The codes associated with each project we finished from SIMIODE (https://www.simiode.org/) written by Ryan Florida, Jeffery Summers, Ben Burton and Puran Nepal.
The complete Python notebook is simiode1.ipynb.
The following codes are separated from simiode1.ipynb and associated with
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M & M Disease Modeling Project (Brian Winkel (2015), "1-017-T-DiseaseSpread," https://www.simiode.org/resources/700.)
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Ebola Modeling: (Jonathan Paynter; Patrick Mugg; Lamar Adams (2016), "6-015-S-CombatingEbolaEpidemic," https://simiode.org/resources/1551.)
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Malaria Control: (David Culver (2016), "1-024-S-MalariaControl," https://simiode.org/resources/1750.)
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Pendulum Modeling: Brian Winkel (2016), "3-080-S-PendulumModeling," https://simiode.org/resources/2643.
The codes are:
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1(a) Bisection and Newton's Methods to do parameter estimation for the growth rate: --- BiNew_RF.ipynb.
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1(b) Simunated Annealing Method to do parameter estimation for the growth rate: --- growth_rate_R_Parameter_Estimation.ipynb.
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1(c) Gradient Descent Method for parameter estimation for the growth rate: --- GradientDescent.py.
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1(d) Codes to generate the disease spread grid without implementing the experiment using M&Ms: --- Sim.py.
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2(a) Ebola Modeling with sliders to see how the changes in the parameters affect the dynamics of susceptible, exposed, infected and recovered populations: --- Ebola.ipynb
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3 Malaria Control: modelling concentration of two particular drugs, Proguanil and Atovaquone, in the blood stream during a given number of days. --- Malaria-Control.ipynb
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4 Pendulum Modeling: ideal pendulum and dampled pendulum. --- PendulumWithOutResistence.ipynb, ResistancePendulum1.ipynb and ResistancePendulum2.ipynb