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@article{Gonzalez2002mis,
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@article{chavali2008cep,
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	month = {December},
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	posted-at = {2008-11-22 12:00:20},
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}
 


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@INPROCEEDINGS{860359,
    author = {Dominique Gro\ss\ and Barry McMullin},
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    pages = {400--409},
    publisher = {MIT Press}
} 

@inproceedings{DBLP:conf/eurogp/DecraeneMMK07,
  author    = {James Decraene and
               George G. Mitchell and
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  booktitle = {EuroGP},
  year      = {2007},
  pages     = {361-370},
  ee        = {http://dx.doi.org/10.1007/978-3-540-71605-1_34},
  crossref  = {DBLP:conf/eurogp/2007},
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@proceedings{DBLP:conf/eurogp/2007,
  editor    = {Marc Ebner and
               Michael O'Neill and
               Anik{\'o} Ek{\'a}rt and
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               Anna Esparcia-Alc{\'a}zar},
  title     = {{Genetic Programming, 10th European Conference, EuroGP 2007,
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@Article{pmid16230365,
   Author="M. Mukai  and T. Kusama and Y. Hamanaka and T. Koga and H. Endo and M. Tatsuta Masaharu and M. Inoue",
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   Volume="65",
   Number="20",
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@Article{pmid10791773,
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   Journal="J Mammary Gland Biol Neoplasia",
   Year="2000",
   Volume="5",
   Number="1",
   Pages="107--115",
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@article{citeulike:447368,
  title={{Origins of Extrinsic Variability in Eukaryotic Gene Expression}},
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 @article{genoud1999,
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pages={503-507},
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@article{bray2000eml,
  title={{Extensible Markup Language (XML) 1.0}},
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 @article{citeulike:488811,
	author = {H. Goto and T. Kiyono and Y. Tomono and A. Kawajiri and T. Urano and K. Furukawa and E.A. Nigg and M Inagaki},
	citeulike-article-id = {488811},
	doi = {10.1038/ncb1350},
	issn = {1465-7392},
	journal = {Nature Cell Biology},
	month = {December},
	number = {2},
	pages = {180--187},
	publisher = {Nature Publishing Group},
	title = {{Complex Formation of Plk1 and INCENP required for Metaphase–Anaphase Transition}},
	url = {http://dx.doi.org/10.1038/ncb1350},
	volume = {8},
	year = {2005}
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@article{citeulike:1303,
	abstract = {Cells use complex networks of interacting molecular components to transfer and process information. These "computational devices of living cells" are responsible for many important cellular processes, including cell-cycle regulation and signal transduction. Here we address the issue of the sensitivity of the networks to variations in their biochemical parameters. We propose a mechanism for robust adaptation in simple signal transduction networks. We show that this mechanism applies in particular to bacterial chemotaxis. This is demonstrated within a quantitative model which explains, in a unified way, many aspects of chemotaxis, including proper responses to chemical gradients. The adaptation property is a consequence of the network's connectivity and does not require the 'fine-tuning' of parameters. We argue that the key properties of biochemical networks should be robust in order to ensure their proper functioning.},
	address = {Department of Physics, Princeton University, New Jersey 08544, USA.},
	author = {N. Barkai  and S. Leibler },
	citeulike-article-id = {1303},
	doi = {10.1038/43199},
	issn = {0028-0836},
	journal = {Nature},
	keywords = {chemotaxis computational dynamics modelling robustness},
	month = {June},
	number = {6636},
	pages = {913--917},
	title = {{Robustness in Simple Biochemical Networks.}},
	url = {http://dx.doi.org/10.1038/43199},
	volume = {387},
	year = {1997}
}

@article{citeulike:447014,
	author = {A.M. Arias and P. Hayward},
	citeulike-article-id = {447014},
	doi = {10.1038/nrg1750},
	issn = {1471-0056},
	journal = {Nature Reviews Genetics},
	keywords = {noise transcription},
	number = {1},
	pages = {34--44},
	priority = {0},
	publisher = {Nature Publishing Group},
	title = {{Filtering Transcriptional Noise during Development: Concepts and Mechanisms}},
	url = {http://dx.doi.org/10.1038/nrg1750},
	volume = {7},
	year={2005},
	
