Agent-based models of cellular systems

Methods in Molecular Biology

Volumn 930, Issue , 2013, Pages 399-426

  Cannata, Nicola ^a   Corradini, Flavio ^a   Merelli, Emanuela ^a   Tesei, Luca ^a  

^a UNIVERSITY OF CAMERINO   (Italy)

Author keywords

Agent based modeling and simulation; Agent oriented software engineering; Behavioral models of biological systems; Multi agent systems

Indexed keywords

EID: 84870502658     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-059-5_18     Document Type: Article

References (93)

1. Milner R (1989) Communication and concurrency. Prentice-Hall, New York, London
2. Wooldridge M (1997) Agent-based software engineering. IEE proceedings on software engineering: 26-37
3. Wooldridge M (2002) An introduction to MultiAgent systems. Wiley, West Sussex, UK
4. Vallurupalli V, Purdy C (2007) Agent-based modeling and simulation of biomolecular reactions. Scalable Computing: Practice and Experience 8(2):185-196
5. Bonabeau E (2002) Agent-based modeling: methods and techniques for simulating human systems. Proc Natl Acad Sci USA 99 (Suppl 3): 7280-7287
6. Kitano H (2001) Foundations of systems biology. MIT Press, Cambridge, MA
7. González PP, Cárdenas M, Camacho D et al (2003) Cellulat: an agent-based intracellular signalling model. Biosystems 68 (2-3): 171-185
8. Wolfram S (1984) Cellular automata as models of complexity. Nature 311:419-424
9. Wishart DS, Yang R, Arndt D et al (2005) Dynamic cellular automata: an alternative approach to cellular simulation. Silico Biol 5 (2):139-161
10. Troisi A, Wong V, Ratner MA (2005) An agent-based approach for modeling molecular self-organization. Proc Natl Acad Sci U S A 102(2): 255-260
11. Emonet T, Macal CM, North MJ et al (2005) AgentCell: a digital single-cell assay for bacterial chemotaxis. Bioinformatics 21 (11): 2714-2721
12. Korobkova E, Emonet T, Vilar JM et al (2004) From molecular noise to behavioural variability in a single bacterium. Nature 428 (6982): 574-578
13. Lemerle C, Di Ventura B, Serrano L (2005) Space as the final frontier in stochastic simulations of biological systems. FEBS Lett 579 (8): 1789-1794
14. Lloyd CM, Halstead MD, Nielsen PF (2004) CellML: its future, present and past. Prog Biophys Mol Biol 85(2-3): 433-450
15. Hucka M, Finney A, Sauro HM et al (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4): 524-531
16. Takahashi K, Arjunan SN, Tomita M (2005) Space in systems biology of signaling pathways-towards intracellular molecular crowding in silico. FEBS Lett 579 (8): 1783-1788
17. Tang J, Ley KF, Hunt CA (2007) Dynamics of in silico leukocyte rolling, activation, and adhesion. BMC Syst Biol 1: 14
18. The breve simulation environment. http:// www.spiderland.org/. Accessed 19 Nov 2010
19. Guo Z, Sloot PM, Tay JC (2008) A hybrid agent-based approach for modeling microbiological systems. J Theor Biol 255(2): 163-175
20. Guo Z, Tay JC (2008) Multi-timescale eventscheduling in multi-agent immune simulation models. Biosystems 91(1): 126-145
21. Walker DC, Southgate J, Hill G et al (2004) The epitheliome: agent-based modelling of the social behaviour of cells. Biosystems 76 (1-3): 89-100
22. MATLAB—The language of technical computing. http://www.mathworks.com/pro ducts/matlab/. Accessed 19 Nov 2010
23. Pogson M, Smallwood R, Qwarnstrom E et al (2006) Formal agent-based modelling of intracellular chemical interactions. Biosystems 85 (1): 37-45
24. Walker DC, Southgate J (2009) The virtual cell-a candidate co-ordinator for ‘middle-out’ modelling of biological systems. Brief Bioinform 10(4): 450-461
25. Adra S, Sun T, MacNeil S et al (2010) Development of a three dimensional multiscale computational model of the human epidermis. PLoS One 5(1): e8511
26. Hoops S, Sahle S, Gauges R et al (2006) COPASI-a COmplex PAthway SImulator. Bioinformatics 22(24): 3067-3074
27. Galva˜o V, Miranda JG (2010) A threedimensional multi-agent-based model for the evolution of Chagas’ disease. Biosystems 100 (3): 225-230
28. Pennisi M, Pappalardo F, Palladini A (2010) Modeling the competition between lung metastases and the immune system using agents. BMC Bioinformatics 11(Suppl 7): S13
29. Bauer AL, Beauchemin CA, Perelson AS (2009) Agent-based modeling of hostpathogen systems: the successes and challenges. Inf Sci (Ny) 179(10): 1379-1389
