Pharm Res 2009, 26:2369-2400. 10.1007/s11095-009-9958-3, 2763179, 19756975.
10. Che S, Boyer M, Meng J, Tarjan D, Sheaffer JW, Skadron K. A performance study of general-purpose applications on graphics processors using CUDA. J Parallel Distrib Comput 2008, 68:1370-1380.
11. Kondo D, Javadi B, Malecot P, Cappello F, Anderson DP. Cost-benefit analysis of cloud computing versus desktop grids. 18th International Heterogeneity in Computing Workshop 2009, Rome.
12. Davis IW, Baker D. RosettaLigand Docking with Full Ligand and Receptor Flexibility. J Mol Biol 2009, 385:381-392. 10.1016/j.jmb.2008.11.010, 19041878.
13. Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D. Kemp elimination catalysts by computational enzyme design. Nature 2008, 453:190-195.
14. Roberts MS, Anissimov YG. Modeling of Hepatic Elimination and Organ Distribution Kinetics with the Extended Convection-Dispersion Model. J Pharmacokin Biopharm 1999, 27:343-382.
15. Hung DY, Chang P, Cheung K, McWhinney B, Masci PP, Weiss M, Roberts MS. Cationic drug pharmacokinetics in diseased livers determined by fibrosis index, hepatic protein content, microsomal activity, and nature of drug. J Pharmaco Exp Ther 2002, 301:1079-1087.
16. BOINC Open-source software for volunteer computing and grid computing. (accessed 04/17/10), BOINC., http://boinc.berkeley.edu/
17. Hunt CA, Ropella GE, Yan L, Hung DY, Roberts MS. Physiologically based synthetic models of hepatic disposition. J Pharmacokinet Pharmacodyn 2006, 33:737-772. 10.1007/s10928-006-9031-3, 17051440.