}

@article{citeulike:841,
	abstract = {Networks of interacting proteins orchestrate the responses of living cells to a variety of external stimuli, but how sensitive is the functioning of these protein networks to variations in their biochemical parameters? One possibility is that to achieve appropriate function, the reaction rate constants and enzyme concentrations need to be adjusted in a precise manner, and any deviation from these 'fine-tuned' values ruins the network's performance. An alternative possibility is that key properties of biochemical networks are robust; that is, they are insensitive to the precise values of the biochemical parameters. Here we address this issue in experiments using chemotaxis of Escherichia coli, one of the best-characterized sensory systems. We focus on how response and adaptation to attractant signals vary with systematic changes in the intracellular concentration of the components of the chemotaxis network. We find that some properties, such as steady-state behaviour and adaptation time, show strong variations in response to varying protein concentrations. In contrast, the precision of adaptation is robust and does not vary with the protein concentrations. This is consistent with a recently proposed molecular mechanism for exact adaptation, where robustness is a direct consequence of the network's architecture.},
	address = {Department of Molecular Biology, Princeton University, New Jersey 08544, USA.},
	author = {U. Alon and M.G. Surette  and N. Barkai and S. Leibler},
	citeulike-article-id = {841},
	doi = {10.1038/16483},
	issn = {0028-0836},
	journal = {Nature},
	keywords = {chemotaxis dynamics no-tag robustness},
	month = {January},
	number = {6715},
	pages = {168--171},
	title = {{Robustness in Bacterial Chemotaxis.}},
	volume = {397},
	year = {1999}
}

@article{hiyama2005mc,
  title={{Molecular Communication}},
  author={S. Hiyama and Y. Moritani and T. Suda  and R. Egashira  and A. Enomoto  and M. Moore and T. Nakano},
  journal={Proc. of the 2005 NSTI Nanotechnology Conference, May},
  year={2005}
}

@article{reed2000cm,
  title={{Computing With Molecules}},
  author={M.A. Reed and J.M. Tour},
  journal={Computing},
  year={2000}
}


@article{desilva2004msl,
  title={{Molecular-Scale Logic Gates}},
  author={A.P. de Silva and N.D. McClenaghan},
  journal={Chemistry- A European Journal},
  volume={10},
  number={3},
  pages={574--586},
  year={2004}
}

@inproceedings{alifexi_decraene_158,
	author = {Decraene, J.  and Mitchell, G.  and Mcmullin, B. },
	booktitle = {Artificial Life XI: Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems},
	citeulike-article-id = {3365909},
	editor = {Bullock, S.  and Noble, J.  and Watson, R.  and Bedau, M. A. },
	pages = {158--165},
	posted-at = {2008-10-02 12:17:25},
	priority = {2},
	publisher = {MIT Press, Cambridge, MA},
	title = {{Unexpected Evolutionary Dynamics in a String-based Artificial Chemistry}},
	url = {http://www.alifexi.org/papers/ALIFExi\_pp158-165.pdf},
	year = {2008}
}

	
	

@incollection{decraene2007eac,
  author    = {James Decraene and
               George G. Mitchell and
               Barry McMullin},
  title     = {{Evolving Artificial Cell Signaling Networks: Perspectives
               and Methods}},
  booktitle = {Advances in Biologically Inspired Information Systems},
  year      = {2007},
  pages     = {165-184},
  ee        = {http://dx.doi.org/10.1007/978-3-540-72693-7_9},
  crossref  = {DBLP:series/sci/2007-69},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}
@book{DBLP:series/sci/2007-69,
  editor    = {Falko Dressler and
               Iacopo Carreras},
  title     = {Advances in Biologically Inspired Information Systems: Models,
               Methods, and Tools},
  publisher = {Springer},
  series    = {Studies in Computational Intelligence},
  volume    = {69},
  year      = {2007},
  isbn      = {978-3-540-72692-0},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

 @book{Helmreich,
 author = {Ernst J. M. Helmreich },
 title = {{The Biochemistry of Cell Signalling}},
 year = {2001},
 isbn = {0198508204},
 publisher = {Oxford University Press},
 address = {USA},
 }
 
 @article{stock1992stb,
  title={{Signal Transduction in Bacterial Chemotaxis}},
  author={Stock, JB and Surette, MG and McCleary, WR and Stock, AM},
  journal={Journal of Biological Chemistry},
  volume={267},
  number={28},
  pages={19753--19756},
  year={1992},
  publisher={ASBMB}
}

