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--- cst-317:classes2014 [2014/07/10 18:16]
gilberto
+++ cst-317:classes2014 [2014/09/10 11:03]
gilberto [Software Description]
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 Students should read the TerraME EMS paper first, to get a sense of the language. Then they should read the Lua papers, to learn about programming in Lua.
-\\
+Please also install the {{http://www.dpi.inpe.br/gilberto/terrame/contrib/terrameaddons.zip|terrame_addons}} and the {{http://www.dpi.inpe.br/gilberto/terrame/contrib/viewer.zip|viewer}} package.
+\\
 ===== Classes =====
@@ Line 34: / Line 35: @@
 |4   |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-feedbacks.ppt|Feedbacks}}                       |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-feedbacks.zip|Feedbacks}}          |                                                | |
 |5  | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-epidemics.ppt|Epidemics}}                       |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-epidemics.zip|Epidemics}}          |                                                 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-epidemics.pdf|Epidemics scenarios}}|
-|6 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-resources.ppt| Renewable Resources }}                       | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-resources.zip|Mono Lake Example}}         |          |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-resources.pdf|Renewable Resources}} |
+|6 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-mono-lake.ppt| Renewable Resources }}                       | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-monolake.zip|Mono Lake Example}}         |          |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-resources.pdf|Renewable Resources}} |
 |7 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-daisyworld.ppt|Daisyworld}}              | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-daisyworld.zip|Daisyworld model}}      |                               | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/exercise-daisyworld.pdf| Daisyworld}} |
 |8 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lecture-predator-prey.ppt|Ecological Models}}              | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-predator-prey.zip|Predator Prey Models}}      |                               | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-predator-prey.pdf| Fitting Predator Prey Models}} |
-|9 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-cellular-automaton.ppt|Cellular Automaton}}	              | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lifemodel.lua|Game of Life}}	              |CellularSpace, Neighborhood, Legend | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-cellular-automata.pdf|Variations on the Game of Life}}|
+|9 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-cellular-automata.ppt|Cellular Automata}}	              | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lifemodel.lua|Game of Life}}	              |CellularSpace, Neighborhood, Legend | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-cellular-automata.pdf|Variations on the Game of Life}}|
 |9a| {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-fire-in-the-forest.ppt|Fire in the Forest (CA example)}}             | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-fire-in-the-forest.zip|Fire in the forest}}|                  | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-fire-in-the-forest.pdf|Fire Scenarios}}|
 |10| {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-hydrological-model.ppt|Hydrological Models}}   | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/data-cabeca_de_boi-mdb.zip|Database}}, {{http://www.dpi.inpe.br/terraview/dow/terraView420.exe|TerraView}}, {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-runoff.zip|Source code}}|                                            | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-hydro-models.pdf|Hydrological Modelling}} |
@@ Line 43: / Line 44: @@
 |11a | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-deforestation-2-database.ppt|Deforestation-part2}}     | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/data-amazonia.zip|Deforestation data}}  |                             | |
 |11b | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-deforestation-3-modelling.ppt|Deforestation-part3}}     | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/amazonia-database.zip|Databases}}, {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-deforestation.zip|Scripts}}  | Trajectory                            | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-deforestation.pdf|Deforestation Model}} + {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-modelling-deforestation.zip|Scripts}}|
-|12 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-agent-based-modelling.ppt|Agent-based modelling}}    | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-segregation-model.zip|SegregationModel}}|       Agent, Society      | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/exercise-segregation.pdf| Segregation Models}} |
+|12 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-agent-based-modelling.ppt|Agent-based modelling}}    | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-butterfly.zip|ButterflyModel}}|       Agent, Society      | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-segregation.pdf| Segregation Models}} |
+|  |     | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-barros-model.zip|BarrosModel}}|         |  |
 |13 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-game-theory.ppt|Game Theory}}             | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-game-theory.zip|Prisioner's Dilemma}}     |                   | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-game-theory.pdf| Variations on Prisioner's Dilemma}} |
 |14 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lecture-cooperation.ppt|Evolution of Cooperation}}              |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-cooperation.zip|Code Evolution of Cooperation}}     |            | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/exercise-evolution-cooperation.pdf| Cooperation Models}} |
 \\
 ===== Additional Reading =====
@@ Line 60: / Line 61: @@
 The final project consists of an implementation and discussion of one of the following papers.
