Rule-based multi-level modeling of cell biological systems

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  Maus, Carsten ^a   Rybacki, Stefan ^a   Uhrmacher, Adelinde M ^a  

^a UNIVERSITY OF ROSTOCK   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; CELL COMMUNICATION; CELL DIVISION; CYTOLOGY; KINETICS; METHODOLOGY; SCHIZOSACCHAROMYCES; SYSTEMS BIOLOGY;

CELL COMMUNICATION; CELL DIVISION; KINETICS; MODELS, BIOLOGICAL; SCHIZOSACCHAROMYCES; SYSTEMS BIOLOGY;

EID: 80054062207     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-166     Document Type: Article

References (91)

1. Campbell DT. 'Downward causation' in hierarchically organised biological systems. Studies in the philosophy of biology: Reduction and related problems 1974, 179-186. Macmillan Press, Ayala FJ, Dobzhansky T.
2. Noble D. The Music of Life: Biology Beyond the Genome 2006, Oxford University Press.
3. Noble D. Claude Bernard, the first systems biologist, and the future of physiology. Exp Physiol 2008, 93:16-26.
4. Kitano H. Computational systems biology. Nature 2002, 420(6912):206-210. 10.1038/nature01254, 12432404.
5. Sackmann A, Heiner M, Koch I. Application of Petri net based analysis techniques to signal transduction pathways. BMC Bioinformatics 2006, 7:482. 10.1186/1471-2105-7-482, 1686943, 17081284.
6. Priami C, Regev A, Shapiro E, Silverman W. Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters 2001, 80:25-31.
7. Danos V, Laneve C. Formal molecular biology. Theoretical Computer Science 2004, 325:69-110.
8. Pedersen M, Plotkin G. A Language for Biochemical Systems. Computational Methods in Systems Biology, Volume 5307 of Lecture Notes in Computer Science 2008, 63-82. Springer Berlin/Heidelberg, Heiner M, Uhrmacher A.
9. Chabrier-Rivier N, Fages F, Soliman S. The Biochemical Abstract Machine BIOCHAM. Computational Methods in Systems Biology: International Conference CMSB 2004, Volume 3082/2005 of Lecture Notes in Computer Science 2005, 172-191. Springer, Danos V, Schachter V.
10. Ciocchetta F, Hillston J. Bio-PEPA: A framework for the modelling and analysis of biological systems. Theoretical Computer Science 2009, 410(33-34):3065-3084.
11. Faeder JR, Blinov ML, Hlavacek WS. Rule-Based Modeling of Biochemical Systems with BioNetGen. Systems Biology, Volume 500 of Methods in Molecular Biology 2009, 113-167. Humana Press.
12. Rohr C, Marwan W, Heiner M. Snoopy-a unifying Petri net framework to investigate biomolecular networks. Bioinformatics 2010, 26(7):974-975. 10.1093/bioinformatics/btq050, 20139470.
13. Klemm JD, Schreiber SL, Crabtree GR. Dimerization as a regulatory mechanism in signal transduction. Annu Rev Immunol 1998, 16:569-592. 10.1146/annurev.immunol.16.1.569, 9597142.
14. Cobb MH, Goldsmith EJ. Dimerization in MAP-kinase signaling. Trends Biochem Sci 2000, 25:7-9. 10.1016/S0968-0004(99)01508-X, 10637602.
15. John M, Lhoussaine C, Niehren J, Versari C. Biochemical Reaction Rules with Constraints. European Symposium on Programming Languages. Volume 6602 of Lecture Notes in Computer Science 2011, 338-357. Springer, Barthe G.
16. Danos V, Feret J, Fontana W, Harmer R. Rule-Based Modelling of Cellular Signalling. CONCUR 2007 - Concurrency Theory: 18th International Conference, Volume 4703 of Lecture Notes in Computer Science 2007, 17-41. Springer, Caires L, Vasconcelos VT.
17. Faeder JR, Blinov ML, Goldstein B, Hlavacek WS. Rule-based modeling of biochemical networks. Complexity 2005, 10(4):22-41.
18. Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W. Rules for modeling signal-transduction systems. Sci STKE 2006, 2006(344):re6. 10.1126/stke.3442006re6, 16849649.
19. Barua D, Faeder JR, Haugh JM. A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases. PLoS Comput Biol 2009, 5(4):e1000364. 10.1371/journal.pcbi.1000364, 2667146, 19381268.
20. Kühn C, Prasad KVS, Klipp E, Gennemark P. Formal representation of the high osmolarity glycerol pathway in yeast. Genome Inform 2010, 22:69-83. 10.1142/9781848165786_0007, 20238420.
21. Feinerman O, Jentsch G, Tkach KE, Coward JW, Hathorn MM, Sneddon MW, Emonet T, Smith KA, Altan-Bonnet G. Single-cell quantification of IL-2 response by effector and regulatory T cells reveals critical plasticity in immune response. Mol Syst Biol 2010, 6:437. 3010113, 21119631.
22. Selivanov VA, Votyakova TV, Pivtoraiko VN, Zeak J, Sukhomlin T, Trucco M, Roca J, Cascante M. Reactive oxygen species production by forward and reverse electron fluxes in the mitochondrial respiratory chain. PLoS Comput Biol 2011, 7(3):e1001115. 10.1371/journal.pcbi.1001115, 3068929, 21483483.
23. MacNamara S, Burrage K. Stochastic Modeling of Naïve T Cell Homeostasis for Competing Clonotypes via the Master Equation. Multiscale Modeling & Simulation 2010, 8:1325. 10.1137/09077182X, 22105191.
24. Walker DC, Southgate J, Hill G, Holcombe M, Hose DR, Wood SM, Neil SM, Smallwood RH. The epitheliome: agent-based modelling of the social behaviour of cells. Biosystems 2004, 76(1-3):89-100. 10.1016/j.biosystems.2004.05.025, 15351133.
25. Kuttler C, Lhoussaine C, Nebut M. Rule-Based Modeling of Transcriptional Attenuation at the Tryptophan Operon. Transactions on Computational Systems Biology XII, Volume 5945 of Lecture Notes in Computer Science 2010, 199-228. Springer Berlin/Heidelberg, Priami C, Breitling Rilbert D, Heiner M, Uhrmacher A.
26. Milner R. Communicating and Mobile Systems: The Pi-Calculus 1999, Cambridge University Press.
27. Sauro HM. Enzyme Kinetics for Systems Biology 2011, Future Skill Software (Ambrosius Publishing).
28. John M, Lhoussaine C, Niehren J, Uhrmacher A. The Attributed Pi Calculus. Computational Methods in Systems Biology, Volume 5307 of Lecture Notes in Computer Science 2008, 83-102. Berlin/Heidelberg, Heiner M, Uhrmacher A, Springer.
29. John M, Lhoussaine C, Niehren J, Uhrmacher A. The Attributed Pi-Calculus with Priorities. Transactions on Computational Systems Biology XII, Volume 5945 of Lecture Notes in Computer Science 2010, 13-76. Springer Berlin/Heidelberg, Priami C, Breitling Rilbert D, Heiner M, Uhrmacher A.
30. Sneddon MW, Faeder JR, Emonet T. Efficient modeling, simulation and coarse-graining of biological complexity with NFsim. Nat Methods 2011, 8(2):177-183. 10.1038/nmeth.1546, 21186362.
31. Zeigler BP. Multifacetted Modelling and Discrete Event Simulation 1984, Academic Press.
32. Himmelspach J, Uhrmacher A. Plug'n Simulate. Simulation Symposium, 2007. ANSS '07. 40th Annual 2007, 137-143.
33. Gillespie D. Exact Stochastic Simulation of Coupled Chemical Reactions. The Journal of Physical Chemistry 1977, 81(25):2340-2361.
34. Ewald R, Himmelspach J, Jeschke M, Leye S, Uhrmacher AM. Flexible experimentation in the modeling and simulation framework JAMES II-implications for computational systems biology. Brief Bioinform 2010, 11(3):290-300. 10.1093/bib/bbp067, 20118105.
35. Jeschke M, Ewald R, Uhrmacher AM. Exploring the performance of spatial stochastic simulation algorithms. Journal of Computational Physics 2011, 230(7):2562-2574.