 
   @book{Krauss2003,
 author = {G. Krauss},
 title = {{Biochemistry of Signal Transduction and Regulation}},
 year = {2003},
 isbn = {3527305912},
 publisher = {John Wiley \& Sons},
 }
@article{citeulike:96164,
	abstract = {Due to the variety and importance of roles performed by signalling networks, understanding their function and evolution is of great interest. Signalling networks allow organisms to process and react to changes in their internal and external environment. Current estimates suggest that two to three percent of all genomes code for proteins involved in signalling networks. The study of signalling networks is hindered by the complexities of the networks and difficulties in ascribing function to form. For example, a very complex dense network might comprise eighty or more densely connected proteins. In the majority of cases there is very little understanding of how these networks process signals. Unlike in electronics, where there is a broad practical and theoretical understanding of how to construct devices that can process almost any kind of signal, in biological signalling networks there is no equivalent theory. Part of the problem stems from the fact that in most cases it is unknown what particular signal processing circuits would look like in a biological form. This paper describes the evolutionary methods used to generate networks with particular signal- and computational-processing capabilities. The techniques involved are described, and the approach is illustrated by evolving computational circuits such as multiplication, radicals and logarithmic functions. The experiments also illustrate the evolution of modularity within biochemical reaction networks.},
	address = {Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.},
	author = {A. Deckard and H.M. Sauro},
	citeulike-article-id = {96164},
	comment = {How to do GP with a biological network.

- Set a goal function to build an analogue computer to compute a square root, cube root, etc.

> Survival of the least deviant

- Seems to work. There's some evidence that it evolves something which computes a taylor series approximation.

- You can't stick two square root modules together to get a fourth root one for the same reason that you can't stick two amplifiers together in electronics - you get impedance problems. Interesting to think about how nature arranginges modules together, maybe like an electrical engineer here?

> The evolved networks look nothing like real biological signalling networks. Whereas biological signalling networks are composed of repeated cyclic motifs, the artificially evolved networks lacked this kind of artchitecture.},
	doi = {10.1002/cbic.200400178},
	issn = {1439-4227},
	journal = {Chembiochem},
	keywords = {from-kell impedance networks},
	month = {October},
	number = {10},
	pages = {1423--1431},
	priority = {0},
	title = {{Preliminary Studies on the in silico Evolution of Biochemical Networks.}},
	volume = {5},
	year = {2004}
}

@article{bray1994cse,
  title={{Computer Simulated Evolution of a Network of Cell-Signaling Molecules}},
  author={Bray, D. and Lay, S.},
  journal={Biophysical Journal},
  volume={66},
  number={4},
  pages={972--977},
  year={1994},
  publisher={Elsevier}
}


@article{bray1995pmc,
  title={{Protein Molecules as Computational Elements in Living Cells}},
  author={D. Bray},
  journal={Nature},
  volume={376},
  number={6538},
  pages={307--312},
  year={1995}
}

@article{binder2004ibd,
  title={{Interrelations between Dynamical Properties and Structural Characteristics of Signal Transduction Networks}},
  author={B. Binder and R. Heinrich},
  journal={Genome Inform Ser Workshop Genome Inform},
  volume={15},
  number={1},
  pages={13--23},
  year={2004}
  }
  
@article{blossey:17,
  author =	 {Ralf Blossey and Luca Cardelli and Andrew Phillips},
  collaboration ={},
  title =	 {{Compositionality, Stochasticity, and Cooperativity
                  in Dynamic Models of Gene Regulation}},
  publisher =	 {HFSP},
  year =	 2008,
  journal =	 {HFSP Journal},
  volume =	 2,
  number =	 1,
  pages =	 {17-28},
  keywords =	 {biochemistry; differential equations; genetics;
                  molecular biophysics; pi calculus; reaction
                  kinetics; stochastic processes},
  url =		 {http://link.aip.org/link/?HFS/2/17/1},
  doi =		 {10.2976/1.2804749}
}

@inproceedings{DBLP:conf/psb/RegevSS01,

 author    = {Aviv Regev and
              William Silverman and
              Ehud Y. Shapiro},
 title     = {{Representation and Simulation of Biochemical Processes Using
              the $\pi$-Calculus Process Algebra.}},
 booktitle = {Pacific Symposium on Biocomputing},
 year      = {2001},
 pages     = {459-470},
 ee        = {http://helix-web.stanford.edu/psb01/regev.pdf},
 bibsource = {DBLP, http://dblp.uni-trier.de}
 }
 
