![Introduction Related Work The calculus Research Questions
Motivation: Study cases
• Climate change risks [TY11]
• Extinction of species in Catalunya [CCM+
10]
• Wildfire risk in Cyprus and Greece [SYF+
07]
• Malaria risk in the Amazon forest [Mai08]](https://image.slidesharecdn.com/spatially-explicit-2012-180901185010/85/Spatially-explicit-individual-based-modeling-4-320.jpg)
![Introduction Related Work The calculus Research Questions
Stochastic Simulation
• Models each component with random behavior
• Spatially-explicit stochastic simulation: [JEU11]
• when the molecules are not homogeneously distributed or
• the time they take to move from where they are to
where they have to react is not the same among all.](https://image.slidesharecdn.com/spatially-explicit-2012-180901185010/85/Spatially-explicit-individual-based-modeling-7-320.jpg)
![Introduction Related Work The calculus Research Questions
Paun’s P Systems
• A P system is defined as a series of membranes
containing chemicals (in finite quantities), catalysts and
rules which determine possible ways in which chemicals
may react with one another to form products. [Pau]
• Rules may also cause chemicals to pass through
membranes or even cause membranes to dissolve.
• A system in which each membrane represents a region
and contains a multiset of objects that communicate
among them.](https://image.slidesharecdn.com/spatially-explicit-2012-180901185010/85/Spatially-explicit-individual-based-modeling-8-320.jpg)
![Introduction Related Work The calculus Research Questions
Process calculi
• Behavioral Hybrid Process Calculus [KS05]
• Continuous Pi-calculus [KS08]
• Stochastic Non-deterministic Timed Concurrent
Constraint (sntcc) [OR05]](https://image.slidesharecdn.com/spatially-explicit-2012-180901185010/85/Spatially-explicit-individual-based-modeling-9-320.jpg)
![Introduction Related Work The calculus Research Questions
Process Algebra with Locations for Population
Systems (PALPS)
• A communicating sequential processes (CSP)-based
process calculus.
• There are individuals, species, locations and a
neighborhood relation, attributes of the locations,
communication channels among the species (e.g.,
reproduction and preying) [AP11].](https://image.slidesharecdn.com/spatially-explicit-2012-180901185010/85/Spatially-explicit-individual-based-modeling-11-320.jpg)
Spatially explicit individual based modeling
- 1. Introduction Related Work The calculus Research Questions Towards extensions to a spatially-explicit process calculus for ecological models Mauricio Toro Berm´udez AVISPA, Pontificia Universidad Javeriana de Cali Seminario de AVISPA November 9th 2012
- 2. Introduction Related Work The calculus Research Questions Outline of the presentation 1. Introduction 2. Related Work 3. The calculus 4. Research questions
- 3. Introduction Related Work The calculus Research Questions Spatially-explicit ecological models • A formalism to model meta-populations • A meta-population is a population of populations • A population is a group of individuals of the same specie that lives in the same place
- 4. Introduction Related Work The calculus Research Questions Motivation: Study cases • Climate change risks [TY11] • Extinction of species in Catalunya [CCM+ 10] • Wildfire risk in Cyprus and Greece [SYF+ 07] • Malaria risk in the Amazon forest [Mai08]
- 5. Introduction Related Work The calculus Research Questions Outline of the presentation 1. Introduction 2. Related Work 3. The calculus 4. Research questions
- 6. Introduction Related Work The calculus Research Questions Chemical reaction simulation • A chemical reaction is a process that results in a change of chemical substances • There are two frameworks to model chemical reactions: • continuous and deterministic (e.g., differential equation modeling) • discrete and stochastic
- 7. Introduction Related Work The calculus Research Questions Stochastic Simulation • Models each component with random behavior • Spatially-explicit stochastic simulation: [JEU11] • when the molecules are not homogeneously distributed or • the time they take to move from where they are to where they have to react is not the same among all.
- 8. Introduction Related Work The calculus Research Questions Paun’s P Systems • A P system is defined as a series of membranes containing chemicals (in finite quantities), catalysts and rules which determine possible ways in which chemicals may react with one another to form products. [Pau] • Rules may also cause chemicals to pass through membranes or even cause membranes to dissolve. • A system in which each membrane represents a region and contains a multiset of objects that communicate among them.
- 9. Introduction Related Work The calculus Research Questions Process calculi • Behavioral Hybrid Process Calculus [KS05] • Continuous Pi-calculus [KS08] • Stochastic Non-deterministic Timed Concurrent Constraint (sntcc) [OR05]
- 10. Introduction Related Work The calculus Research Questions Outline of the presentation 1. Introduction 2. Related Work 3. The calculus 4. Research questions
- 11. Introduction Related Work The calculus Research Questions Process Algebra with Locations for Population Systems (PALPS) • A communicating sequential processes (CSP)-based process calculus. • There are individuals, species, locations and a neighborhood relation, attributes of the locations, communication channels among the species (e.g., reproduction and preying) [AP11].