36. Danos V, Feret J, Fontana W, Krivine J. Scalable Simulation of Cellular Signaling Networks. Programming Languages and Systems, Volume 4807 of Lecture Notes in Computer Science 2007, 139-157. Springer Berlin/Heidelberg, Shao Z.
37. Yang J, Monine MI, Faeder JR, Hlavacek WS. Kinetic Monte Carlo method for rule-based modeling of biochemical networks. Phys Rev E Stat Nonlin Soft Matter Phys 2008, 78(3 Pt 1):031910. 2652652, 18851068.
38. Mura I, Prandi D, Priami C, Romanel A. Exploiting non-Markovian Bio-Processes. Electronic Notes in Theoretical Computer Science 2009, 253(3):83-98. [Proceedings of Seventh Workshop on Quantitative Aspects of Programming Languages (QAPL 2009)].
39. Takahashi K, Kaizu K, Hu B, Tomita M. A multi-algorithm, multi-timescale method for cell simulation. Bioinformatics 2004, 20(4):538-546. 10.1093/bioinformatics/btg442, 14990450.
40. Kim SM, Huberman JA. Regulation of replication timing in fission yeast. EMBO J 2001, 20(21):6115-6126. 10.1093/emboj/20.21.6115, 125695, 11689451.
41. Tyson JJ, Novak B. Regulation of the eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions. J Theor Biol 2001, 210(2):249-263. 10.1006/jtbi.2001.2293, 11371178.
42. Tyson JJ, Csikasz-Nagy A, Novak B. The dynamics of cell cycle regulation. Bioessays 2002, 24(12):1095-1109. 10.1002/bies.10191, 12447975.
43. Kar S, Baumann WT, Paul MR, Tyson JJ. Exploring the roles of noise in the eukaryotic cell cycle. Proc Natl Acad Sci USA 2009, 106(16):6471-6476. 10.1073/pnas.0810034106, 2672517, 19246388.
44. Moseley JB, Mayeux A, Paoletti A, Nurse P. A spatial gradient coordinates cell size and mitotic entry in fission yeast. Nature 2009, 459(7248):857-860. 10.1038/nature08074, 19474789.
45. Sawin KE. Cell cycle: Cell division brought down to size. Nature 2009, 459(7248):782-783. 10.1038/459782a, 19516326.
46. Tyson JJ. Modeling the cell division cycle: cdc2 and cyclin interactions. Proc Natl Acad Sci USA 1991, 88(16):7328-7332. 10.1073/pnas.88.16.7328, 52288, 1831270.
47. Novak B, Tyson JJ. Modeling the control of DNA replication in fission yeast. Proc Natl Acad Sci USA 1997, 94(17):9147-9152. 10.1073/pnas.94.17.9147, 23080, 9256450.
48. Sveiczer A, Tyson JJ, Novak B. A stochastic, molecular model of the fission yeast cell cycle: role of the nucleocytoplasmic ratio in cycle time regulation. Biophys Chem 2001, 92(1-2):1-15. 10.1016/S0301-4622(01)00183-1, 11527575.
49. Qu Z, MacLellan WR, Weiss JN. Dynamics of the cell cycle: checkpoints, sizers and timers. Biophys J 2003, 85(6):3600-3611. 10.1016/S0006-3495(03)74778-X, 1303665, 14645053.
50. Miyata H, Miyata M, Ito M. The cell cycle in the fission yeast, Schizosaccharomyces pombe. I. Relationship between cell size and cycle time. Cell Struct Funct 1978, 3:39-46.
51. Leupold U. Studies on recombination in Schizosaccharomyces pombe. Cold Spring Harb Symp Quant Biol 1958, 23:161-170.
52. Beach D. Cell type switching by DNA transposition in fission yeast. Nature 1983, 305:682-688.
53. Beach DH, Klar AJ. Rearrangements of the transposable mating-type cassettes of fission yeast. EMBO J 1984, 3(3):603-610. 557395, 6325178.