 @article{regev2004cab,
  title={{The $\pi$-calculus as an Abstraction for Biomolecular Systems}},
  author={Regev, A. and Shapiro, E.},
  journal={Modelling in Molecular Biology},
  pages={219},
  year={2004},
  publisher={Springer}
}

 @book{329902,

 author = {Robin Milner},
 title = {{Communicating and Mobile Systems: the $\pi$-calculus}},
 year = {1999},
 isbn = {0-521-65869-1},
 publisher = {Cambridge University Press},
 address = {New York, NY, USA},
 }
 
 @article{358021,

 author = {C. A. R. Hoare},
 title = {{Communicating Sequential Processes}},
 journal = {Commun. ACM},
 volume = {26},
 number = {1},
 year = {1983},
 issn = {0001-0782},
 pages = {100--106},
 doi = {http://doi.acm.org/10.1145/357980.358021},
 publisher = {ACM Press},
 address = {New York, NY, USA},
 }
 
 @article{citeulike:273,

 author = {Pinney, J. W.  and Westhead, D. R.  and McConkey, G. A. },
 citeulike-article-id = {273},
 comment = {Doesn't really tell you anything earth-shattering.},
 issn = {0300-5127},
 journal = {Biochem Soc Trans},
 keywords = {networks petri-net sysbio},
 number = {Pt 6},
 pages = {1513--1515},
 title = {{Petri Net Representations in Systems Biology.}},
 volume = {31},
 year = {2003}
 }
 
 @article{reddy1993pnr,

 title={{Petri Net Representations in Metabolic Pathways.}},
 author={Reddy, VN and Mavrovouniotis, ML and Liebman, MN},
 journal={Proc Int Conf Intell Syst Mol Biol},
 volume={1},
 pages={328--36},
 year={1993}
 }


@book{539513,

 author = {James Lyle Peterson},
 title = {{Petri Net Theory and the Modeling of Systems}},
 year = {1981},
 isbn = {0136619835},
 publisher = {Prentice Hall PTR},
 address = {Upper Saddle River, NJ, USA},
 }
 
 @book{Petri62,
  title={{Kommunikation mit Automaten}},
  author={Petri, C.A.},
  year={1962},
  publisher={Auch im Handel als: Schriften d. Rheinisch-Westf{\"a}lischen Instituts f. instrumentelle Mathematik an d. Universit{\"a}t Bonn. Nr 2.}
}
 
 @article{conway1970gl,
  title={{The Game of Life}},
  author={Conway, J.},
  journal={Scientific American},
  volume={223},
  pages={120--123},
  year={1970}
}

@article{holcombe1988xmb,
  title={{X-machines as a Basis for Dynamic System Specification}},
  author={Holcombe, M.},
  journal={Software Engineering Journal},
  volume={3},
  number={2},
  pages={69--76},
  year={1988}
}

@article{paun1998dcn,
  author    = {Gheorghe Paun and
               Grzegorz Rozenberg},
  title     = {{A Guide to Membrane Computing}},
  journal   = {Theor. Comput. Sci.},
  volume    = {287},
  number    = {1},
  year      = {2002},
  pages     = {73-100},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@article{bernstein-05,
  title={{Simulating Mesoscopic Reaction-Diffusion Systems using the Gillespie Algorithm}},
  author={Bernstein, D.},
  journal={Physical Review E},
  volume={71},
  number={4},
  pages={41103},
  year={2005},
  publisher={APS}
}

@article{chatterjee-vlachos-05,
	abstract = {Recently, Gillespie introduced the tau-leap approximate, accelerated stochastic Monte Carlo method for well-mixed reacting systems [J. Chem. Phys. 115, 1716 (2001)]. In each time increment of that method, one executes a number of reaction events, selected randomly from a Poisson distribution, to enable simulation of long times. Here we introduce a binomial distribution tau-leap algorithm (abbreviated as BD-tau method). This method combines the bounded nature of the binomial distribution variable with the limiting reactant and constrained firing concepts to avoid negative populations encountered in the original tau-leap method of Gillespie for large time increments, and thus conserve mass. Simulations using prototype reaction networks show that the BD-tau method is more accurate than the original method for comparable coarse-graining in time.},
	address = {Department of Chemical Engineering and Center for Catalytic Science and Technology, University of Delaware, Newark, Delaware 19716, USA.},
	author = {Chatterjee, A.  and Vlachos, D. G.  and Katsoulakis, M. A. },
	citeulike-article-id = {2105214},
	doi = {10.1063/1.1833357},
	issn = {0021-9606},
	journal = {Journal of Chemical Physics},
	keywords = {gillespie\_algorithm, simulation, stochastic, tau\_leap},
	month = {January},
	number = {2},
	posted-at = {2007-12-13 16:13:54},
	priority = {0},
	title = {{Binomial Distribution based Tau-Leap Accelerated Stochastic Simulation.}},
	url = {http://dx.doi.org/10.1063/1.1833357},
	volume = {122},
	year = {2005}
}



