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E oNet slide 1
E oNetA web based software for e ologi almodelingCaner Kazan �Department of Mathemati sFa ulty of EngineeringUniversity of Georgia
http://e o.engr.uga.edu
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 2
E oNet Model Stru ture
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 3
Detritus −> Microbiota Detritus −> Meiofauna Microbiota −> Meiofauna
Meiofauna −> * Microbiota −> *
* −> Detritus
Flows among ompartments
E oNet Model Stru ture
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 3
Detritus −> Microbiota c=0.15Detritus −> Meiofauna c=0.2Microbiota −> Meiofauna c=0.5
Meiofauna −> * c=.23Microbiota −> * c=.01
* −> Detritus c=10
Flow types and rate oe� ients
E oNet Model Stru ture
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 3
Detritus −> Microbiota c=0.15Detritus −> Meiofauna c=0.2
Microbiota = 50Meiofauna = 10
Microbiota −> Meiofauna c=0.5
Meiofauna −> * c=.23 Microbiota −> * c=.01
* −> Detritus c=10
Detritus = 100
Initial onditions
E oNet Model Stru ture
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 3
# Below is a simple model example
Detritus −> Microbiota c=0.15 # flowsDetritus −> Meiofauna c=0.2 # among
Microbiota = 50Meiofauna = 10
Microbiota −> Meiofauna c=0.5 # compartments
Meiofauna −> * c=.23 # outputsMicrobiota −> * c=.01
* −> Detritus c=10 # Input to Detritus
Detritus = 100 # initial stock values
Comments
E oNet Model Stru ture
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 3
# Below is a simple model example
Detritus −> Microbiota c=0.15 # flowsDetritus −> Meiofauna c=0.2 # among
Microbiota = 50Meiofauna = 10
Microbiota −> Meiofauna c=0.5 # compartments
Meiofauna −> * c=.23 # outputsMicrobiota −> * c=.01
* −> Detritus c=10 # Input to Detritus
Detritus = 100 # initial stock values
Flow type and coefficients Comments
Flows
Initial storage values
E oNet Model Stru ture
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 3
c=0.5, c=.23, c=.01
Detritus −> Meiofauna c=0.2
Microbiota = 50, Meiofauna = 10
Microbiota −> Meiofauna, Meiofauna −> *, Microbiota −> *
Detritus −> Microbiota c=0.15
Detritus = 100 * −> Detritus c=10
Flexibility
What does E oNet do?
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 4
■ Creates a �ow hart of the model
Based on your method of hoi e, it onverts themodel into:An Ordinary Di�erential Equation (ODE)A Sto hasti Di�erential Equation (SDE)A Dis rete Sto hasti Pro ess (Gillespie)Solves the appropriate equations numeri allyPlots the temporal evolution of sto k valuesPerforms e ologi al network analysis
What does E oNet do?
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 4
■ Creates a �ow hart of the model■ Based on your method of hoi e, it onverts themodel into:
◆ An Ordinary Di�erential Equation (ODE)◆ A Sto hasti Di�erential Equation (SDE)◆ A Dis rete Sto hasti Pro ess (Gillespie)
Solves the appropriate equations numeri allyPlots the temporal evolution of sto k valuesPerforms e ologi al network analysis
What does E oNet do?
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 4
■ Creates a �ow hart of the model■ Based on your method of hoi e, it onverts themodel into:
◆ An Ordinary Di�erential Equation (ODE)◆ A Sto hasti Di�erential Equation (SDE)◆ A Dis rete Sto hasti Pro ess (Gillespie)
■ Solves the appropriate equations numeri ally
Plots the temporal evolution of sto k valuesPerforms e ologi al network analysis
What does E oNet do?
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 4
■ Creates a �ow hart of the model■ Based on your method of hoi e, it onverts themodel into:
◆ An Ordinary Di�erential Equation (ODE)◆ A Sto hasti Di�erential Equation (SDE)◆ A Dis rete Sto hasti Pro ess (Gillespie)
■ Solves the appropriate equations numeri ally
■ Plots the temporal evolution of sto k values
Performs e ologi al network analysis
What does E oNet do?
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 4
■ Creates a �ow hart of the model■ Based on your method of hoi e, it onverts themodel into:
◆ An Ordinary Di�erential Equation (ODE)◆ A Sto hasti Di�erential Equation (SDE)◆ A Dis rete Sto hasti Pro ess (Gillespie)
■ Solves the appropriate equations numeri ally
■ Plots the temporal evolution of sto k values
■ Performs e ologi al network analysis
E oNet model format?
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 5
E oNet uses a �exible text format to a ept models.Be ause, it is:
■ Qui k and easy to enter■ Human readable
PortableCan be automated easilyEasy to manipulate
E oNet model format?