30. Christley S, Lee B, Dai X et al (2010) Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms. BMC Syst Biol 4: 107
31. Dematté L, Prandi D (2010) GPU computing for systems biology. Brief Bioinform 11 (3): 323-333
32. Halling-Brown M, Pappalardo F, Rapin N et al (2010) ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale. Philos Transact A Math Phys Eng Sci 368(1920): 2799-2815
33. Viceconti M, Clapworthy G, Van Sint JS (2008) The virtual physiological human—a European initiative for in silico human modeling. J Physiol Sci 58(7): 441-446
34. Shah I, Wambaugh J (2010) Virtual tissues in toxicology. J Toxicol Environ Health B Crit Rev 13(2-4): 314-328
35. Devillers J, Devillers H, Decourtye A (2010) Internet resources for agent-based modelling. SAR QSAR Environ Res 21(3-4): 337-50
36. Gilbert N, Bankes S (2002) Platforms and methods for agent-based modeling. Proc Natl Acad Sci USA 99(Suppl 3): 7197-7198
37. REPAST - Recursive porous agent simulation toolkit. http://repast.sourceforge.net/. Accessed 19 Nov 2010
38. A resource for agent- and individual-based modelers and the home of Swarm. http:// www.swarm.org/index.php/Main_Page. Accessed 19 Nov 2010
39. JADE—Java Agent DEvelopment Framework. http://jade.tilab.com/. Accessed 19 Nov 2010
40. JADE—A White Paper. http://jade.tilab. com/papers/2003/WhitePaperJADEEXP. pdf. Accessed 19 Nov 2010
41. IEEE foundation for intelligent physical agents. http://www.fipa.org/. Accessed 19 Nov 2010
42. IEEE—the world’s largest professional association for the advancement of technology. http://www.ieee.org/index.html. Accessed 19 Nov 2010
43. Java-based intelligent agent componentware. http://jiac.de/. Accessed 19 Nov 2010
44. SPADE—Smart python multi-agent development environment. http://code.google.com/ p/spade2/. Accessed 19 Nov 2010
45. JACK autonomous software. http://aosgrp. com/products/jack/index.html. Accessed 19 Nov 2010
46. Comparison of agent-based modeling software. http://en.wikipedia.org/wiki/Comparison_ of_agent-based_modeling_software. Accessed 19 Nov 2010
47. Macal CM, North MJ (2008) Agent-based modeling and simulation: desktop ABMS. In proc. of winter simulation conference 2007: 95-106
48. Sánchez D, Isern D, Rodríguez-Rozas A et al (2010) Agent-based platform to support the execution of parallel tasks. Expert Syst Appl. doi:10.1016/j.eswa.2010.11.073
49. CUDA Zone—Official Website. http://www. nvidia.com/object/cuda_home_new.html. Accessed 19 Nov 2010
50. Allan R (2009) Survey of agent based modelling and simulation tools. Technical report. computational science and engineering department, STFC Daresbury laboratory, Daresbury, Warrington. http://epubs.cclrc.ac.uk/workdetails? w¼50398. Accessed 19 Nov 2010
51. Nikolai C, Madey G (2009) Tools of the trade: a survey of various agent based modeling platforms. J Artif Soc Soc Simulat 12(2): 2
52. Railsback SF, Lytinen SL, Jackson SK (2006) Agent-based simulation platforms: review and development recommendations. Simulation 82: 609-623
53. Tobias R, Hofmann C (2004) Evaluation of free Java-libraries for social-scientific agent based simulation. J Artif Soc Soc Simulat 7 (1): 6
54. Groovy—An agile dynamic language for the Java platform. http://groovy.codehaus.org/. Accessed 19 Nov 2010
55. Mason multiagent simulation toolkit. http:// cs.gmu.edu/~eclab/projects/mason/. Accessed 19 Nov 2010
56. AgentSheets. http://www.agentsheets.com/. Accessed 19 Nov 2010
57. NetLogo Home Page. http://ccl.northwest ern.edu/netlogo/. Accessed 19 Nov 2010
58. SeSAm—Integrated environment for multiagent simulation. http://www.simsesam.de/. Accessed 19 Nov 2010
59. StarLogo on the Web. http://education.mit. edu/starlogo/. Accessed 19 Nov 2010
60. Why AnyLogic simulation software? http:// www.xjtek.com/anylogic/why_anylogic/. Accessed 19 Nov 2010
61. SimBioSys class framework. http://www.luci fer.com/~david/SimBioSys/. Accessed 19 Nov 2010
62. Unified modeling language, resource page. http://www.uml.org/. Accessed 19 Nov 2010
63. Rational unified process: best practices for software development teams whitepaper. http:// www.augustana.ab.ca/~mohrj/courses/2000. winter/csc220/papers/rup_best_practices/ rup_bestpractices.html. Accessed 19 Nov 2010
64. Bernon C, Cossentino M, Pavo´n J (2005) Agent-oriented software engineering. Knowl Eng Rev 20(2): 99-116
