567
Views
22
CrossRef citations to date
0
Altmetric
Original Articles

Cellular automata modelling of biomolecular networks dynamics

, , &
Pages 77-102 | Received 06 Jul 2009, Accepted 03 Nov 2009, Published online: 06 Apr 2010

References

  • Kitano , H . 2001 . Foundations of Systems Biology , Cambridge, MA : MIT Press .
  • Systems biology, Science 295 (2002), Special Issue, L. Chong and L.B. Ray, Eds., pp. 1661–1682
  • Alon , U . 2006 . An Introduction to Systems Biology: Design Principles of Biological Circuits , Boca Raton, FL : Chapman & Hall/CRC, Taylor and Francis Group .
  • Barabási , A-L . 2002 . Linked. The New Science of Networks , Cambridge, MA : Perseus .
  • Newman , M , Barabási , A-L and Watts , DJ . 2006 . The Structure and Dynamics of Networks , Princeton, NJ : Princeton University Press .
  • Wasserman , S and Faust , K . 1994 . Social Network Analysis: Methods and Applications , Cambridge : Cambridge University Press .
  • Ingenuity Pathway Analysis (IPA), Ingenuity Systems Inc., Redwood City, CA; available at www.ingenuity.com/products/prod_overview/html
  • Pathway Studio, Ariadne Genomics, Inc., Rockville, MD; available at www.ariadnegenomics.com/products/pathway-studio/
  • Cytoscape, An open source platform for network analysis and visualization, available at http://cytoscape.org/download.php
  • Haefner , JW . 2005 . Modeling Biological Systems: Principles and Applications , 2nd , New York : Springer .
  • Szallasi , Z , Stelling , J and Periwal , V . 2006 . Systems Modeling in Cellular Biology , Cambridge, MA : MIT Press .
  • Wilkinson , DJ . 2006 . Stochastic Modelling for Systems Biology , Boca Raton, FL : Chapman & Hall/CRC Press .
  • Dreyer , TP . 1993 . Modeling with Ordinary Differential Equations , Boca Raton, FL : CRC Press .
  • Taubes , CH . 2008 . Modeling Differential Equations in Biology , 2nd , Cambridge, MA : Cambridge University Press .
  • Bonchev , D . 2003 . “ Shannon's information and complexity ” . In Complexity in Chemistry, Mathematical Chemistry Series , Edited by: Bonchev , D and Rouvray , DH . Vol. 7 , 155 – 187 . Boca Raton, FL : Taylor & Francis .
  • Bonchev , D . 2003 . “ Complexity of protein-protein interaction networks, complexes and pathways ” . In Handbook of Proteomics Methods , Edited by: Conn , M . 451 – 462 . New York : Humana .
  • Bonchev , D and Buck , GA . 2005 . “ Quantitative measures of network complexity ” . In Complexity in Chemistry, Biology and Ecology , Edited by: Bonchev , D and Rouvray , DH . 191 – 235 . New York : Springer .
  • J. von Neumann, Theory of Self-Reproducing Automata, edited and completed by A.W. Burks, University of IL Press, Urbana, IL, 1966
  • Burks , AW . 1971 . Essays on Cellular Automata , Urbana, IL : University of IL Press .
  • Doyne-Farmer , J , Toffoli , T and Wolfram , S . 1983 . Cellular Automata , Amsterdam : Elsevier .
  • Wolfram , S . 1986 . “ Theory and Applications of Cellular Automata ” . In Advanced Series on Complex Systems , Singapore : World Scientific .
  • Wolfram , S . 2002 . The New Kind of Science , Champaign, IL : Wolfram Media .
  • Rucker , R . 2005 . The Lifebox, the Seashell, and the Soul , New York : Thunder's Mouth Press .
