Relational grounding facilitates development of scientifically useful multiscale models

Theoretical Biology and Medical Modelling

Volumn 8, Issue 1, 2011, Pages

  Hunt, C Anthony ^a   Ropella, Glen Ep ^b   Lam, Tai ^c   Gewitz, Andrew D ^d  

^a San Francisco   (United States)

^b TEMPUS DICTUM INC   (United States)

^c CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

^d STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MODEL; DECISION MAKING; HUMAN; PRACTICE GUIDELINE; REPRODUCIBILITY; REVIEW; TRANSLATIONAL RESEARCH; UNCERTAINTY;

DECISION MAKING; GUIDELINES AS TOPIC; HUMANS; MODELS, BIOLOGICAL; REPRODUCIBILITY OF RESULTS; TRANSLATIONAL MEDICAL RESEARCH; UNCERTAINTY;

EID: 80053362261     PISSN: None     EISSN: 17424682     Source Type: Journal    
DOI: 10.1186/1742-4682-8-35     Document Type: Review

References (30)

1. A review of multiscale analysis: examples from systems biology, materials engineering, and other fluid-surface interacting systems. Vlachos DG, Adv Chem Eng 2005 30 1 61 (Pubitemid 43589062)
2. BioShape: a spatial shape-based scale-independent simulation environment for biological systems. Butia F, Cacciagranoa D, Corradinia F, Merellia E, Teseia L, Procedia Comp Sci 2010 1 827 835 10.1016/j.procs.2010.04.090
3. At the biological modeling and simulation frontier. Hunt CA, Ropella GEP, Lam TN, Tang J, Kim SHJ, Engelberg JA, Sheikh-Bahaei S, Pharm Res 2009 26 2369 2400 10.1007/s11095-009-9958-3 19756975
4. Computational investigation of epithelial cell dynamic phenotype in vitro. Kim SHJ, Park S, Mostov K, Debnath J, Hunt CA, Theo Biol Med Model 2009 6 8 10.1186/1742-4682-6-8
5. Identifying the rules of engagement enabling leukocyte rolling, activation, and adhesion. Tang J, Hunt CA, PLoS Comput Biol 2010 6 1000681 10.1371/journal.pcbi.1000681 20174606
6. Tracing multiscale mechanisms of drug disposition in normal and diseased livers. Park S, Kim SH, Ropella GE, Roberts MS, Hunt CA, J Pharmacol Exp Ther 2010 334 124 136 10.1124/jpet.110.168526 20406856
7. MDCK cystogenesis driven by cell stabilization within computational analogues. Engelberg JA, Datta A, Mostov KE, Hunt CA, PLoS Comput Biol 2011 7 1002030 10.1371/journal.pcbi.1002030 21490722
8. Computational experiments reveal plausible mechanisms for changing patterns of hepatic zonation of xenobiotic clearance and hepatotoxicity. Sheikh-Bahaei S, Maher JJ, Hunt CA, J Theor Biol 265 718 733
9. An algebraic theory of actors and its application to a simple object-based language ("From Object-Orientation To Formal Methods"). Agha G, Thati P, Lec Notes Comp Sci 2004 2635 26 57 10.1007/978-3-540-39993-3-4
10. Actor Model. http://en.wikipedia.org/wiki/Actor-model
11. Physiologically-based pharmacokinetic (PBPK) model to predict IgG tissue kinetics in wild-type and FcRn-knockout mice. Garg A, Balthasar JP, J Pharmacokinet Pharmacodyn 2007 34 687 709 10.1007/s10928-007-9065-1 17636457 (Pubitemid 47477039)
12. PBPK model for radioactive iodide and perchlorate kinetics and perchlorate-induced inhibition of iodide uptake in humans. Merrill EA, Clewell RA, Robinson PJ, Jarabek AM, Gearhart JM, Sterner TR, Fisher JW, Toxicol Sci 2005 83 25 43 15509666 (Pubitemid 40123328)
13. 131I radioimmunotherapy of refractory non-Hodgkin's lymphoma. Roberson PL, Amro H, Wilderman SJ, Avram AM, Kaminski MS, Schipper MJ, Dewaraja YK, Eur J Nucl Med Mol Imaging 2011 38 874 83 10.1007/s00259-010-1699-3 21174088
