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===== CST-323: Introduction to Earth System Modelling/CAP-465: Modelling and Simulation of Earth Systems (INPE Course 2019) =====

  * Professors: Mariane Coutinho, Pedro R. Andrade, [[http://www.dpi.inpe.br/gilberto|Gilberto Câmara]] 
  * Lectures: Mondays and Tuesdays, 9h00-11h30, Room 12, 1st floor, CCST building

===== Software =====

  * [[http://www.terrame.org|TerraME 2.0-RC9]]
  * [[https://studio.zerobrane.com/download?not-this-time|ZeroBrane 1.70]]
  * [[https://github.com/TerraME/terrame/wiki/ZB|How to configure ZeroBrane]]

===== Classes =====
^ ^  Title	                  ^  Models  ^  Scenarios                ^  Concepts  ^  Exercises  |
|1  |Introduction | | | | |
|2  |Programming Basics| | | | |
|   |{{:cst-317:1-lua-for-terrame.ppt|Lua for TerraME}}     | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/code-introduction.zip|Lua scripts}}      | | nil, number, boolean, string, table, function | {{:cst-317:exercicios-lua.pdf|Lua exercises}} |
|3  |{{:cst-317:2-system-dynamics.ppt|Systems Dynamics}}      | {{https://raw.githubusercontent.com/pedro-andrade-inpe/sysdyn/master/lua/Tub.lua|Tub}} (sysdyn) | {{https://raw.githubusercontent.com/pedro-andrade-inpe/sysdyn/master/examples/tub-scenarios.lua|tub-scenarios}} (sysdyn) | Model, Event, Timer, Chart |  |
|4  | {{:cst-317:3-feedbacks.ppt|Feedbacks}} | {{https://raw.githubusercontent.com/pedro-andrade-inpe/sysdyn/master/lua/Coffee.lua|Coffee}}, {{https://raw.githubusercontent.com/pedro-andrade-inpe/sysdyn/master/lua/PopulationGrowth.lua|PopulationGrowth}} (sysdyn) | {{https://raw.githubusercontent.com/pedro-andrade-inpe/sysdyn/master/examples/coffee-scenarios.lua|coffee-scenarios}}, {{https://raw.githubusercontent.com/pedro-andrade-inpe/sysdyn/master/examples/population-scenarios-1.lua|population-scenarios-1}}, {{https://raw.githubusercontent.com/pedro-andrade-inpe/sysdyn/master/examples/population-scenarios-1.lua|population-scenarios-2}} (sysdyn) | Environment, instance of Model | {{:cst-317:exercise1.pdf|Water in the Dam}} |
|5  | {{:cst-317:4-epidemics.ppt|Epidemics}} | {{https://raw.githubusercontent.com/pedro-andrade-inpe/sysdyn/master/lua/SIR.lua|SIR}} (sysdyn) | {{https://raw.githubusercontent.com/pedro-andrade-inpe/sysdyn/master/examples/infection-scenarios-1.lua|infection-scenarios-1}}, {{https://raw.githubusercontent.com/pedro-andrade-inpe/sysdyn/master/examples/infection-scenarios-2.lua|infection-scenarios-2}}, {{https://raw.githubusercontent.com/pedro-andrade-inpe/sysdyn/master/examples/infection-scenarios-3.lua|infection-scenarios-3}} (sysdyn) | | |
|6  | {{:cst-317:6-daisyworld.ppt|Daisyworld}} | {{https://raw.githubusercontent.com/pedro-andrade-inpe/sysdyn/master/lua/Daisyworld.lua|Daisyworld}} (sysdyn) | {{https://raw.githubusercontent.com/pedro-andrade-inpe/calibration/master/examples/daisy-calibration.lua|daisy-calibration}} (calibration)| MultipleRuns (calibration) |
|7 | {{:cst-317:chaos.ppt|Chaos}}           | {{https://raw.githubusercontent.com/pedro-andrade-inpe/sysdyn/master/lua/ChaoticGrowth.lua|ChaoticGrowth}} (sysdyn), {{https://raw.githubusercontent.com/pedro-andrade-inpe/sysdyn/master/lua/Lorenz.lua|Lorenz}} (sysdyn)| | | |
|8 |Celular Automata | | | | |
| | {{:cst-317:8-cellular-automaton.ppt|Cellular Automata}}	              | {{https://raw.githubusercontent.com/pedro-andrade-inpe/ca/master/lua/Life.lua|Life}} (ca)         |      |Cell, CellularSpace, Neighborhood, Map, Random | |
| | {{:cst-317:9-fire-in-the-forest.ppt|Fire in the Forest}}             | {{https://raw.githubusercontent.com/pedro-andrade-inpe/ca/master/lua/Fire.lua|Fire}} (ca) |      |             | {{:cst-317:exercise2.pdf|Fire in the Forest}}|
| | {{:cst-317:10-runoff.ppt|Runoff}} | {{https://raw.githubusercontent.com/TerraME/terrame/master/packages/gis/examples/runoff.lua|Runoff}} (gis) | | |


===== Papers for Final Projects =====

The final project consists of an implementation and discussion of one of the models available
[[http://www.easterbrook.ca/steve/2013/01/simple-climate-models-to-play-with-in-the-classroom/|here]]
or the following papers.