- 12. Introduction Related Work The calculus Research Questions Process Algebra with Locations for Population Systems (PALPS) IndividualsSpecies Channels Locations Attributes reps preys myLoc Ψ Ψ s s
- 13. Introduction Related Work The calculus Research Questions Operational Semantics of PALPS • Defined on labeled transition systems • Three levels of abstraction • Individual level • Species level • System level
- 14. Introduction Related Work The calculus Research Questions Simulation of PALPS • Philippou et al. proposed to use stochastic simulation to foresee the system behavior
- 15. Introduction Related Work The calculus Research Questions Model Checking of PALPS • Philippou et al. proposed to verify Probabilistic Computational Time Logic (PCTL) properties • An an example, “after a request, a task will be accomplished within 5 minutes with a probability of at least 95%”
- 16. Introduction Related Work The calculus Research Questions Example of a problem modeled with PALPS • A sequence of events in the lifetime of a dispersing species
- 17. Introduction Related Work The calculus Research Questions Example of a problem modeled with PALPS10 A process calculus for spatially-explicit ecological models !#$%'(# )*$%+,-./+' 0-1*'2*3 4+5$*//+' 6#$*%#72 8-%11'(3+#$%'(# 6#$*%#'(3 +#$%'(# 9+':,#$*%#'(3 +#$%'(# 33333;,-2/# 55(%7'/3 ,#$*%#*%# ;,-2/# Figure 1: The sequence of events in the lifetime of a dispersing species
- 18. Introduction Related Work The calculus Research Questions Outline of the presentation 1. Introduction 2. Related Work 3. The calculus 4. Research questions
- 19. Introduction Related Work The calculus Research Questions Research questions 1. Extend with continuous time. Does the model checking problem becomes much more complex and intractable? 2. Extend with dynamic parameters. Is it worth it without continuous time? 3. Translate to and from stochastic simulation models. Translate to and from P systems. What is the advantage of a process calculus over the other approaches? 4. Model checking is an advantage of process calculus over the other approaches. Is there any other?
- 20. Introduction Related Work The calculus Research Questions Research questions 1. Extend with continuous time. Does the model checking problem becomes much more complex and intractable? 2. Extend with dynamic parameters. Is it worth it without continuous time? 3. Translate to and from stochastic simulation models. Translate to and from P systems. What is the advantage of a process calculus over the other approaches? 4. Model checking is an advantage of process calculus over the other approaches. Is there any other?
- 21. Introduction Related Work The calculus Research Questions Research questions 1. Extend with continuous time. Does the model checking problem becomes much more complex and intractable? 2. Extend with dynamic parameters. Is it worth it without continuous time? 3. Translate to and from stochastic simulation models. Translate to and from P systems. What is the advantage of a process calculus over the other approaches? 4. Model checking is an advantage of process calculus over the other approaches. Is there any other?
- 22. Introduction Related Work The calculus Research Questions Research questions 1. Extend with continuous time. Does the model checking problem becomes much more complex and intractable? 2. Extend with dynamic parameters. Is it worth it without continuous time? 3. Translate to and from stochastic simulation models. Translate to and from P systems. What is the advantage of a process calculus over the other approaches? 4. Model checking is an advantage of process calculus over the other approaches. Is there any other?
- 23. Introduction Related Work The calculus Research Questions G R A C I A S. Tienen alguna pregunta?
- 24. Introduction Related Work The calculus Research Questions Margarita Antonaki and Anna Philippou. A process calculus for spatially-explicit ecological models. In Proc. of MeCBIC 2011, 2011. M´onica Cardona, M. Angels Colomer, Antoni Margalida, Ignacio P´erez-Hurtado, Mario J. P´erez-Jim´enez, and Delf´ı Sanuy. A p system based model of an ecosystem of some scavenger birds. In Proceedings of the 10th international conference on Membrane Computing, WMC’09, pages 182–195, Berlin, Heidelberg, 2010. Springer-Verlag. Matthias Jeschke, Roland Ewald, and Adelinde M. Uhrmacher. Exploring the performance of spatial stochastic simulation algorithms. J. Comput. Phys., 230(7):2562–2574, April 2011.
- 25. Introduction Related Work The calculus Research Questions Tomas Krilaviˇcius and Helen Schonenberg. Discrete simulation of behavioural hybrid process calculus. In J.M.T. Romijn, G.P. Smith, and J.C. Pol van de, editors, Fifth International Conference on Integrated Formal Methods, IFM 2005, pages 33–38, Eindhoven, the Netherlands, 2005. Technical University of Eindhoven, Department of Mathematics. KriSch05. Marek Kwiatkowski and Ian Stark. The Continuous pi-Calculus: A Process Algebra for Biochemical Modelling. 2008. N. Maire. Stochastic Simulation Models of Plasmodium Falciparum Malaria Epidemiology and Control. 2008.
- 26. Introduction Related Work The calculus Research Questions C. Olarte and C. Rueda. A Stochastic Non-deterministic Temporal Concurrent Constraint Calculus. In International Conference of the Chilean Computer Science Society (SCCC 2005). IEEE-CS, 2005. Gheorghe Paun. Chapter 1 introduction to membrane computing. Alexandra D. Syphard, Jian Yang, Janet Franklin, Hong S. He, and Jon E. Keeley. Calibrating a forest landscape model to simulate frequent fire in mediterranean-type shrublands. Environ. Model. Softw., 22(11):1641–1653, November 2007. James Thurlow and Winston Yu. A stochastic simulation approach to estimating the economic impacts of climate change in bangladesh.
- 27. Introduction Related Work The calculus Research Questions Working Papers UNU-WIDER Research Paper, World Institute for Development Economic Research (UNU-WIDER), 2011.