-| Christiane e Anahi | {{http://www.leg.ufpr.br/~pedro/final-projects/Balzter-97.pdf|H. Balzter, P. W. Braun, W. Köhler (1998) Cellular automata models for vegetation dynamics. Ecological Modelling 107(2-3):113-125}}|
+|  | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Balzter1998.pdf|H. Balzter, P. W. Braun, W. Köhler (1998) Cellular automata models for vegetation dynamics. Ecological Modelling 107(2-3):113-125}}|
-|  | {{http://www.leg.ufpr.br/~pedro/final-projects/Silvertown-92.pdf|J. Silvertown, S. Holtier, J. Johnson and P. Dale (1992) Cellular Automaton Models of Interspecific Competition for Space-The Effect of Pattern on Process. Journal of Ecology, 80(3):527-533}}|
+|  | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Silvertown-92.pdf|J. Silvertown, S. Holtier, J. Johnson and P. Dale (1992) Cellular Automaton Models of Interspecific Competition for Space-The Effect of Pattern on Process. Journal of Ecology, 80(3):527-533}}|
-| Felipe | {{http://www.leg.ufpr.br/~pedro/final-projects/Chase-91.pdf|Chase, C. (1992) Fluvial landsculpting and the fractal dimension of topography. Geomorphology, 5(1-2):39-57.}}|
+|  | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Berjak-01.pdf|S. G. Berjak,  J. W. Hearne (2002) An improved cellular automaton model for simulating fire in a spatially heterogeneous Savanna system. Ecological Modelling 148(2):133–15}}|
-|  | {{http://www.leg.ufpr.br/~pedro/final-projects/Berjak-01.pdf|S. G. Berjak,  J. W. Hearne (2002) An improved cellular automaton model for simulating fire in a spatially heterogeneous Savanna system. Ecological Modelling 148(2):133–15}}|
+|Marcos Sanches, Diego Jatobá  | {{http://www.dpi.inpe.br/gilberto/cursos/papers//Dunkerley-96.pdf|D. L. Dunkerley (1997) Banded vegetation: development under uniform rainfall from a simple cellular automaton model. Plant Ecology 129(2):103-111}}|
-|  | {{http://www.leg.ufpr.br/~pedro/final-projects/Dunkerley-96.pdf|D. L. Dunkerley (1997) Banded vegetation: development under uniform rainfall from a simple cellular automaton model. Plant Ecology 129(2):103-111}}|
+|  | {{http://www.dpi.inpe.br/gilberto/cursos/papers//Dunkerley-96-b.pdf|D.L Dunkerley (1997) Banded vegetation: survival under drought and grazing pressure based on a simple cellular automaton model. Journal of Arid Environments 35(3):419–428}}|
-|  | {{http://www.leg.ufpr.br/~pedro/final-projects/Dunkerley-96-b.pdf|D.L Dunkerley (1997) Banded vegetation: survival under drought and grazing pressure based on a simple cellular automaton model. Journal of Arid Environments 35(3):419–428}}|
+| | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Sirakoulis-00.pdf|G.Ch Sirakoulis, I. Karafyllidis, A. Thanailakis (2000) A cellular automaton model for the effects of population movement and vaccination on epidemic propagation. Ecological Modelling 133(3): 209–223}}|
-|Jaidson e Rafael  | {{http://www.leg.ufpr.br/~pedro/final-projects/Sirakoulis-00.pdf|G.Ch Sirakoulis, I. Karafyllidis, A. Thanailakis (2000) A cellular automaton model for the effects of population movement and vaccination on epidemic propagation. Ecological Modelling 133(3): 209–223}}|
+|  | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Beauchemina-05.pdf|C. Beauchemina, J. Samuelb, J. Tuszynskia (2005) A simple cellular automaton model for influenza A viral infections. Journal of Theoretical Biology 232(2) 223–234}}|
