Process algebra-based computational tools in ecological modelling

Abstract Ecological systems and processes are inherently variable. The multiplicity of interacting processes and the variety of components call for multi-level, integrative models that keep track of stochasticity and quantify its consequences. Mathematics and physics already helped biologists a lot, but the composability feature of process algebra-based computational tools may provide additional help in modelling interacting stochastic processes. Compositional models can be built in a modular way, and can be easily standardized and evaluated rigorously. Following initial applications in systems biology, the concepts of parallelism and concurrency can also be of key importance to future systems ecology. We provide an overview of process algebra-based approaches in ecology, discuss the perspectives of this research line and provide a toy and a real example for illustration.

[1]  Paola Lecca,et al.  Identifying key species in ecosystems with stochastic sensitivity analysis , 2011 .

[2]  M. Pascual,et al.  Ecological networks : Linking structure to dynamics in food webs , 2006 .

[3]  C. S. Holling.  Understanding the Complexity of Economic, Ecological, and Social Systems , 2001, Ecosystems.

[4]  Lev R Ginzburg,et al.  Rules of thumb for judging ecological theories. , 2004, Trends in ecology & evolution.

[5]  D. Doak,et al.  The Keystone-Species Concept in Ecology and ConservationManagement and policy must explicitly consider the complexity of interactions in natural systems , 1993 .

[6]  B. Enquist,et al.  Rebuilding community ecology from functional traits. , 2006, Trends in ecology & evolution.

[7]  Neo D. Martinez,et al.  Scaling up keystone effects from simple to complex ecological networks , 2005 .

[8]  M. Loreau.  Linking biodiversity and ecosystems: towards a unifying ecological theory , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[9]  Marten Scheffer,et al.  Super-individuals a simple solution for modelling large populations on an individual basis , 1995 .

[10]  G. Polis,et al.  Food webs: integration of patterns and dynamics , 1997 .

[11]  Terrie M. Williams,et al.  KILLER APPETITES: ASSESSING THE ROLE OF PREDATORS IN ECOLOGICAL COMMUNITIES , 2004 .

[12]  Toshinori Okuyama,et al.  Local interactions between predators and prey call into question commonly used functional responses , 2009 .

[13]  G. Belovsky.  Food Plant Selection by a Generalist Herbivore: The Moose , 1981 .

[14]  Thomas A. Okey,et al.  Shifted community states in four marine ecosystems : some potential mechanisms , 2004 .

[15]  J. Stinchcombe,et al.  An emerging synthesis between community ecology and evolutionary biology. , 2007, Trends in ecology & evolution.

[16]  Nigel R. Franks,et al.  Task allocation in ant colonies within variable environments (A study of temporal polyethism: Experimental) , 1993 .

[17]  L. Ginzburg,et al.  The nature of predation: prey dependent, ratio dependent or neither? , 2000, Trends in ecology & evolution.

[18]  Ádám Kun,et al.  THE EFFECT OF CLONAL INTEGRATION ON PLANT COMPETITION FOR MOSAIC HABITAT SPACE , 2000 .

[19]  Jurek Kolasa,et al.  Complexity, system integration, and susceptibility to change: Biodiversity connection , 2005 .

[20]  Carron Shankland,et al.  Developing the Use of Process Algebra in the Derivation and Analysis of Mathematical Models of Infectious Disease , 2003, EUROCAST.

[21]  Corrado Priami,et al.  Algorithmic systems biology , 2009, CACM.

[22]  A. Seth.  The ecology of action selection: insights from artificial life , 2007, Philosophical Transactions of the Royal Society B: Biological Sciences.

[23]  Enn Tyugu,et al.  Eco-logic: Logic-based approaches to ecological modelling : D Robertson, A Bundy, R Muetzelfeldt, M Haggith and M Uschold , 1992, Knowledge-Based Systems.

[24]  S. Levin,et al.  Mathematical and Computational Challenges in Population Biology and Ecosystems Science , 1997, Science.

[25]  B. Ebenman,et al.  Using community viability analysis to identify fragile systems and keystone species. , 2005, Trends in ecology & evolution.

[26]  D. Gillespie.  Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[27]  Anja Gronewold,et al.  Event-based modelling of ecological systems with asynchronous cellular automata , 1998 .

[28]  R. James,et al.  Tradeoffs and the evolution of thermal reaction norms , 2003 .

[29]  D J Sumpter,et al.  Ants and agents: A process algebra approach to modelling ant colony behaviour , 2001, Bulletin of mathematical biology.

[30]  S. Levin.  Ecosystems and the Biosphere as Complex Adaptive Systems , 1998, Ecosystems.

[31]  F. Clements.  Scientific Books: Plant Succession. An Analysis of the Development of Vegetation , 2009 .

[32]  Carron Shankland,et al.  From Individuals to Populations: A Symbolic Process Algebra Approach to Epidemiology , 2009, Math. Comput. Sci..

[33]  Peter C de Ruiter and Volkmar Wolters.  DYNAMIC FOOD WEBS: MULTISPECIES ASSEMBLAGES, ECOSYSTEM DEVELOPMENT, AND ENVIRONMENTAL CHANGE , 2005 .

[34]  Corrado Priami,et al.  The BlenX Language: A Tutorial , 2008, SFM.

[35]  J. Thompson,et al.  VARIATION IN INTERSPECIFIC INTERACTIONS , 1988 .