 @article{gibson-bruck-00,

 title={{Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels}},
 author={Gibson, MA and Bruck, J},
 journal={J. Phys. Chem. A},
 volume={104},
 pages={1876--1889},
 year={2000}
 }


@article{meng2004mas,
  title={{Modeling and Simulation of Biological Systems with Stochasticity}},
  author={Meng, T.C.},
  journal={In Silico Biology},
  volume={4},
  number={3},
  pages={293--309},
  year={2004},
  publisher={IOS Press}
}

@article{gillespie1976gmn,
  title={{A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions}},
  author={Gillespie, D.T.},
  journal={J. Comput. Phys},
  volume={22},
  number={4},
  pages={403--434},
  year={1976}
}

@article{gillespie1977ess,
  title={{Exact Stochastic Simulation of Coupled Chemical Reactions}},
  author={Gillespie, D.T. and others},
  journal={The journal of physical chemistry},
  volume={81},
  number={25},
  pages={2340--2361},
  year={1977},
  publisher={American Chemical Society}
}

@article{gillespie-01,

 title={{Approximate Accelerated Stochastic Simulation of Chemically Reacting Systems}},
 author={Daniel T. Gillespie},
 journal={Journal of Chemical Physics},
 volume={115},
 number={4},
 pages={1716--1733},
 year={2001}
 }
 
 
 @article{lenovere-shimizu-01,
 title={{StochSim: Modelling of Stochastic Biomolecular Processes}},
 author={Le Nov\`{e}re, N. and Shimizu, T. S.},
 journal={Bioinformatics},
 volume={17},
 pages={575--576},
 year={2001}
 }
 
 @article{citeulike:470218,

 address = {Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. dpeer@genetics.med.harvard.edu},
 author = {Pe'er, D. },
 citeulike-article-id = {470218},
 doi = {10.1126/stke.2812005pl4},
 issn = {1525-8882},
 journal = {Sci STKE},
 keywords = {a_exam bayesian bayesnet inference network signaling toread},
 number = {281},
 title = {{Bayesian Network Analysis of Signaling Networks: a Primer.}},
 url = {http://dx.doi.org/10.1126/stke.2812005pl4},
 volume = {2005},
 year = {2005}
 }
 
 @article{citeulike:126817,

 author = {Woolf, J.  and Wendy, Prudhomme   and Laurence, Daheron   and Daley, Q.  and Lauffenburger, A. },
 citeulike-article-id = {126817},
 doi = {10.1093/bioinformatics/bti056},
 issn = {1367-4803},
 journal = {Bioinformatics},
 number = {6},
 pages = {741--753},
 publisher = {Oxford University Press},
 title = {{Bayesian Analysis of Signaling Networks Governing Embryonic Stem Cell Fate Decisions}},
 url = {http://dx.doi.org/10.1093/bioinformatics/bti056},
 volume = {21},
 year = {2005}
 }
 
 @article{deJong2002mas,

 author = {de Jong, H. },
 citeulike-article-id = {411464},
 doi = {10.1089/10665270252833208},
 journal = {Journal of Computational Biology},
 keywords = {genetic_regulatory_networks kinematics},
 month = {January},
 number = {1},
 pages = {67--103},
 priority = {2},
 title = {{Modeling and Simulation of Genetic Regulatory
 Systems: A Literature Review}},
 url = {http://dx.doi.org/10.1089/10665270252833208},
 volume = {9},
 year = {2002}
 }
 
 @InCollection{Ch96,

 author =	"D. M. Chickering",
 title =	{{Learning {B}ayesian Networks is {NP}-complete}},
 editor =	"D. Fisher and H.-J. Lenz",
 booktitle =	"Learning from data: {AI} and statistics {V}",
 pages =	"121--130",
 chapter =	"12",
 publisher =	"Springer",
 year = 	"1996",
 }
 