-|Ana Gabriela e Lucinéia  | {{http://www.leg.ufpr.br/~pedro/final-projects/Beauchemina-05.pdf|C. Beauchemina, J. Samuelb, J. Tuszynskia (2005) A simple cellular automaton model for influenza A viral infections. Journal of Theoretical Biology 232(2) 223–234}}|
+|Phillip Edson, Raquel Melo | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Medeiros-11.pdf|Medeiros, L. C., Castilho, C. A. R., Braga, C., de Souza, W. V., Regis, L., Monteiro, A. M. V. (2011). Modeling the dynamic transmission of dengue fever: investigating disease persistence. PLOS neglected tropical diseases, 5(1), e942.}}|
-| | {{http://www.leg.ufpr.br/~pedro/final-projects/Medeiros-11.pdf|Medeiros, L. C., Castilho, C. A. R., Braga, C., de Souza, W. V., Regis, L., Monteiro, A. M. V. (2011). Modeling the dynamic transmission of dengue fever: investigating disease persistence. PLOS neglected tropical diseases, 5(1), e942.}}|
+| | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Nakanishi-90.pdf|H. Nakanishi (1990) Cellular-automaton model of earthquakes with deterministic dynamics. Phys. Rev. A 41:7086–7089}}|
-|Carla e Ian | {{http://www.leg.ufpr.br/~pedro/final-projects/Avolio-00.pdf|M.V. Avolio, S. Gregorio, F. Mantovani, A. Pasuto, R. Rongo, S. Silvano, W. Spataro (2000) Simulation of the 1992 Tessina landslide by a cellular automata model and future hazard scenarios. International Journal of Applied Earth Observation and Geoinformation 2(1):41–50}}|
+|Raquel Carvalho | {{http://www.hks.harvard.edu/netgov/files/fellows/onnela_j/papers/A7.pdf| R. Toivonen, J. Onnela, J. Saramaki, J. Hyvonen, K. Kaski (2006) A model for social networks. Physica A: Statistical Mechanics and its Applications 371(2):851–860}}|
-| Sandro e Lira | {{http://www.leg.ufpr.br/~pedro/final-projects/Nakanishi-90.pdf|H. Nakanishi (1990) Cellular-automaton model of earthquakes with deterministic dynamics. Phys. Rev. A 41:7086–7089}}|
+|  | {{http://www.dpi.inpe.br/gilberto/cursos/papers//joana_barros.pdf|Barros, J. Urban Growth in Latin American Cities. PhD thesis, CASA/UCL}} |
-| | {{http://www.hks.harvard.edu/netgov/files/fellows/onnela_j/papers/A7.pdf| R. Toivonen, J. Onnela, J. Saramaki, J. Hyvonen, K. Kaski (2006) A model for social networks. Physica A: Statistical Mechanics and its Applications 371(2):851–860}}|
+| Iane | Cycles in Predator and Prey Populations, Chapter 20 of A. Ford, Modeling the Environment|
-|  | {{http://www.leg.ufpr.br/~pedro/final-projects/joana_barros.pdf|Barros, J. Urban Growth in Latin American Cities. PhD thesis, CASA/UCL}} |
+|  | {{http://www.dpi.inpe.br/gilberto/cursos/papers/gas_book_chap3.pdf|Sex, Culture and Conflict in SugarScape}}. From J Epstein, R. Axtell, Growing Artificial Societies: Social Science from the Bottom Up. MIT Press, 1996.|
-| Lis e Ana Paula | Cycles in Predator and Prey Populations, Chapter 20 of A. Ford, Modeling the Environment|
+|  | {{http://www.dpi.inpe.br/gilberto/cursos/papers/gas_book_chap4.pdf|Trade in SugarScape}}. From J Epstein, R. Axtell, Growing Artificial Societies: Social Science from the Bottom Up. MIT Press, 1996.|
