IGEM:IMPERIAL/2006/project/Oscillator/project browser/Predator Construct: Difference between revisions

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!height="25pt" width="80pt"| Super Parts
!height="25pt" width="80pt"| Super Parts
!colspan="2" | [[IGEM:IMPERIAL/2006/project/Oscillator/project browser/Full_System | Molecular Prey-Predator Oscillator]]
!colspan="2" | [[IGEM:IMPERIAL/2006/project/Oscillator/project browser/Full_System | Molecular Prey-Predator Oscillator]]
|- style="background:#FF9966"
|-  
!height="50" width="80pt"|Actual Part
! style="background:#FF9966" height="50" width="80pt"|Actual Part
!colspan="2"| Logo of the Part
!colspan="2"| [[Image:J37036 parts pic.PNG|300px]]
|- style="background:#CCCCFF"
|- style="background:#CCCCFF"
!height="25pt" width="80pt"|Sub Parts
!height="25pt" width="80pt"|Sub Parts
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==Motivations==
==Motivations==
*This part is driving the '''molecular''' events associated with the '''Predator''' in the [[IGEM:IMPERIAL/2006/project/Oscillator/Modelling/LV|Lotka-Volterra model]].  
*This part is driving the '''molecular''' events associated with the '''Predator''' in the '''[[IGEM:IMPERIAL/2006/project/Oscillator/Theoretical_Analyses/2D_Model1|Lotka-Volterra model]]'''.  
*This part is supposed to interface with the [[IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Prey_Construct|'''prey-construct''']].
*This part has to interface with the [[IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Prey_Construct|'''Prey-construct''']].
*To satify the Lotka-Volterra dynamic of the predator, this part has to fullfil 3 properties:
*To satify the Lotka-Volterra dynamic of the predator, this part has to fulfill 3 properties:
**'''Promote the growth of the predator-molecule''' according to the prey and predator populations.
**'''Promote the growth of the predator-molecule''' according to the prey and predator populations.
**'''Kill the prey-molecule''' according to the population of preys and predators
**'''Kill the prey-molecule''' according to the population of preys and predators
**enable the natural '''death of the predator-molecules'''
**Enable the natural '''death of the predator-molecule'''


==Part interface==
==Part interface==
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! style="background:#66CC99"| INPUTS !!style="background:#FF3333"| OUTPUTS  
! style="background:#66CC99"| INPUTS !!style="background:#FF3333"| OUTPUTS  
|-
|-
| Prey  || Predator growth
| rowspan = "2" | Prey molecule || Prey molecule
|-
|rowspan = "2" | Predator  || Prey killing
|-
|-
| Predator death
| Predator molecule
|}
|}
||
||
[[Image:iGEM_IMPERIAL_PreadatorConstructSystemIcon.png|right|350px]]
[[Image:iGEM_IMPERIAL_PreadatorConstructSystemIcon.png|right|350px]]
|}
|}
The '''prey-molecules''' are an '''input''' of the device. They trigger the production of predator-molecules. As a consequence, the '''output''' of this device is a new level of '''prey-molecules''', due to killing, in association with a new level of '''predator-molecules''', due to the balance between growth and natural death.


==Expected behavior and performances==
==Expected behavior and performances==
(try to write your specifications in tables. Here are just 2 examples)
{| border="1" width="100%"
Interface specifications
|-
! style="background:lightgrey"|Characteristics !! Prey !! Predator !! Predator expression !! Predator Killing
|-
| Range || Sensitivity to the prey should at least match the dynamic range of the prey || Sensitivity to the predator should at least match the dynamic range of the predator || To be characterized || To be characterized
|-
| Transfer function ||  n/a  || n/a || [[Image:IGEM_IMPERIAL_TransferFunctionPredator1.png|250px]]  ||  [[Image:IGEM_IMPERIAL_TransferFunctionPredator2.png|250px]]
|-
| Variability||  n/a    || n/a    || population level + day-to-day variability low  ||  population level + day-to-day variability low   
|}


{| border="1" width="100%"
{| border="1" width="100%"
System level specifications
System level specifications
|-  
|-  
! style="background:lightgrey" width="100pt" |Properties !! Comments
! style="background:lightgrey" width="100pt" |Properties !! colspan="2" | Specifications
|-
|-
| Range||
| Input Range(s)|| colspan="2" | Input range of the prey should at least match the dynamic range of the prey.
|-
|-
| Transfer function ||
| rowspan="2"| Output Range(s)|| colspan="2" | Output range of the prey should at least match the dynamic range of the prey.
|-
|-
| Latency ||
| colspan="2" | Output range of the predator to be defined.
|-
|-
| Robustness ||
| Transfer function(s) || [[Image:IGEM_IMPERIAL_TransferFunctionPredator1.png|250px]] <br> Transfer function inspired by the pure Lotka-Volterra equations, growth predator = C*prey_population_*predator_population|| [[Image:IGEM_IMPERIAL_TransferFunctionPredator2.png|250px]] <br>Transfer function inspired by the pure Lotka-Volterra equations, prey killing = B*prey_population_*predator_population.
|-
|-
| Variability  ||
| Robustness || colspan="2" | Device should work for at least 10 cycles of the oscillator to match system level oscillator specifications.
|-
|-
| properties 3 ||  
| Variability || colspan="2" | Variability at the device population level (day to day, device to device) should be as low as possible.
|-
| properties 4 ||
 
|}
|}


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*Getting linear relationship is going to be challenging in a biological system.
*Getting linear relationship is going to be challenging in a biological system.
*Saturation in the response may have to be taken into account (characterized and defined).
*Saturation in the response may have to be taken into account (characterized and defined).
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Latest revision as of 09:43, 30 October 2006

Super Parts Molecular Prey-Predator Oscillator
Actual Part
Sub Parts Test Sensing Predator Construct Test Killing Predator Construct


Motivations

  • This part is driving the molecular events associated with the Predator in the Lotka-Volterra model.
  • This part has to interface with the Prey-construct.
  • To satify the Lotka-Volterra dynamic of the predator, this part has to fulfill 3 properties:
    • Promote the growth of the predator-molecule according to the prey and predator populations.
    • Kill the prey-molecule according to the population of preys and predators
    • Enable the natural death of the predator-molecule

Part interface

INPUTS OUTPUTS
Prey molecule Prey molecule
Predator molecule

The prey-molecules are an input of the device. They trigger the production of predator-molecules. As a consequence, the output of this device is a new level of prey-molecules, due to killing, in association with a new level of predator-molecules, due to the balance between growth and natural death.

Expected behavior and performances

System level specifications
Properties Specifications
Input Range(s) Input range of the prey should at least match the dynamic range of the prey.
Output Range(s) Output range of the prey should at least match the dynamic range of the prey.
Output range of the predator to be defined.
Transfer function(s)
Transfer function inspired by the pure Lotka-Volterra equations, growth predator = C*prey_population_*predator_population
Transfer function inspired by the pure Lotka-Volterra equations, prey killing = B*prey_population_*predator_population.
Robustness Device should work for at least 10 cycles of the oscillator to match system level oscillator specifications.
Variability Variability at the device population level (day to day, device to device) should be as low as possible.

Open issues

  • Getting linear relationship is going to be challenging in a biological system.
  • Saturation in the response may have to be taken into account (characterized and defined).

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