[36]  Corrado Priami,et al.  Modelling the dynamics of biosystems , 2004, Briefings Bioinform..

[37]  A. Houston,et al.  Integrating function and mechanism. , 2009, Trends in ecology & evolution.

[38]  O P Judson,et al.  The rise of the individual-based model in ecology. , 1994, Trends in ecology & evolution.

[39]  D. DeAngelis,et al.  Individual-Based Models and Approaches in Ecology , 1992 .

[40]  J. Dunne,et al.  Stochastic ecological network occupancy (SENO) models: a new tool for modeling ecological networks across spatial scales , 2010, Theoretical Ecology.

[41]  Barbara Drossel,et al.  Models of Food-Web Evolution , 2006 .

[42]  Axel Kowald,et al.  Systems Biology in Practice: Concepts, Implementation and Application , 2005 .

[43]  John D. Stevens,et al.  The effects of fishing on sharks, rays, and chimaeras (chondrichthyans), and the implications for marine ecosystems , 2000 .

[44]  Daniel Pauly,et al.  Trophic Mass-Balance Model of Alaska's Prince William Sound Ecosystem, for the Post-Spill Period 1994-1996 , 1999 .

[45]  Craig R Powell,et al.  The effects of stochastic population dynamics on food web structure. , 2008, Journal of theoretical biology.

[46]  M. Bertness,et al.  Positive interactions in communities. , 1994, Trends in ecology & evolution.

[47]  D S Broomhead,et al.  Shape and dynamics of thermoregulating honey bee clusters. , 2000, Journal of theoretical biology.

[48]  N. Stenseth,et al.  Cycles and trends in cod populations. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[49]  N. Franks,et al.  Social resilience in individual worker ants and its role in division of labour , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[50]  Steven F. Railsback,et al.  Individual-based modeling and ecology , 2005 .

[51]  Jennifer A. Dunne,et al.  The Network Structure of Food Webs , 2005 .

[52]  Corrado Priami,et al.  Application of a stochastic name-passing calculus to representation and simulation of molecular processes , 2001, Inf. Process. Lett..

[53]  Michel Loreau,et al.  Parallel ecological networks in ecosystems , 2009, Philosophical Transactions of the Royal Society B: Biological Sciences.

[54]  B. C. Patten,et al.  Throughflow analysis: A stochastic approach , 2009 .

[55]  Jane Hillston,et al.  Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA , 2008, Theor. Comput. Sci..

[56]  Neo D. Martinez,et al.  Network structure and biodiversity loss in food webs: robustness increases with connectance , 2002, Ecology Letters.

[57]  D. DeAngelis,et al.  Individual-based modeling of ecological and evolutionary processes , 2005 .

[58]  S. Pimm.  The Balance of Nature?: Ecological Issues in the Conservation of Species and Communities , 1992 .

[59]  D. Roff.  Evolutionary Quantitative Genetics , 1997, Springer US.

[60]  Chris Tofts.  Algorithms for task allocation in ants. (A study of temporal polyethism: Theory) , 1993 .

[61]  D. Sumpter,et al.  The dynamics of virus epidemics in Varroa -infested honey bee colonies , 2004 .

[62]  Paolo Milazzo,et al.  The Calculus of Looping Sequences , 2008, SFM.

[63]  Thomas Stützle,et al.  Ant Colony Optimization Theory , 2004 .

[64]  H. Gleason.  The individualistic concept of the plant association , 1926 .

[65]  Ricard V. Solé,et al.  Complexity and fragility in ecological networks , 2000, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[66]  F. Berkes.  Rethinking Community‐Based Conservation , 2004 .

[67]  D S Broomhead,et al.  Relating individual behaviour to population dynamics , 2001, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[68]  R. J. Pool,et al.  Plant Succession. An Analysis of the Development of Vegetation , 1917 .

[69]  D. DeAngelis,et al.  New Computer Models Unify Ecological TheoryComputer simulations show that many ecological patterns can be explained by interactions among individual organisms , 1988 .

[70]  James S Clark,et al.  Beyond neutral science. , 2009, Trends in ecology & evolution.

[71]  F. Ayala,et al.  Complexity in Ecology and Conservation: Mathematical, Statistical, and Computational Challenges , 2005 .

[72]  Birgit Müller,et al.  A standard protocol for describing individual-based and agent-based models , 2006 .

[73]  P. Yodzis,et al.  Must top predators be culled for the sake of fisheries? , 2001, Trends in ecology & evolution.

[74]  Mercedes Pascual,et al.  Computational Ecology: From the Complex to the Simple and Back , 2005, PLoS Comput. Biol..

[75]  Corrado Priami,et al.  Evolving BlenX programs to simulate the evolution of biological networks , 2008, Theor. Comput. Sci..

[76]  R. Lande.  Genetics and demography in biological conservation. , 1988, Science.

[77]  Maria Luisa Guerriero,et al.  Modelling Biological Compartments in Bio-PEPA , 2008, MeCBIC.

[78]  J. Jeffers,et al.  Theoretical Studies of Ecosystems: The Network Perspective , 2009 .

[79]  Uta Berger,et al.  Pattern-Oriented Modeling of Agent-Based Complex Systems: Lessons from Ecology , 2005, Science.

[80]  David J. Mladenoff,et al.  Increasing the reliability of ecological models using modern software engineering techniques , 2010 .

[81]  Ernest W. Tollner,et al.  Cycling in ecosystems: An individual based approach , 2009 .