54. Egel R. The pedigree pattern of mating-type switching in Schizosaccharomycespombe. Current Genetics 1984, 8:205-210.
55. Egel R. Two tightly linked silent cassettes in the mating-type region of Schizosaccharomyces pombe. Current Genetics 1984, 8:199-203.
56. Klar AJ, Bonaduce MJ, Cafferkey R. The mechanism of fission yeast mating type interconversion: seal/replicate/cleave model of replication across the double-stranded break site at mat1. Genetics 1991, 127(3):489-496. 1204376, 2016051.
57. Yamada-Inagawa T, Klar AJS, Dalgaard JZ. Schizosaccharomyces pombe switches mating type by the synthesis-dependent strand-annealing mechanism. Genetics 2007, 177:255-265. 10.1534/genetics.107.076315, 2013724, 17660548.
58. Klar AJ. Developmental choices in mating-type interconversion in fission yeast. Trends Genet 1992, 8(6):208-213. 10.1016/0168-9525(92)90235-V, 1496556.
59. Nielsen O, Davey J. Pheromone communication in the fission yeast Schizosaccharomyces pombe. Semin Cell Biol 1995, 6(2):95-104. 10.1016/1043-4682(95)90006-3, 7548848.
60. Stern B, Nurse P. Fission yeast pheromone blocks S-phase by inhibiting the G1 cyclin B-p34cdc2 kinase. EMBO J 1997, 16(3):534-544. 10.1093/emboj/16.3.534, 1169657, 9034336.
61. Imai Y, Yamamoto M. Schizosaccharomyces pombe sxa1+ and sxa2+ encode putative proteases involved in the mating response. Mol Cell Biol 1992, 12(4):1827-1834. 369626, 1549128.
62. Hurtley S. Spatial cell biology. Location, location, location. Science 2009, 326(5957):1205. 10.1126/science.326.5957.1205, 19965460.
63. Elf J, Ehrenberg M. Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases. Syst Biol (Stevenage) 2004, 1(2):230-236.
64. Bittig AT, Jeschke M, Uhrmacher AM. Towards Modelling and Simulation of Crowded Environments in Cell Biology. AIP Conference Proceedings, Volume 1281 2010, 1326-1329. AIP, Simos TE, Psihoyios G, Tsitouras C.
65. Bittig AT, Haack F, Maus C, Uhrmacher AM. Adapting Rule-based Model Descriptions for Simulating in Continuous and Hybrid Space. Proceedings of the 9th International Conference on Computational Methods in Systems Biology, CMSB '11 2011, ACM.
66. Uhrmacher A. Reasoning about changing structure: a modeling concept for ecological systems. Applied artificial intelligence 1995, 9(2):157-180.
67. Oury N, Plotkin G. Multi-Level Modelling via Stochastic Multi-Level Multiset Rewriting. Mathematical Structures in Computer Science, Special Issue on DCM 2010 to appear
68. Lemons NW, Hu B, Hlavacek WS. Hierarchical graphs for rule-based modeling of biochemical systems. BMC Bioinformatics 2011, 12:45. 10.1186/1471-2105-12-45, 3152790, 21288338.
69. Calzone L, Fages F, Soliman S. BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics 2006, 22(14):1805-1807. 10.1093/bioinformatics/btl172, 16672256.
70. Mallavarapu A, Thomson M, Ullian B, Gunawardena J. Programming with models: modularity and abstraction provide powerful capabilities for systems biology. J R Soc Interface 2009, 6(32):257-270. 10.1098/rsif.2008.0205, 2659579, 18647734.
71. Harris L, Hogg J, Faeder J. Compartmental rule-based modeling of biochemical systems. Proceedings of the 2009 Winter Simulation Conference (WSC), IEEE 2009, 908-919.
72. Regev A, Panina EM, Silverman W, Cardelli L, Shapiro E. BioAmbients: an abstraction for biological compartments. Theoretical Computer Science 2004, 325:141-167.
73. Laneve C, Tarissan F. A simple calculus for proteins and cells. Theoretical Computer Science 2008, 404(1-2):127-141.
74. Cardelli L. Brane Calculi. Interactions of Biological Membranes. Computational Methods in Systems Biology, Volume 3082 of Lecture Notes in Computer Science 2005, 257-278. Springer Berlin/Heidelberg, Danos V, Schachter V.