 @article{DBLP:journals/jcb/LiL05,

 author    = {Lei M. Li and
              Henry Horng-Shing Lu},
 title     = {{Explore Biological Pathways from Noisy Array Data by Directed
              Acyclic Boolean Networks.}},
 journal   = {Journal of Computational Biology},
 volume    = {12},
 number    = {2},
 year      = {2005},
 pages     = {170-185},
 ee        = {http://dx.doi.org/10.1089/cmb.2005.12.170},
 bibsource = {DBLP, http://dblp.uni-trier.de}
 }
 
 @article{citeulike:461395,

 author = {Needham, Chris  J.  and Bradford, James  R.  and Bulpitt, Andrew  J.  and Westhead, David  R. },
 citeulike-article-id = {461395},
 doi = {10.1038/nbt0106-51},
 issn = {1087-0156},
 journal = {Nature Biotechnology},
 keywords = {ai algorithms computation fun graphs mathematics networks printed},
 number = {1},
 pages = {51--53},
 priority = {3},
 publisher = {Nature Publishing Group},
 title = {{Inference in Bayesian Networks}},
 url = {http://dx.doi.org/10.1038/nbt0106-51},
 volume = {24},
 year = {2006}
 }
 
 @article{kim2003ign,
  title={{Inferring Gene Networks from Time Series Microarray Data using Dynamic Bayesian Networks}},
  author={Kim, S.Y. and Imoto, S. and Miyano, S.},
  journal={Briefings in Bioinformatics},
  volume={4},
  number={3},
  pages={228--235},
  year={2003},
  publisher={Oxford Univ Press}
}

 @Article{sachs02,
 title =	{{Bayesian Network Approach to Cell Signaling Pathway Modeling.}},
 author =	"Karen Sachs and David Gifford and Tommi Jaakkola and Peter Sorger and Douglas A. Lauffenburger",
 journal =	"Sci STKE",
 year = 	"2002",
 number =	"EG10",
 volume =	"148"
 }
 
 @book{534975,
 author = {Judea Pearl},
 title = {{Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference}},
 year = {1988},
 isbn = {1558604790},
 publisher = {Morgan Kaufmann Publishers Inc.},
 address = {San Francisco, CA, USA},
 }


 

@article{1268671,
 author = {Tominaga,, Kazuto and Watanabe,, Tooru and Kobayashi,, Keiji and Nakamura,, Masaki and Kishi,, Koji and Kazuno,, Mitsuyoshi},
 title = {{Modeling Molecular Computing Systems by an Artificial Chemistry---Its Expressive Power and Application}},
 journal = {Artif. Life},
 volume = {13},
 number = {3},
 year = {2007},
 issn = {1064-5462},
 pages = {223--247},
 doi = {http://dx.doi.org/10.1162/artl.2007.13.3.223},
 publisher = {MIT Press},
 address = {Cambridge, MA, USA},
 }


 @book{press-etal-book-88,
 author = {William H. Press and Brian P. Flannery and Saul A. Teukolsky and William T. Vetterling},
 title = {{Numerical Recipes in C}},
 year = {1988},
 publisher = {Cambridge University Press},
 address = {Cambridge, UK},
 }
 
 @Book{fritz,

 author =       {Fritz, John},
 title =        {{Partial Differential Equations}},
 publisher =    {Springer-Verlag},
 year =         1982,
 series =       {Applied Mathematical Sciences},
 address =      {New York, NY},
 edition =      {4th}
 }
 
 @article{lenser2007ten,
  title={{Towards Evolutionary Network Reconstruction Tools for Systems Biology}},
  author={Lenser, T. and Hinze, T. and Ibrahim, B. and Dittrich, P.},
  journal={Lecture Notes in Computer Science},
  volume={4447},
  pages={132--142},
  year={2007},
  publisher={Springer}
}

@article{fontana1994aft,
  title={{“The Arrival of the Fittest”: Toward a Theory of Biological Organization}},
  author={Fontana, W. and Buss, L.W.},
  journal={Bulletin of Mathematical Biology},
  volume={56},
  number={1},
  pages={1--64},
  year={1994},
  publisher={Springer}
}