+|  | {{http://www.openabm.org/model/3163/version/2/view|S Bergin (2012). Torsten Hägerstrand’s Spatial Innovation Diffusion Model. Available in CoMSES Computational Model Library.}}|
+|  | {{http://jasss.soc.surrey.ac.uk/16/4/11.html|S Heckbert (2013). MayaSim: An agent-based model of the ancient Maya social-ecological system.}}{{http://www.openabm.org/model/3063/version/4/view| Available in CoMSES Computational Model Library.}}|
+| |{{http://www.openabm.org/model/3705/version/2/view| R Axelrod (1997). “The dissemination of culture - A model with local convergence and global polarization.” Journal of Conflict Resolution 41: 203-226.Replicated in CoMSES Computational Model Library.}}|
+| | {{http://www.openabm.org/model/3377/version/1/view|J Pepper and B Smuts (2000). The evolution of cooperation in an ecological context: an agent-based model. Replicated in CoMSES Computational Model Library.}}|
+|  | {{http://www.openabm.org/model/3890/version/2/view|K Kahn (2013) A model of the Spanish Flu Pandemic. Available in CoMSES Computational Model Library.}}|
+| | {{http://www.openabm.org/model/3051/version/1/view|Schindler J (2012) A simple Multi-Agent System of the Tragedy Of the Commons. Available in CoMSES Computational Model Library.}}|
+| | {{http://www.openabm.org/model/2762/version/1/view| A K Knittel, R Riolo and R Snow (2011). Development and evaluation of an agent-based model of sexual partnership. Adaptive Behavior (available at CoMSES Computational Model Library.}}|.
+| | {{http://www.openabm.org/model/2274/version/2/view| M Janssen and N.D. Rollins (2012). Evolution of cooperation in asymmetric commons dilemmas. Journal of Economic Behavior and Organization, 81: 220-229. Available in CoMSES Computational Model Library).}}|
+|Marcio, Eduardo | {{http://www.openabm.org/model/2222/version/2/view|Axtell, Epstein, et al. (2002) Population Growth and Collapse in a Multi-Agent Model of the Kayenta Anasazi in Long House Valley. PNAS 99(3): 7275-7279.  Replicated in M Janssen and available in CoMSES Computational Model Library.}}|
+| | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Bandini2007.pdf|S Bandini, F Celada, S Manzoni, G Vizzari (2007). Modelling the immune system: the case of situated cellular agents, Natural Computing, 6(1):19-32.}}|
+| | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Yassemi2008.pdf|S. Yassemi, S. Dragićevića, M. Schmidt(2008), Design and implementation of an integrated GIS-based cellular automata model to characterize forest fire behaviour
+, Ecological Modelling, 210(1–2), 71–84}}|
+|  | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Sirakoulis2000.pdf|G.Ch Sirakoulis, I. Karafyllidis, A. Thanailakis (2000) A cellular automaton model for the effects of population movement and vaccination on epidemic propagation. Ecological Modelling 133(3): 209–223}}|
+| | {{http://www.dpi.inpe.br/gilberto/cursos/papers/White2007.pdf|S. Hoya White, A. Martín del Rey, G. Rodríguez Sánchez(2007), Modeling epidemics using cellular automata. Applied Mathematics and Computation, 186(1):193-202}}|
+| | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Feitosa2012.pdf| F. Feitosa, A.M. Monteiro, Urban Conventions and Residential Location Choice. CAMUSS Conference (Cellular Automata Modeling forUrban and Spatial Systems 2012)}}|

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