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 5
E oNet uses a �exible text format to a ept models.Be ause, it is:
■ Qui k and easy to enter■ Human readable
■ Portable
Can be automated easilyEasy to manipulate
E oNet model format?
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 5
E oNet uses a �exible text format to a ept models.Be ause, it is:
■ Qui k and easy to enter■ Human readable
■ Portable
■ Can be automated easily
Easy to manipulate
E oNet model format?
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 5
E oNet uses a �exible text format to a ept models.Be ause, it is:
■ Qui k and easy to enter■ Human readable
■ Portable
■ Can be automated easily■ Easy to manipulate
E oNet model format?
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 5
E oNet uses a �exible text format to a ept models.Be ause, it is:
■ Qui k and easy to enter■ Human readable
■ Portable
■ Can be automated easily■ Easy to manipulate
What is E oNet made of?
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 6
■ A set of intera ting odes based on:◆ C++ odes: Computing intensive pro esses(simulations)
◆ Matlab odes: Graphing, Statisti al Analysisof simulation outputs◆ Linux/Unix shell s ripts: Intera tion and ommuni ation among separate modules
◆ Awk, Sed and Grep: Parsing of human input
◆ Graphviz: Forming network graphs
◆ CGI: Web interfa e (under development)
What is E oNet made of?
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 6
■ A set of intera ting odes based on:◆ C++ odes: Computing intensive pro esses(simulations)
◆ Matlab odes: Graphing, Statisti al Analysisof simulation outputs◆ Linux/Unix shell s ripts: Intera tion and ommuni ation among separate modules
◆ Awk, Sed and Grep: Parsing of human input
◆ Graphviz: Forming network graphs
◆ CGI: Web interfa e (under development)
What is E oNet made of?
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 6
■ A set of intera ting odes based on:◆ C++ odes: Computing intensive pro esses(simulations)
◆ Matlab odes: Graphing, Statisti al Analysisof simulation outputs◆ Linux/Unix shell s ripts: Intera tion and ommuni ation among separate modules
◆ Awk, Sed and Grep: Parsing of human input
◆ Graphviz: Forming network graphs
◆ CGI: Web interfa e (under development)
What is E oNet made of?
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 6
■ A set of intera ting odes based on:◆ C++ odes: Computing intensive pro esses(simulations)
◆ Matlab odes: Graphing, Statisti al Analysisof simulation outputs◆ Linux/Unix shell s ripts: Intera tion and ommuni ation among separate modules
◆ Awk, Sed and Grep: Parsing of human input
◆ Graphviz: Forming network graphs
◆ CGI: Web interfa e (under development)
What is E oNet made of?
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 6
■ A set of intera ting odes based on:◆ C++ odes: Computing intensive pro esses(simulations)
◆ Matlab odes: Graphing, Statisti al Analysisof simulation outputs◆ Linux/Unix shell s ripts: Intera tion and ommuni ation among separate modules
◆ Awk, Sed and Grep: Parsing of human input
◆ Graphviz: Forming network graphs
◆ CGI: Web interfa e (under development)
What is E oNet made of?
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 6
■ A set of intera ting odes based on:◆ C++ odes: Computing intensive pro esses(simulations)
◆ Matlab odes: Graphing, Statisti al Analysisof simulation outputs◆ Linux/Unix shell s ripts: Intera tion and ommuni ation among separate modules
◆ Awk, Sed and Grep: Parsing of human input
◆ Graphviz: Forming network graphs
◆ CGI: Web interfa e (under development)
Advantages of E oNet
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 7
E oNet is:
■ Combines ODE solution with network analysis
E� ient and fastWeb basedEasy to useFeatures sto hasti solutionsModular and �exible stru ture
Advantages of E oNet
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 7
E oNet is:
■ Combines ODE solution with network analysis■ E� ient and fast
Web basedEasy to useFeatures sto hasti solutionsModular and �exible stru ture
Advantages of E oNet
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 7
E oNet is:
■ Combines ODE solution with network analysis■ E� ient and fast
■ Web based
Easy to useFeatures sto hasti solutionsModular and �exible stru ture
Advantages of E oNet
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 7
E oNet is:
■ Combines ODE solution with network analysis■ E� ient and fast
■ Web based
■ Easy to use
Features sto hasti solutionsModular and �exible stru ture
Advantages of E oNet
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 7
E oNet is:
■ Combines ODE solution with network analysis■ E� ient and fast
■ Web based
■ Easy to use
■ Features sto hasti solutions
Modular and �exible stru ture
Advantages of E oNet
Interfa eModel stru tureWhat E oNet doesE oNet modelformat?What is E oNetmade of?AdvantagesE oNet slide 7
E oNet is:
■ Combines ODE solution with network analysis■ E� ient and fast
■ Web based
■ Easy to use
■ Features sto hasti solutions■ Modular and �exible stru ture
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