  • Math Forum Internet Mathematical Library; available at http://mathforum.org/library/topics/cellular_auto/
  • M. Wojtowicz, Cellular automata - be in the know; available at http://www.mirekw.com/ca/beintheknow.html; http://www.mirekw.com/ca/other_ca.html
  • C.G. Langton, My Zooland; available at http://sites.google.com/site/myzooland/
  • D. Adalsteinsson, D. McMillen, and T. C. Elston, Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks; available at http://biospice.sourceforge.net/
  • E.M. Francis, CAGE (Cellular Automata generation Engine), v. 1.1.4, 29 March 2002; software available at http://www.alcyone.com/software/cage/cage-latest.tar.gz
  • R. Rucker, CALife, a DOS based cellular automata simulator; software available at http://switch.sjsu.edu/switch/alife/rucker/download1.html/
  • M. Schaller, CAOS, cellular automata; software available at http://nicewww.cern.ch/~schaller/complex/CA1d/CA1d.html
  • R. Rucker, Capow, cellular automata, 23 January 2003; software available at http://www.mathcs.sjsu.edu
  • R. Rucker and J. Walker, CelLab, CA, 1989; software available at http://www.fourmilab.ch/cellab; http://www.cs.sjsu.edu/faculty/rucker/cellab.htm
  • Cell Springs/Web; Cell Springs/DT, CA, 21 June 2000; software available at http://jmge.net/java/csprings/
  • Cellular Automata Viewer; available at http://www.rennard.org/alife/english/cavgb.html
  • J. Gleick, R. Rucker, J. Gordon, and J. Walker, Chaos: The software, 4 January 1999; available at http://www.mathcs.sjsu.edu/faculty/rucker
  • A. Wuensche, DDLab, July 1995; available at www.ddlab.org
  • C. Gordon-Smith, FlexiCA v. 1.2, Jan 1997; available at http://www.simsoup.info/Flexica_Download.html
  • A. Hensel, Conway's Game of Life. At http://mindspring.com/~alanh/life/
  • J. Bontes, Life32, CA simulator of artificial life, v. 2.15, 10 August 2002; available at http://psoup.math.wiscedu/Life32.html.; http://www.xs4all.nl/~jbontes/
  • M. Wojtovicz, MCell (Mirek celebration), v. 1.50, CA explorer, 11 January 1999; available at http://www.mirekw.com/ca/; http://psoup.math.wisc.edu/mcell
  • G. Maydwell, ModernCA; available at http://www.collidoscope.com/modernca/
  • U. Wilensky, NetLogo, CA, April 2002; software available at ccl.northwestern.edu/netlogo/
  • E. Klopfer, StarLogo TNG, 2D and 3D CA simulations, February 2000; software available at en.wikipedia.org/wiki/StarLogo; http://education.mit.edu/drupal/starlogo-tng
  • B. Prentice, Tiled CA, available at http://linuxenvy.com/bprentice/TiledCA/TiledCA.html
  • J. Rampe, Visions of Chaos, v. 43.9, 9 September 2009; software available at http://www.freeyellow.com/freeyellow/upgrade_plans2.bml
  • B. Fisch and D. Griffeath, WinCA; software available at http://psoup.math.wisc.edu/kitchen.html
  • M. Gerits, WinLife, CA software; available at ftp://ftp.digital.com/pub/games/winlife.zip
  • XToys, Linux CA software, 1995; available at http://thy.phy.bnl.gov/www/xtoys/xtoys.html
  • Five Cellular Automata, v. 7.31, Hermetic Systems Inc.; software available at http://www.hermetic.ch
  • Cells, Breeding Gliders with Cellular Automata, Ventrella.com; available at http://www.ventrella.com/Alife/alife.html
  • Mathematica, Wolfram, 23 June 1988; available at http://www.wolfram.com/products/mathematica/index.html
  • Kier , LB and Witten , T . 2005 . “ Cellular automata modeling of complex biological systems ” . In Complexity in Chemistry, Biology, and Ecology , Edited by: Bonchev , D and Rouvray , DH . New York : Springer .
  • A. Deutsch, Modeling interacting cell systems in biology and medicine with cellular automata; available at http://www.bioinfo.de/isb/gcb01/talks/deutsch/main.html
  • Rost , B , Ermentrout , GB and Edelstein-Keshet , L . 1993 . Cellular automata approaches to biological modelling . J. Theor. Biol. , 160 : 97 – 133 .
  • Wootton , JT . 2001 . Local interactions predict large-scale pattern in empirically derived cellular automata . Nature , 413 : 841 – 844 .
  • Wishart , DS , Yang , R , Arndt , D , Tang , P and Cruz , J . 2005 . Dynamic cellular automata: An alternative approach to cellular simulation . In Silico Biol. , 5 : 139 – 161 .
  • Sander , C . 1993 . Prediction of protein secondary structure at better than 70% accuracy . J. Mol. Biol. , 232 : 584 – 599 .
  • Chopra , P and Bender , A . 2007 . Evolved cellular automata for protein secondary structure prediction imitate the determinants for folding observed in nature . In Silico Biol. , 7 : 87 – 93 .
  • Woolf , PJ and Linderman , JJ . 2003 . Self organization of membrane proteins via dimerization . Biophys. Chem. , 104 : 217 – 227 .