@article{church1932spf,
     jstor_articletype = {primary_article},
     title = {{A Set of Postulates for the Foundation of Logic}},
     author = {Church, Alonzo},
     journal = {The Annals of Mathematics},
     jstor_issuetitle = {},
     volume = {33},
     number = {2},
     series = {Second Series},
     jstor_formatteddate = {Apr., 1932},
     pages = {346--366},
     url = {http://www.jstor.org/stable/1968337},
     ISSN = {0003486X},
     abstract = {},
     language = {},
     year = {1932},
     publisher = {Annals of Mathematics},    
     copyright = {Copyright Â© 1932 Annals of Mathematics},
    }

 @article{decraene2006msm,
  title={{A Multidisciplinary Survey of Modeling Techniques for Biochemical Networks}},
  author={Decraene, J. and Dittrich, P. and Hinze, T. and Lenser, T. and McMullin, B. and Mitchell, G.},
  journal={Proceedings of the Integrative Post-Genomics (IPG’06), Lyon, France},
  year={2006}
}


@TECHREPORT{esignet41,
  title={{Deliverable number 4.1 Specification of the Properties of Cell Signalling Systems Document Describing Formats for Phenotypic Representation}},
  author={ESIGNET},
   INSTITUTION={University of Jena},
 note={http://esignet.net/dokumente/WP4-D41/},
 TYPE={EU technical report},
  year={2006},
}


@TECHREPORT{esignet31,
  title={{Deliverable number 3.1 Cell Signalling Networks: State of the Art Report}},
  author={ESIGNET},
   INSTITUTION={Dublin City University},
 note={http://esignet.net/dokumente/WP3-D31/},
 TYPE={EU technical report},
  year={2006},
}

 }
 
 
 


@article{decraene2008mae,
author = {J. Decraene and G.G. Mitchell and B. McMullin},
collaboration = {},
title = {{Modeling and Evolving Biochemical Networks: Insights into Communication and Computation from the Biological Domain}},
publisher = {IEE},
year = {2008},
journal = {IET Conference Publications},
volume = {2008},
number = {CP544},
pages = {235-239},
keywords = {biochemical networks; cellular activities; artificial cell signaling networks; evolutionary computation; engineering crosstalking systems},
url = {http://link.aip.org/link/abstract/IEECPS/v2008/iCP544/p235/s1},
doi = {10.1049/cp:20080798}
}


@book{rumbaugh1991oom,
  title={{Object-Oriented Modeling and Design}},
  author={Rumbaugh, J. and Blaha, M. and Premerlani, W. and Eddy, F. and Lorensen, W.},
  year={1991},
  publisher={Prentice-Hall, Inc. Upper Saddle River, NJ, USA}
}

@book{bersini2004ooo,
  title={{La Programmation Orient{\'e}e Objet. Cours et Exercices en UML 2 avec Java 5, C++, Python, PHP 5 et LINQ (4 {\'E}d.)}},
  author={Bersini, H.},
  year={2008},
  publisher={Eyrolles}
}

@article{DBLP:journals/cj/Priami95,

 author    = {Corrado Priami},
 title     = {Stochastic $\pi$-calculus.},
 journal   = {Comput. J.},
 volume    = {38},
 number    = {7},
 year      = {1995},
 pages     = {578-589},
 bibsource = {DBLP, http://dblp.uni-trier.de}
 }
 
