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