  • J. Hilke, J. Reggia, R. Navarro-Gonzalez, and J. Lohn, A modified cellular automata model of nucleotide interactions and non-enzymatic transcription of DNA, in the First International Symposium on Intelligence in Neural and Biological Systems (INBS'95), 1995
  • Nilsson , M and Rasmussen , S . 2003 . Cellular automata for simulating molecular self-assembly . Discr. Math. Theor. Comput. Sci. AB(DMCS) , 6 : 31 – 42 .
  • Kier , LB , Cheng , C-K and Testa , B . 1999 . Cellular automata models of biochemical phenomena . Future Generation Comput. Syst. , 16 : 273 – 289 .
  • Weimar , JR . 2002 . Cellular automata approaches to enzymatic reaction networks . Lect. Notes Comput. Sci. , 2493 : 294 – 303 .
  • Graner , F and Glazier , JA . 1992 . Simulation of biological cell sorting using a two-dimensional extended Potts model . Phys. Rev. Lett. , 69 : 2013 – 2016 .
  • Glazier , JA and Graner , F . 1993 . Simulation of the differential driven rearrangement of biological cells . Phys. Rev. E , 47 : 2128 – 2154 .
  • Ben-Jacob , E , Shochet , O , Tenenbaum , A , Cohen , I , Czirók , A and Vicsek , T . 1994 . Generic modeling of cooperative growth patterns in bacterial colonies . Nature, , 368 : 46 – 49 .
  • Le Sceller , L , Ripoll , C , Demarty , M , Cabin-Flamand , A , Nyström , T , Saier , M Jr and Norris , V . 2006 . Modelling bacterial hyperstructures with cellular automata, in Unifying Themes in Complex Systems , Edited by: Minai , AA and Bar-Yam , Y . 147 – 156 . New York : Springer .
  • Piotrowska , MJ and Angus , SD . 2009 . A quantitative cellular automaton model of in vitro multicellular spheroid tumor growth . J. Theor. Biol. , 258 : 165 – 178 .
  • Mallet , DG and De Pillis , LG . 2006 . A cellular automata model of tumor–immune system interactions . J. Theor. Biol. , 239 : 334 – 350 .
  • Holland , JH and Miller , JH . 1991 . Artificial adaptive agents in economic theory . Amer. Econom. Rev. , 81 : 365 – 371 .
  • Bonabeau , E . 2002 . Agent-based modeling: Methods and techniques for simulating human systems . Proc. Natl. Acad. Sci. Unit. States Am. , 99 : 7280 – 7287 .
  • Holland , JH . 1995 . Hidden Order: How Adaptation Builds Complexity , Reading, MA : Addison-Wesley .
  • O'Sullivan , D and Haklay , M . 2000 . Agent-based models and individualism: Is the world agent-based? . Environ. Plann. A , 32 : 1409 – 1425 .
  • Grimm , V , Revilla , E , Berger , U , Jeltsch , F , Mooij , WM , Railsback , SF , Thulke , HH , Weiner , J , Wiegand , T and DeAngelis , DL . 2005 . Pattern-oriented modeling of agent-based complex systems: Lessons from ecology . Science , 310 : 987 – 891 .
  • A. Tobias and C. Hoffman, Agent Based Models in Biology and Medicine, 2004, available at http://www.swarm.org/index.php/
  • Samuelson , DA and Macal , CM . 2006 . Agent-based modeling comes of age . OR/MS Today , 33 : 34 – 38 .
  • Yoav , S and Leyton-Brown , K . 2009 . Multi-agent systems: algorithmic, game-theoretic, and logical foundations , Cambridge : University Press .
  • Casti , J . 1997 . Agent-based modeling: Methods and techniques for simulating human systems . Proc. Natl. Acad. Sci. Unit. States Am. , 99 : 7280 – 7297 .
  • Jennings , NR . 2000 . On agent-based software engineering . Artif. Intel. , 117 : 277 – 296 .
  • C.M. Macal and M.J. North, Tutorial on agent-based modeling and simulation part 2: How to model with agents, Proc. 2006 Winter Simulation Conference, (2006), pp. 73–83
  • M. North, M. Altaweel, D. Blachowicz, N. Collier, T. Howe, B. Najlis, J. Ozik, M. Parker, E. Tatara, and J. R. Vos, 2006, Repast (Recursive Porous Agent Simulation Toolkit), available at http://repast.sourceforge.net/
  • Center for the Study of Complex Systems at the University of Michigan, Swarm, 2006; available at http://www.swarm.org
  • S. Luke, G.C. Balan, K. Sullivan, and L. Panait, 2006, MASON (Multi-Agent Simulator of Neighborhoods), GMU; available at http://cs.gmu.edu/~eclab/tools.html
  • XJ Technologies, AnyLogic, 2006, available at http://www.xjtek.com/
  • J. Devillers, H. Devillers, A. Decourtye, and A. Aupinel, Internet resources for agent-based modelling, SAR QSAR Environ. Res. 21 (2010), in press
  • Kier , LB , Seybold , PG and Cheng , C-K . 2005 . Modeling Chemical Systems Using Cellular Automata , New York : Springer .
