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===== CST-323: Introduction to Earth System Modelling (INPE Course 2017) =====

  * Professors: Mariane Coutinho, Pedro R. Andrade,[[http://www.dpi.inpe.br/gilberto|Gilberto Câmara]] 
  * Lectures: Mondays and Thursdays, 14h00-16h30, Room 12, 1st floor, CCST building



===== Classes =====
^ ^  Title	                  ^  Models  ^  Scenarios                ^  Concepts  ^  Exercises  |
|1  |Introduction | | | | |
|   |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2017/lecture-introd-2017.ppt|Introduction}}| | | | |
|2  |Modelling 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  |System Dynamics| | | | |
|    |{{http://www.dpi.inpe.br/gilberto/cursos/st-society/lecture-systems-theory.ppt|Systems Theory}}    | | | | |
|    |{{:cst-317:2-system-dynamics.ppt|Systems Dynamics}}     |{{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/Tub.lua|Tub}} (sysdyn) | {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/tub-scenarios.lua|tub-scenarios}} (sysdyn) | Model, Event, Timer, Chart | {{:cst-317:exercise1.pdf|Water in the Dam}} |
|  | {{:cst-317:3-feedbacks.ppt|Feedbacks}} | {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/Coffee.lua|Coffee}}, {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/PopulationGrowth.lua|PopulationGrowth}} (sysdyn) | {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/coffee-scenarios.lua|coffee-scenarios}}, {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/population-scenarios-1.lua|population-scenarios-1}}, {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/population-scenarios-1.lua|population-scenarios-2}} (sysdyn) | Environment, instance of Model | |
|    |{{http://www.dpi.inpe.br/gilberto/cursos/st-society/lecture-mono-lake.ppt|Water Flows in Mono Lake}}   | {{:cst-317:monolake.zip|Mono Lake Code in TerraME}} | | | |
|    |{{http://www.dpi.inpe.br/gilberto/cursos/st-society/lecture-daisyworld.pptx|Daisyworld}}  | {{http://www.dpi.inpe.br/gilberto/cursos/st-society/daisyworld.lua| Daisyworld model}} | | | |
|4 |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:exercise3.pdf|Fire in the Forest}}|
|5| Spatial Models |  |      |             | |
| | {{:cst-317:10-runoff.ppt|Runoff}} | {{https://raw.githubusercontent.com/TerraME/terrame/master/packages/terralib/examples/runoff.lua|Runoff}} (terralib) | | |
| | {{:cst-317:11-geospatial-data.ppt|Geospatial data}} | | | Project, Layer (terralib) | |
| | {{:cst-317:12-deforestation.ppt|Deforestation}}   | {{:cst-317:deforestation.zip|}}| | Trajectory | {{:cst-317:exercise4.pdf|Deforestation}}, {{:cst-317:exercise4.zip|database}}|
|6  |Climate Change Scenarios| | |
|   | {{http://climatemodels.uchicago.edu/kaya/|Kaya Identity}} |  |      || |
|  | {{http://climatemodels.uchicago.edu/slugulator|Methane vs. CO2}} |  | | | |
|7| {{http://climatemodels.uchicago.edu/maps/|Climate models}} | | | |



===== Additional Reading =====

  * {{http://www.leg.ufpr.br/~pedro/final-projects/Wood-08.pdf|Wood, A. J., G. J. Ackland, J. G. Dyke, H. T. P. Williams, and T. M. Lenton (2008), Daisyworld: A review, Rev. Geophys., 46, RG1001}}.
  * W. von Bloh. Daisyworld: a tutorial approach to geophysiological modelling [[http://www.pik-potsdam.de/~bloh/]]
  * {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lenton1998.pdf|Timothy M. Lenton(1998). Gaia and Natural Selection. Nature 394, 439-447 (30 July 1998)}} 

===== 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.

|  | {{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/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/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/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/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. |
| | [[https://en.wikipedia.org/wiki/Belousov–Zhabotinsky_reaction|Belousov–Zhabotinsky reaction]]|
| | 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://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.]] |
|  | 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-
 eld 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.|

===== Papers for Final Projects: Secondary Choices =====

You can also choose from the following papers if you did not find a suitable paper in the above list.

| | {{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://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}}|
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