 @article{513277,

 author = {Corrado Priami and Aviv Regev and Ehud Shapiro and William Silverman},
 title = {{Application of a Stochastic Name-passing Calculus to Representation and Simulation of Molecular Processes}},
 journal = {Inf. Process. Lett.},
 volume = {80},
 number = {1},
 year = {2001},
 issn = {0020-0190},
 pages = {25--31},
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@article{1480452,
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@article{gabora2008ces,
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@book{kauffman1993oos,
	abstract = {{Stuart Kauffman here presents a brilliant new paradigm for evolutionary biology, one that extends the basic concepts of Darwinian evolution to accommodate recent findings and perspectives from the fields of biology, physics, chemistry and mathematics.  The book drives to the heart of the exciting debate on the origins of life and maintenance of order in complex biological systems.  It focuses on the concept of self-organization: the spontaneous emergence of order that is widely observed throughout nature Kauffman argues that self-organization plays an important role in the Darwinian process of natural selection. Yet until now no systematic effort has been made to incorporate the concept of self-organization into evolutionary theory. The construction requirements which permit complex systems to adapt are poorly understood, as is the extent to which selection itself can yield systems able to adapt more successfully. This book explores these themes.  It shows how complex systems, contrary to expectations, can spontaneously exhibit stunning degrees of order, and how this order, in turn, is essential for understanding the emergence and development of life on Earth.  Topics include the new biotechnology of applied molecular evolution, with its important implications for developing new drugs and vaccines; the balance between order and chaos observed in many naturally occurring systems; new insights concerning the predictive power of statistical mechanics in biology; and other major issues.  Indeed, the approaches investigated here may prove to be the new center around which biological science itself will evolve.  The work is written for all those interested in the cutting edge of research in the life sciences.}},
	author = {Kauffman, Stuart  A. },
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@article{szathmary1997rrf,
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@article{holland1976sse,
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@inproceedings{DecraeneBiosignal09,
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  booktitle = {BIOSIGNALS},
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  pages     = {107-114},
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@proceedings{DBLP:conf/biostec/2009bs,
  editor    = {Pedro Encarna\c{c}{\~a}o and
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  title     = {BIOSIGNALS 2009 - Proceedings of the International Conference
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@article{dittich2007,
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@proceedings{DBLP:conf/cec/2009,
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@inproceedings{DBLP:conf/ecal/McMullinKO07,
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@proceedings{DBLP:conf/ecal/2007,
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  year      = {2007},
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}

@inproceedings{DBLP:conf/cec/Decraene09,
  author    = {James Decraene and
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  title     = {{Crosstalk and the Cooperation of Collectively Autocatalytic Reaction Networks}},
  booktitle = {IEEE Congress on Evolutionary Computation},
  year      = {2009},
  note     = {To appear}
}



@techreport{ALL-06-01,
  author =         {James Decraene},
  title =          {{The Holland Broadcast Language}},
  institution =    {RINCE, Dublin City University},
  number =         {ALL-06-01},
  year =           {2006},
  url=							{http://elm.eeng.dcu.ie/\~{}alife/jd/ALL-06-01/},
  note= 			{http://elm.eeng.dcu.ie/\~{}alife/jd/ALL-06-01/},
}

@book{holland1975ana,
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@book{holland1992ana,
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@conference{cramer1985rag,
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@book{rechenberg1973eot,
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@article{wolkenhauer2007acm,
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@book{fogel2007iec,
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@article{ dittrich-articial,

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 @book{1015.34001,
	abstract = {Exact solutions of differential equations continue to play an important role
in the understanding of many phenomena and processes throughout the natural
sciences in that they can verify the correctness of or estimate errors in
solutions reached by numerical, asymptotic, and approximate analytical
methods. The new edition of this bestselling handbook now contains the exact
solutions to more than 6200 ordinary differential equations. The authors have
made significant enhancements to this edition, including:· An introductory
chapter that describes exact, asymptotic, and approximate analytical methods
for solving ordinary differential equations · The addition of solutions to
more than 1200 nonlinear equations· An improved format that allows for an
expanded table of contents that makes locating equations of interest more
quickly and easily· Expansion of the supplement on special functionsThis
handbook's focus on equations encountered in applications and on equations
that appear simple but prove particularly difficult to integrate make it an
indispensable addition to the arsenals of mathematicians, scientists, and
engineers alike.},
	author = {Polyanin, Andrei  D.  and Zaitsev, Valentin  F. },
	citeulike-article-id = {3976331},
	edition = {2},
	howpublished = {Hardcover},
	isbn = {1584882972},
	month = {October},
	posted-at = {2009-01-29 06:15:48},
	publisher = {Chapman \& Hall/CRC},
	title = {{Handbook of Exact Solutions for Ordinary Differential Equations, Second Edition}},
	url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&amp;path=ASIN/1584882972},
	year = {2002}
}
 

@Book{hand,
 author =       {Zwillinger, D.},
 title =        {{Handbook of Differential Equations}},
 publisher =    "Academic Press",
 year =         1992,
 address =      "San Diego, CA",
 edition =      "2nd"
 }

@article{dittrich2007,
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  publisher={Springer}
}

@article{1182079,
 author = {R. Machn\'{e} and A. Finney and S. M\"{u}ller and J. Lu and S. Widder and C. Flamm},
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 pages = {1406--1407},
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 publisher = {Oxford University Press},
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 }