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
!colspan="2" | This is the whole system!!!!
!colspan="2" | Not Applicable
|-
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!height="25pt" width="80pt"|Actual Part
!height="25pt" width="80pt"|Actual Part
!colspan="2"| [[Image:J37036 logo.png]]
!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/Prey_Construct| Prey Construct]]  
! [[IGEM:IMPERIAL/2006/project/Oscillator/project browser/Prey_Construct| Prey Molecule Generator]]  
! [[IGEM:IMPERIAL/2006/project/Oscillator/project browser/Predator_Construct| Predator Construct]]   
! [[IGEM:IMPERIAL/2006/project/Oscillator/project browser/Predator_Construct| Predator Molecule Generator]]   
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<div class="tabs-blue">
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==Motivations==
==Motivations==
*describe briefly the reasons behind the creation of this part (bullet point style)
 
*add links to other parts if necessary or other part of the wiki.
*'''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)
 
*Based on these past limitations, we have defined the''' specifications for our oscillator'''.
==System Specifications==
 
{| border="1" width="100%"
|- style="background:blue"
!  width="100pt" |Properties !! Comments
|-
| 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==
==Part interface==


(describe your black-box approach, define properties of inputs/outputs)
{| border="0" width="100% align="center"
{| border="0" width="100% align="center"
|-
|-
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! style="background:#66CC99"| INPUTS !!style="background:#FF3333"| OUTPUTS  
! style="background:#66CC99"| INPUTS !!style="background:#FF3333"| OUTPUTS  
|-
|-
| Prey molecule || Prey molecule
| On/Off || rowspan="3"| Output signal
|-
| Frequency tuning 
|-
| Amplitude tuning
|}
|}
||
|[[Image:Oscillatorblkbox2.png|450px]]
[[Image:Oscillator black box.png|right|350px]]
|}
|}
(don't forget to insert a relevant image of your black box.)


==Expected behavior and performances==
==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.


{| border="1" width="100%"
System level specifications
|-
! style="background:lightgrey" width="100pt" |Properties !! Comments
|-
| Range||<font color='red'>?</font>||||
|-
| Expected output ||


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[[Image:Oscillator output.png|200px]]
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||
|-
| Latency ||<font color='red'>?</font>||
|-
| Robustness ||Oscillations should be stable for greater then 10 cycles||
|-
| Variability  ||There should be a high signal to noise ratio||
|}
 
==Open issues==
*list known issues

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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