  • Kier , LB , Cheng , C-K , Testa , B and Karrupt , P-A . 1996 . Cellular automata model of enzyme kinetics . J. Molec. Graphics , 14 : 227 – 231 .
  • F. Barra and P. Gaspard, Classical dynamics on graphs, (2000). Available at arxiv.org/abs/nlin.CD/0011045
  • P. Gács, Reliable cellular automata with self-organization, (2001). Available at arxiv.org/abs/math.PR/0003117
  • Gagneur , J and Casari , G . 2005 . From molecular networks to qualitative cell behavior . FEBS Lett., , 579 : 1867 – 1871 .
  • A. Shreim, P. Grassberger, W. Nadler, B. Samuelsson, and J.E.S. Socolar, Network analysis of the state space of discrete dynamical systems, (2007). Available at arxiv.org/abs/cond-mat/0610447
  • Mason , O and Verwoerd , M . 2007 . Graph theory and networks in Biology . IET Syst. Biol. , 1 : 89 – 119 .
  • Kier , LB , Bonchev , D and Buck , GA . 2005 . Modeling biochemical networks: A cellular automata approach . Chem. Biodiversity , 2 : 233 – 243 .
  • Huang , C-YF and Ferell , JE . 1996 . Ultrasensitivity in the mitogen activated protein kinase cascade . Proc. Natl. Acad. Sci. Unit. States Am. , 93 : 10078 – 10083 .
  • Bhalla , US and Iyengar , R . 1999 . Emergent properties of networks of biological signaling pathways . Science , 283 : 381 – 387 .
  • Kholodenko , BN . 2000 . Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades . Eur. J. Biochem. , 267 : 1583 – 1588 .
  • Brightman , FA and Fell , DA . 2000 . Differential feedback regulation of the MAPK cascade underlies the quantitative differences the quantitative differences in EGF and NGF signaling in PC12 cells . FEBS Lett. , 482 : 169 – 174 .
  • Shimizu , TS and Bray , D . 2001 . “ Computational cell biology–the stochastic approach ” . In Computational Cell Biology–The Stochastic Approach, Foundations of Systems Biology , Edited by: Kitano , H . Cambridge, MA : MIT Press . Chap. 10
  • Schoeberl , B , Eichler-Jonsson , C , Gilles , ED and Müller , G . 2002 . Computational modeling of the dynamics of MAP cascade activated by surface and internalized EGF receptors . Nat. Biotechnol. , 20 : 370 – 375 .
  • Hatakeyama , M , Kimura , S , Naka , T , Kawasaki , T , Yumoto , N , Ichikawa , M , Kim , J-H , Saito , K , Saeki , M , Shirouzu , M , Yokoyama , S and Konagaya , A . 2003 . A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling . Biochem. J. , 373 : 451 – 463 .
  • Shimizu , TS , Aksenov , SV and Bray , D . 2003 . A spatially extended stochastic model of the bacterial chemotaxis signaling pathway . J. Mol. Biol. , 329 : 291 – 309 .
  • Bonchev , D , Kier , LB and Cheng , C-K . 2006 . Cellular Automata (CA) as a basic method for studying network dynamics . Lect. Ser. Comp. Comput. Sci. , 6 : 581 – 591 .
  • Scott , FL , Stec , B , Pop , C , Dobaczewska , MK , Lee , JEJ , Monosov , E , Robinson , H , Salvesen , GS , Schwarzenbacher , R and Riedl , SJ . 2009 . The Fas–FADD death domain complex structure unravels signalling by receptor clustering . Nature , 457 : 1019 – 1022 .
  • G.S. Salvesen and S.J. Riedl, Structure of the Fas/FADD complex: A conditional death domain complex mediating signaling by receptor clustering, Epub ahead of print (30 September 2009), to appear in Cell Cycle, 8(17)
  • Yangand , YL and Li , XM . 2000 . The IAP family: Endogenous caspase inhibitors with multiple biological activities . Cell Res. , 10 : 169 – 177 .
  • Verhagen , AM , Coulson , EJ and Vaux , DL . 2001 . Inhibitor of apoptosis proteins and their relatives: IAPs and other BIRPs . Genome Biol. , 2 : 1 – 10 .
  • Thome , M and Tschopp , J . 2001 . Regulation of lymphocyte proliferation and death by FLIP . Nature Rev. Immunol. , 1 : 50 – 58 .
