IGEM:IMPERIAL/2006/project/Oscillator/project browser/Full System: Difference between revisions

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!height="25pt" width="80pt"| Super Parts
!height="25pt" width="80pt"| Super Parts
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!colspan="2" | Not Applicable
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!height="25pt" width="80pt"|Actual Part
!height="25pt" width="80pt"|Actual Part
!colspan="2"| Logo of the Part
!colspan="2"| Full System Logo
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!height="25pt" width="80pt"|Sub Parts
!height="25pt" width="80pt"|Sub Parts
! [[IGEM:IMPERIAL/2006/project/Oscillator/project browser/Full System/Prey_Construct| Prey Construct]]  
! [[IGEM:IMPERIAL/2006/project/Oscillator/project browser/Prey_Construct| Prey Molecule Generator]]  
! [[IGEM:IMPERIAL/2006/project/Oscillator/project browser/Full System/Predator_Construct| Predator Construct]]   
! [[IGEM:IMPERIAL/2006/project/Oscillator/project browser/Predator_Construct| Predator Molecule Generator]]   
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*Intro
==Motivations==


*Motivation
*'''Oscillators''' are a '''fundamental building block''' in traditional engineering applications (i.e. computers, radio, clocks) , as well as a recurrent motif in many biological systems (i.e.circadian rhythm, menstrual cycle).
*We intend to build a '''generic''' and '''modular synthetic biological oscillator''' that can become a fundamental building block in future synthetic biological applications.
*Previous oscillators have been attempted (such as the [http://www.nature.com/nature/journal/v403/n6767/abs/403335a0.html  Repressilator] by Elowitz and Leibler in 2000) but they often share the following problems:
::*'''Noisy''' and '''Unstable''' (due to stochastic molecular events at the single cell level, cell-cell variability, cell division)
::*'''Damping''' (i.e.with cell-cell asynchrony)
::*'''Inflexible''' (i.e. lack of control over amplitude and frequency)
::*'''No easy connectivity''' (hard to integrate into larger systems)


* Specification of the oscillator
*Based on these past limitations, we have defined the''' specifications for our oscillator'''.
* Specification of the oscillator
==System Specifications==
* Specification of the oscillator
 
* Specification of the oscillator
{| border="1" width="100%"
* Specification of the oscillator
|- style="background:blue"
* Specification of the oscillator
!  width="100pt" |Properties !! Comments
* Specification of the oscillator
|-
| style="background:lightblue" width="100pt" |'''Expected output''' ||align="center" | [[Image:Oscillator output.png|200px| center]]
|-
| style="background:lightblue" width="100pt" |'''Stability''' ||Oscillations should be stable for greater then 10 cycles. Stable in amplitude, frequency and output profile.
|-
| style="background:lightblue" width="100pt" |'''Variability'''  ||Output signal should have a high signal to noise ratio.
|-
| style="background:lightblue" width="100pt" |'''Flexibility''' ||Amplitude and frequency should be controllable.
|-
| style="background:lightblue" width="100pt" |'''Amplitude Range'''|| Large enough to have an easy detection.
|-
|style="background:lightblue" width="100pt" | '''Frequency Range'''||From a period of the order of the hour to several hours.
|-
| style="background:lightblue" width="100pt" |'''Connectivity''' ||The oscillator should be easily integrated into other more complicated systems. Modular and generic output.
|}
 
==Part interface==
 
{| border="0" width="100% align="center"
|-
|
{| border="1" cellpadding="15" width="100%"
|-
! style="background:#66CC99"| INPUTS !!style="background:#FF3333"| OUTPUTS
|-
| On/Off || rowspan="3"| Output signal
|-
| Frequency tuning 
|-
| Amplitude tuning
|}
|[[Image:Oscillatorblkbox2.png|450px]]
|}
 
==Open issues==
*In electronic, the stability of the oscillations is a key factor, but the profile of the ouput signal is also an important property of an oscillator. There is an important variety of output profiles used in electronic (harmonic, square-wave, triangle-wave). Sometimes, for a given application a given profile is required. [http://en.wikipedia.org/wiki/Electronic_oscillator read more>>]
*Due to biological variability, getting a stable behavior might be challenging.
 
 
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Latest revision as of 04:36, 31 October 2006

Super Parts Not Applicable
Actual Part Full System Logo
Sub Parts Prey Molecule Generator Predator Molecule Generator


Motivations

  • Oscillators are a fundamental building block in traditional engineering applications (i.e. computers, radio, clocks) , as well as a recurrent motif in many biological systems (i.e.circadian rhythm, menstrual cycle).
  • We intend to build a generic and modular synthetic biological oscillator that can become a fundamental building block in future synthetic biological applications.
  • Previous oscillators have been attempted (such as the Repressilator by Elowitz and Leibler in 2000) but they often share the following problems:
  • Noisy and Unstable (due to stochastic molecular events at the single cell level, cell-cell variability, cell division)
  • Damping (i.e.with cell-cell asynchrony)
  • Inflexible (i.e. lack of control over amplitude and frequency)
  • No easy connectivity (hard to integrate into larger systems)
  • Based on these past limitations, we have defined the specifications for our oscillator.

System Specifications

Properties Comments
Expected output
Stability Oscillations should be stable for greater then 10 cycles. Stable in amplitude, frequency and output profile.
Variability Output signal should have a high signal to noise ratio.
Flexibility Amplitude and frequency should be controllable.
Amplitude Range Large enough to have an easy detection.
Frequency Range From a period of the order of the hour to several hours.
Connectivity The oscillator should be easily integrated into other more complicated systems. Modular and generic output.

Part interface

INPUTS OUTPUTS
On/Off Output signal
Frequency tuning
Amplitude tuning

Open issues

  • In electronic, the stability of the oscillations is a key factor, but the profile of the ouput signal is also an important property of an oscillator. There is an important variety of output profiles used in electronic (harmonic, square-wave, triangle-wave). Sometimes, for a given application a given profile is required. read more>>
  • Due to biological variability, getting a stable behavior might be challenging.


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