65. Macal CM, North MJ (2008) Agent-based modeling and simulation: desktop ABMS. In proc. of winter simulation conference 2007, pp. 95-106
66. Axelrod R (1997) Advancing the art of simulation in social sciences. In: Conte R, Hegselmann R, Terna P (eds) Simulating social phenomena. Springer-Verlag, Berlin
67. Wooldridge M, Jennings NR, Kinny D (2000) The Gaia methodology for agent-oriented analysis and design. J Auton Agent Multi- Agent Syst 3(3): 285-312
68. Zambonelli F, Jennings N, Kinny D (2003) Developing multiagent systems: the Gaia methodology. ACM Trans Softw Eng Methodol 12(3): 417-470
69. Bresciani P, Giorgini P, Giunchiglia F et al (2004) Tropos: an agent-oriented software development methodology. J Auton Agent Multi-Agent Syst 8: 203-236
70. Padgham L, Winikoff M (2002) Prometheus: a methodology for developing intelligent agents. In proc. of 3rd international conference on agentoriented software engineering III: 174-185
71. Pavon J, Gomez-Sanz J, Fuentes R (2005) The INGENIAS methodology and tools. In: Henderson-Sellers B, Giorgini P (eds) Agentoriented methodologies. Idea Group, London
72. Cossentino M (2005) From requirements to code with the PASSI methodology. In: Henderson-Sellers B, Giorgini P (eds) Agentoriented methodologies. Idea Group, London
73. Bernon C, Camps V, Gleizes M-P et al (2005) Engineering adaptive multi-agent systems: the ADELFE methodology. In: Henderson-Sellers B, Giorgini P (eds) Agent-oriented methodologies. Idea Group, London
74. Cossentino M, Fortino G, Garro A et al (2008) PASSIM: a simulation-based process for the development of multi-agent systems. Int J Agent-Oriented Softw Eng 2(2): 132-170
75. Henderson-Sellers B, Giorgini P (2005) Agent-oriented methodologies. Idea Group, London
76. The FIPA agent UML Web site. http://www.auml.org/. Accessed 19 Nov 2010
77. Padgham L, Winikoff M, Deloach S, Cossentino M (2009) A unified graphical notation for AOSE. In proc. agent-oriented software engineering IX. doi:10.1007/978-3-642-01338- 6_9
78. García-Magariño I, Gutiérrez C, Fuentes-Fernández R (2009) The INGENIAS development kit: a practical application for crisismanagement. In bio-inspired systems: computational and ambient intelligence. Lect Notes Comput Sci 5517: 537-544
79. PASSI toolkit. http://sourceforge.net/pro1jects/ptk/. Accessed 19 Nov 2010
80. Cossentino M, Fortino G, Gleizes MP et al (2010) Simulation-based design and evaluation of multi-agent systems. Modell Pract Theory 18(10): 1425-1427
81. Fortino G, Garro A, Russo W (2005) An integrated approach for the development and validation of multi-agent systems. Comput Syst Sci Eng 20(4): 94-107
82. Fortino G, Garro A, Mascillaro S et al (2007) ELDATool: a statechart-based tool for prototyping multi-agent systems. Proc. of workshop on objects and agents (WOA ’07)
83. Cannata N, Corradini F, Merelli E et al (2005) An agent-oriented conceptual framework for systems biology. Trans Comput Syst Biol, Lect Notes Comput Sci (3737): 105-122
84. Finkelstein A, Hetherington J, Li L et al (2004) Computational challenges of systems biology. Computer 37(5): 26-33
85. Corradini F, Merelli E, Vita M(2005) A multiagent system for modelling carbohydrate oxidation in cell. Lect Notes Comput Sci 3481: 1264-1273
86. Cannata N, Corradini F, Merelli E (2008) Multiagent modelling and simulation of carbohydrate oxidation in cell. Int J Modell Ident Control 3(1): 17-28
87. Corradini F, Merelli E (2005) Hermes: agentbased middleware for mobile computing. Lect Notes Comput Sci 3465: 234-270
88. Boehm B (1981) Software engineering economics. Prentice Hall, New York, London
89. Merelli E, Young M (2007) Validating MAS with mutation. Int J Multiagent Grid Syst 3 (2): 225-243
90. Berluti E, Corradini F, Leli S et al (2006) Glycolisis and fermetation in cellular energy production. Internal report unicam-cs01-2006, University of Camerino, Department of Computer Science
91. Cannata N, Corradini F, Merelli E et al (2008) A spatial simulator for metabolic pathways. International workshop on multi agents systems and bioinformatics (MAS & BIO 2008) http://www.cs.unicam.it/tesei/updown/ CCMT08b.pdf. Accessed 19 Nov 2010
92. KEGG LIGAND Database. http://www. genome.jp/ligand/. Accessed 19 Nov 2010
93. Software Templates - SwarmWiki. http:// www.swarm.org/index.php/Software_templates. Accessed 19 Nov 2010