  • Chang , DW , Xing , Z , Pan , Y , Algeciras-Schimnich , A , Barnhart , BC , Yaish-Ohad , S , Peter , ME and Yang , X . 2002 . c-FLIPL is a dual function regulator for caspase-8 activation and CD95-mediated apoptosis . EMBO J. , 21 : 3704 – 3714 .
  • Hyung , LS , Sug , KH , Young , KS , Y-Sil , L , Sang , PW , Ho , KS , Young , LJ and Jin , YN . 2003 . Increased expression of FLIP, an inhibitor of FAS-mediated apoptosis, in stomach cancer . APMIS , 111 : 309 – 314 .
  • Temesgen , S , Welsh , K , Lober , T , Togo , SH , Zapata , JM and Reed , JC . 2006 . Distinct BIR domains of cIAP1 mediate binding to and ubiquitination of tumor necrosis factor receptor-associated factor 2 and second mitochondrial activator of caspases . J. Biol. Chem. , 281 : 1080 – 1090 .
  • O'Riordan , MXD , Bauler , LD , Scott , FL and Duckett , CS . 2008 . Inhibitor of apoptosis (IAP) proteins in eukaryotic evolution and development: A model of thematic conservation . Dev. Cell. , 15 : 497 – 508 .
  • Petros , AM , Medek , A , Nettesheim , DG , Kim , DH , Yoon , HS , Swift , K , Matayoshi , ED , Oltersdorf , T and Fesik , SW . 2001 . Solution structure of the antiapoptotic protein bcl-2 . PNAS , 98 : 3012 – 3017 .
  • Ciardiello , F and Tortora , G . 2002 . Inhibition of Bcl-2 as cancer therapy . Ann. Oncol. , 13 : 501 – 502 .
  • Siehs , C , Oberbauer , R , Mayer , G , Lukas , A and Mayer , B . 2002 . Discrete simulation of regulatory homo- and heterodimerization in the apoptosis effector phase . Bioinformatics , 18 : 67 – 76 .
  • Marani , M , Tenev , T , Hancock , D , Downward , J and Lemoine , NR . 2002 . Identification of novel isoforms of the BH3 domain protein Bim which directly activate Bax . Mol. Cell Biol. , 22 : 3577 – 3589 .
  • Xue , L-Y , Chiu , S-M , Fiebig , A , Andrews , DW and Oleinick , NL . 2003 . Photodamage to multiple Bcl-xL isoforms by photodynamic therapy with the phthalocyanine photosensitizer Pc 4 . Oncogene , 22 : 9197 – 9204 .
  • Jourdan , M , Reme , T , Goldschmidt , H , Fiol , G , Pantesco , V , De Vos , J , Rossi , J-F , Hose , D and Klein , B . 2009 . Gene expression of anti- and pro-apoptotic proteins in malignant and normal plasma cells . Br. J. Haematol. , 145 : 45 – 58 .
  • Renouf , DJ , Wood-Baker , R , Ionescu , DN , Leung , S , Masoudi , GH , Cyril , B and Laskin , J . 2009 . BCL-2 expression is prognostic for improved survival in non-small cell lung cancer . J. Thor. Oncol. , 4 : 486 – 491 .
  • Kerrien , S , Alam-Faruque , Y , Aranda , B , Bancarz , I , Bridge , A , Derow , C , Dimmer , E , Feuermann , M , Friedrichsen , A , Huntley , R , Kohler , C , Khadake , J , Leroy , C , Liban , A , Lieftink , C , Montecchi-Palazzi , L , Orchard , S , Risse , J , Robbe , K , Roechert , B , Thorneycroft , D , Zhang , Y , Apweiler , R and Hermjakob , H . 2006 . IntAct–Open source resource for molecular interaction data . Nucleic Acids Res. , 35 : 561 – 565 .
  • Apte , A , Cain , JW , Bonchev , D and Fong , S . 2008 . Topological effects on the dynamics of feed-forward motifs . J. Biol. Eng. , 2 : 2 – 13 .
  • D.T. Taylor, J.W. Cain, D.G. Bonchev, S.S. Fong, A.A. Apte, and L.E. Pace, Toward a classification of isodynamic feed-forward motifs, advanced online publication (28 July 2009), to appear in J. Biol. Dynamics, DOI: 10.1080/17513750903144461
  • Milo , R , Shen-Orr , S , Itzkovitz , S , Kashtan , N , Chklovskii , D and Alon , U . 2002 . Network motifs: Simple building blocks of complex networks . Science , 298 : 824 – 827 .

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.