14. 131I-labelled anti-CD20 MAB IDEC-C2B8 (rituximab) in relapsed non-Hodgkin's lymphoma. Scheidhauer K, Wolf I, Baumgartl HJ, Von Schilling C, Schmidt B, Reidel G, Peschel C, Schwaiger M, Eur J Nucl Med Mol Imaging 2002 29 1276 82 10.1007/s00259-002-0820-7 12271407 (Pubitemid 44392206)
15. TNF and IL-10 are major factors in modulation of the phagocytic cell environment in lung and lymph node in tuberculosis: a next-generation two-compartmental model. Marino S, Myers A, Flynn JL, Kirschner DE, J Theor Biol 2010 265 586 98 10.1016/j.jtbi.2010.05.012 20510249
16. Synergy between individual TNF-dependent functions determines granuloma performance for controlling Mycobacterium tuberculosis infection. Ray JC, Flynn JL, Kirschner DE, J Immunol 2009 182 3706 17 10.4049/jimmunol.0802297 19265149
17. Multiscale computational modeling reveals a critical role for TNF- receptor 1 dynamics in tuberculosis granuloma formation. Fallahi-Sichani M, El-Kebir M, Marino S, Kirschner DE, Linderman JJ, J Immunol 2011 186 3472 83 10.4049/jimmunol.1003299 21321109
18. A hybrid multi-compartment model of granuloma formation and T cell priming in tuberculosis. Marino S, El-Kebir M, Kirschner D, J Theor Biol 2011 280 50 62 10.1016/j.jtbi.2011.03.022 21443879
19. Strategies and tactics in multiscale modeling of cell-to-organ systems. Bassingthwaighte JB, Chizeck HJ, Atlas LE, Proc IEEE Inst Electr Electron Eng 2006 94 819 830 20463841 (Pubitemid 46444987)
20. Ptolemy II. http://ptolemy.eecs.berkeley.edu/
21. Component-based hierarchical modeling of systems with continuous and discrete dynamics. Liu J, Lee E, Proceedings of the 2000 IEEE International Symposium on Computer-Aided Control System Design, CACSD 2000 95 100
22. From syntax to semantics in systems biology towards automated reasoning tools, ("Transactions on Computational Systems Biology IV"). Fages F, Lec Notes Comp Sci 2006 3939 68 70 10.1007/11732488-6 (Pubitemid 350278757)
23. 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)
24. Integration of multi-scale biosimulation models via lightweight semantics. Gennari JH, Neal ML, Carlson BE, Cook DL, Pac Sym Biocomput 2008 414 25
25. Using ontology with semantic web services to support modeling in systems biology, (Web Information Systems Engineering-WISE 2007 Workshops). Sun Z, Finkelstein A, Ashmore J, Lec Notes Comp Sci 2007 4832 41 51 10.1007/978-3-540-77010-7-5
26. Essential operating principles for tumor spheroid growth. Engelberg JA, Ropella GE, Hunt CA, BMC Syst Biol 2008 2 110 10.1186/1752-0509-2-110 19105850
27. Predictions of hepatic disposition properties using a mechanistically realistic, physiologically based model. Yan L, Sheikh-Bahaei S, Park S, Ropella GEP, Hunt CA, Drug Metab Dispos 2008 36 759 768 10.1124/dmd.107.019067 18227144 (Pubitemid 351468384)
28. Mechanistic insight from in silico pharmacokinetic experiments: Roles of P-glycoprotein, Cyp3A4 enzymes, and microenvironments. Lam TN, Hunt CA, J Pharmacol Exp Therap 2010 332 398 412 10.1124/jpet.109.160739
29. Agent-based models in translational systems biology. An G, Mi Q, Dutta-Moscato J, Solovyev A, Vodovotz Y, WIREs Syst Biol Med 2009 1 159 171 10.1002/wsbm.45
30. A specification language and a framework for the execution of composite models in systems biology, (Transactions on Computational Systems Biology VII). Margoninski O, Saffrey P, Hetherington J, Finkelstein A, Warner A, Lec Notes Comp Sci 2006 4230 163 184 10.1007/11905455-9 (Pubitemid 351150629)