75. Pǎun G, Rozenberg G. A guide to membrane computing. Theoretical Computer Science 2002, 287:73-100.
76. Coppo M, Damiani F, Drocco M, Grassi E, Sciacca E, Spinella S, Troina A. Hybrid Calculus of Wrapped Compartments. Proceedings Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC 2010), Volume 40 of EPTCS 2010, 102-120. Ciobanu G, Koutny M.
77. Coppo M, Damiani F, Drocco M, Grassi E, Troina A. Stochastic Calculus of Wrapped Compartment. Proceedings Eighth Workshop on Quantitative Aspects of Programming Languages (QAPL 2010), Volume 28 of EPTCS 2010, 82-98. Pierro AD, Norman G.
78. Milner R. The Space and Motion of Communicating Agents 2009, Cambridge University Press.
79. Krivine J, Milner R, Troina A. Stochastic Bigraphs. Electronic Notes in Theoretical Computer Science 2008, 218:73-96. [Proceedings of the 24th Conference on the Mathematical Foundations of Programming Semantics (MFPS XXIV)].
80. Andrews SS, Addy NJ, Brent R, Arkin AP. Detailed simulations of cell biology with Smoldyn 2.1. PLoS Comput Biol 2010, 6(3):e1000705. 10.1371/journal.pcbi.1000705, 2837389, 20300644.
81. Tolle DP, Novère NL. Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes. BMC Syst Biol 2010, 4:24. 10.1186/1752-0509-4-24, 2848630, 20233406.
82. Chaturvedi R, Huang C, Kazmierczak B, Schneider T, Izaguirre JA, Glimm T, Hentschel HGE, Glazier JA, Newman SA, Alber MS. On multiscale approaches to three-dimensional modelling of morphogenesis. J R Soc Interface 2005, 2(3):237-253. 10.1098/rsif.2005.0033, 1629079, 16849182.
83. Pradal C, Dufour-Kowalski S, Boudon F, Fournier C, Godin C. OpenAlea: a visual programming and component-based software platform for plant modelling. Functional Plant Biology 2008, 35(10):751-760.
84. Qutub AA, Liu G, Vempati P, Popel AS. Integration of angiogenesis modules at multiple scales: from molecular to tissue. Pac Symp Biocomput 2009, 316-327. PMC3077677, 19209711.
85. Pitt-Francis J, Pathmanathan P, Bernabeu MO, Bordas R, Cooper J, Fletcher AG, Mirams GR, Murray P, Osborne JM, Walter A, Chapman SJ, Garny A, van Leeuwen IM, Maini PK, Rodríguez B, Waters SL, Whiteley JP, Byrne HM, Gavaghan DJ. Chaste: A test-driven approach to software development for biological modelling. Computer Physics Communications 2009, 180(12):2452-2471.
86. Meier-Schellersheim M, Fraser IDC, Klauschen F. Multiscale modeling for biologists. Wiley Interdisciplinary Reviews: Systems Biology and Medicine 2009, 1:4-14. 10.1002/wsbm.33, 2862646, 20448808.
87. Giavitto JL, Michel O. MGS: A Rule-Based Programming Language for Complex Objects and Collections. Electronic Notes in Theoretical Computer Science 2001, 59(4):286-304.
88. Michel O, Spicher A, Giavitto JL. Rule-based programming for integrative biological modeling. Natural Computing 2009, 8:865-889.
89. Lomazova I. Nested Petri nets - a Formalism for Specification and Verification of Multi-Agent Distributed Systems. Fundamenta Informaticae 2000, 43(1-4):195-214.
90. Lomazova I. Nested Petri nets: Multi-level and recursive systems. Fundamenta Informaticae 2001, 47(3-4):283-293., http://iospress.metapress.com/content/hxe8qhvaa3j678km/
91. Köhler-Bußmeier M. Hornets: Nets within Nets Combined with Net Algebra. Applications and Theory of Petri Nets, Volume 5606 of Lecture Notes in Computer Science 2009, 243-262. Springer, Franceschinis G, Wolf K.