==== System Dynamics ====

|  | [[http://citeseerx.ist.psu.edu/viewdoc/download;jsessionid=CB3EA777DE19841D563DC6241FA916B6?doi=10.1.1.497.9850&rep=rep1&type=pdf|Scherer A. & McLean A., (2002) Mathematical models of vaccination, British Medical Bulletin 2002;62 187-199.]] |
|  | [[http://calculadora2050brasil.epe.gov.br/calculadora.html|Energy scenarios for Brazil (in portuguese)]]|

==== Cellular Automata ====

|  | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Berjak2002.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.dpi.inpe.br/gilberto/cursos/papers/Beauchemina2005.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}}|
| | {{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/Almeida2011.pdf|Almeida, Rodolfo Maduro, and Elbert EN Macau. "Stochastic cellular automata model for wildland fire spread dynamics." Journal of Physics: Conference Series. Vol. 285. No. 1. IOP Publishing, 2011.}}|
| | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Fisch1991.pdf|Fisch, Robert, Janko Gravner, and David Griffeath. "Threshold-range scaling of excitable cellular automata." Statistics and Computing 1.1 (1991): 23-39.}} |
| | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Fisch1992.pdf|Fisch, Robert. "Clustering in the one-dimensional three-color cyclic cellular automaton." The Annals of Probability (1992): 1528-1548.}} |
| | [[https://qlfiles.net/the-ql-files/next-nearest-neighbors-cellular-automata/|Li, Wentian. "Complex patterns generated by next nearest neighbors cellular automata." Computers & Graphics 13.4 (1989): 531-537.]] |
| | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Chate1990.pdf|Chate, H. & Manneville, P. (1990). Criticality in cellular automata. Physica D (45), 122-135.}}|
| | Li, W., Packard, N., & Langton, C. (1990). Transition Phenomena in Cellular Automata Rule Space. Physica D (45), 77-94. |
| | Colasanti, R. L., R. Hunt, and L. Watrud. "A simple cellular automaton model for high-level vegetation dynamics." Ecological Modelling 203.3 (2007): 363-374.|
| | {{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://pdf.blucher.com.br.s3-sa-east-1.amazonaws.com/designproceedings/sigradi2016/450.pdf| Araujo and Celani (20166), Exploring Weaire-Phelan through Cellular Automata: A proposal for a structural variance-producing engine}}|
|  | [[http://link.aps.org/pdf/10.1103/PhysRevE.58.1425|Rickert, M., Nagel, K., Schreckenberg, M. and Latour, A., 1996. Two lane traffic simulations using cellular automata. Physica A: Statistical Mechanics and its Applications, 231(4), pp.534-550.]]|
|  | [[https://pdfs.semanticscholar.org/a522/5a5633d0ce89c913a65c2e6cde72f808e95f.pdf|White, R. and Engelen, G., 1993. Cellular automata and fractal urban form: a cellular modelling approach to the evolution of urban land-use patterns. Environment and planning A, 25(8), pp.1175-1199.]] |
|  | [[ https://www.sciencedirect.com/science/article/pii/S0169204602002189| Barredo, J.I., Kasanko, M., McCormick, N. and Lavalle, C., 2003. Modelling dynamic spatial processes:  simulation of urban future scenarios through cellular automata. Landscape and urban planning, 64(3), pp.145-160.]]|
|  | [[ http://www.academia.edu/download/30249270/m283xl03.pdf| Karafyllidis, I. and Thanailakis, A., 1997. A model for predicting forest fire spreading using cellular automata. Ecological Modelling, 99(1), pp.87-97.]]|
|  | [[ http://search.proquest.com/openview/6fc409331fb6e6f5a21e4fc783349e7c/1.pdf?pq-origsite=gscholar&cbl=1456339| Ermentrout, G.B. and Edelstein-Keshet, L., 1993. Cellular automata approaches to biological modeling. Journal of theoretical Biology, 160(1), pp.97-133.]]|
|  | [[ https://www.sciencedirect.com/science/article/pii/S0022519303002443| Alarcón, T., Byrne, H.M. and Maini, P.K., 2003. A cellular automaton model for tumour growth in inhomogeneous environment. Journal of theoretical biology, 225(2), pp.257-274.]]|
|  | [[https://www.sciencedirect.com/science/article/pii/S0378437107006085 | Yuan, W. and Tan, K.H., 2007. An evacuation model using cellular automata. Physica A: Statistical Mechanics and its Applications, 384(2), pp.549-566.]]|
| | [[ http://www.bioinfo.de/isb/2002020035/main.html | Dormann, S. and Deutsch, A., 2002. Modeling of self-organized avascular tumor growth with a hybrid cellular automaton. In silico biology, 2(3), pp.393-406.]]|
| | [[https://pdfs.semanticscholar.org/4f78/2bcb7bf2c0d4e1a210a41b80a4f664efc9f8.pdf|Bersini, H. and Detours, V., 1994, July. Asynchrony induces stability in cellular automata based models. In Artificial Life IV (pp. 382-387). MIT Press, MA.]]|

==== Agent-based Modeling ====

| | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Medeiros2011.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.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).}}|
| | {{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.}}|
|  | Pe'er et al. Virtual Corridors for Conservation Management, Conservation Biology (2005): 1997–2003 |
|  | Garcia et al. Predicting evolution of insect resistance to transgenic crops in within field refuge configurations, based on larval movement. Ecol. Complex. 28, 94–103 (2016).|
|  | Malaquias et al. Larval Dispersal of Spodoptera frugiperda Strains on Bt Cotton: A Model for Understanding Resistance Evolution and Consequences for its Management. Scientific reports. 2017 Nov 23;7(1):16109.|
|  | Brown, C.; Bakam, I.; Smith. P.; Matthews, R.B., (2016) An agent-based modelling approach to evaluate factors influencing bioenergy crop adoption in north-east Scotland., Global Change Biology Bioenergy, 8, 226-244.|
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