Team:Paris Bettencourt/RISC

From 2011.igem.org

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<h2>Risc project</h2>
<h2>Risc project</h2>
<p>
<p>
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The risc is a long term project. It consist in a Database of pre-constructed pattern describing minimalist biological behaviours.
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The Risc is a long term project. It consist in a database of pre-constructed pattern describing minimalist biological behaviours.
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<br/>
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</p><p>
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So, it introduce the concept of usualy used Biobrick's pattern database based on the frequency of biobrick construct in Igem team.
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We introduce the concept of Biobrick patterns' database based on the frequency of biobrick construct in Igem team.
 +
</p><p>
 +
The objective is to simplify design of synthetic systems by using intuitive pattern describing the behaviour we need insteed of combining a lot of biobrick.
 +
It is a way of having an abstraction of the biobrick level. Also : for a behaviour, we can find different patterns.
 +
For example, for an inhibition behaviour, we can use a promoter, a RBS or RNA degradation.
 +
The idea is having behind this description a compiler working on those behaviour and choosing the finest pattern for the behaviour we are looking for.
</p>
</p>
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<h2>compilation</h2>
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<h2>Compilation</h2>
<table>
<table>
<tr>
<tr>
<td>
<td>
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<p>This project is based on an other project witch consist in using a high level behavious langage for synthetic biology.
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<p>This project is based on an other project witch consist in using a high level behaviousal langage for synthetic biology.
 +
This compiling top down chain begin with a synthetic system idea.
 +
</p><p>
 +
Then this idea is traduced in a program in an high level langage witch use behaviour description of the synthetic system.
 +
</p><p>
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Next, this program is traduced in a combination of minimalist patterns witch are equivalent to a biobrick construct.
</p>
</p>
</td></tr>
</td></tr>
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<tr><td>
<tr><td>
<p>
<p>
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we will use those minimalist patterns by combination and substitution to simulate the model described by the langage.
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<h2>Assembling pattern</h2>
 +
We will use those minimalist patterns by combination and substitution to simulate the model described by the langage.
 +
 
</p>
</p>
<table>
<table>
<tr>
<tr>
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<td align="center"><h3>Combination</h3></td><td align="right"><img src="https://static.igem.org/mediawiki/2011/e/e6/Igemparis2011Combinaison.png"/></td>
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<td align="center"><h3>Combination</h3><br/>We combine P1's behaviour and P2's behaviour to create a model doing P1's behaviour and next P2's behaviour</td><td align="right"><img src="https://static.igem.org/mediawiki/2011/e/e6/Igemparis2011Combinaison.png"/></td>
</tr><tr>
</tr><tr>
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<td align="center"><h3>Substitution</h3></td><td align="right"><img src="https://static.igem.org/mediawiki/2011/7/74/Paris2011Substitution.png"/></td>
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<td align="center"><h3>Substitution</h3><br/>In the pattern P1, we identify a sub function F witch will be remplaced by the P2 behaviour.</td><td align="right"><img src="https://static.igem.org/mediawiki/2011/7/74/Paris2011Substitution.png"/></td>
</tr>
</tr>
</table>
</table>
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<tr><td>
<tr><td>
<p>
<p>
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Our approach is to propose to creat a comportemental description of those patterns instead of a  structural design. This to facilitate the usage of these construct.
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Our approach is to propose to create a behaviousal description of those patterns instead of a  structural design. This to facilitate the usage of these construct.
-
 
+
</p><p>
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this idea is different from other modeling method by not trying to modelize biologic systems but having the biologic system simulating the model(doing possibly more than the model but not less).
+
This idea is different from other modeling method by not trying to modelize biologic systems but having the biologic system simulating the model(doing possibly more than the model but not less).
</p>
</p>
</td></tr>
</td></tr>
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</table>
</table>
<h2>Example of patterns</h2>
<h2>Example of patterns</h2>
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<table>
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<table border="2px">
<tr>
<tr>
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<td>Mechanism</td>
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<td><h3>Mechanism</h3></td>
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<td>Pattern description</td>
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<td><h3>Pattern description</h3></td>
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<td>Pattern code</td>
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<td><h3>Pattern code</h3></td>
</tr><tr>
</tr><tr>
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<td>Transposon<img src="https://static.igem.org/mediawiki/2011/2/27/Paris2011Transposon.png" width="300"/></td>
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<td>Transposon<img src="https://static.igem.org/mediawiki/2011/2/27/Paris2011Transposon.png" width="200"/></td>
<td><ul><li>in : one sequence with 2 extraction site</li><li>out : 1 sequence extracted and the original sequence regenerated</li><li>behaviours : extract a part of a sequence and potentialy active another</li></ul></td>
<td><ul><li>in : one sequence with 2 extraction site</li><li>out : 1 sequence extracted and the original sequence regenerated</li><li>behaviours : extract a part of a sequence and potentialy active another</li></ul></td>
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<td><img src="https://static.igem.org/mediawiki/2011/d/d7/Igem2011Transposoncode.png" width="300"/></td>
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<td><img src="https://static.igem.org/mediawiki/2011/d/d7/Igem2011Transposoncode.png" width="400"/></td>
</tr><tr>
</tr><tr>
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<td>Phage<img src="https://static.igem.org/mediawiki/2011/2/2e/Paris2011Phage.png" width="300"/></td>
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<td>Phage<img src="https://static.igem.org/mediawiki/2011/2/2e/Paris2011Phage.png" width="200"/></td>
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<td></td>
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<td><ul><li>in : 1 sequence with 2 insertion site and 1 plasmid with 2 attachment sites</li><li>out : 1 sequence combination of the two first</li><li>behaviours : insert a subsequence in a DNA sequence</li></ul></td>
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<td><img src="https://static.igem.org/mediawiki/2011/c/c0/Paris2011Phagecode.png" width="300"/></td>
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<td><img src="https://static.igem.org/mediawiki/2011/c/c0/Paris2011Phagecode.png" width="400"/></td>
</tr>
</tr>
</table>
</table>

Latest revision as of 14:05, 21 September 2011

Team IGEM Paris 2011

Risc project

The Risc is a long term project. It consist in a database of pre-constructed pattern describing minimalist biological behaviours.

We introduce the concept of Biobrick patterns' database based on the frequency of biobrick construct in Igem team.

The objective is to simplify design of synthetic systems by using intuitive pattern describing the behaviour we need insteed of combining a lot of biobrick. It is a way of having an abstraction of the biobrick level. Also : for a behaviour, we can find different patterns. For example, for an inhibition behaviour, we can use a promoter, a RBS or RNA degradation. The idea is having behind this description a compiler working on those behaviour and choosing the finest pattern for the behaviour we are looking for.

Compilation

This project is based on an other project witch consist in using a high level behaviousal langage for synthetic biology. This compiling top down chain begin with a synthetic system idea.

Then this idea is traduced in a program in an high level langage witch use behaviour description of the synthetic system.

Next, this program is traduced in a combination of minimalist patterns witch are equivalent to a biobrick construct.

Assembling pattern

We will use those minimalist patterns by combination and substitution to simulate the model described by the langage.

Combination


We combine P1's behaviour and P2's behaviour to create a model doing P1's behaviour and next P2's behaviour

Substitution


In the pattern P1, we identify a sub function F witch will be remplaced by the P2 behaviour.

Our approach is to propose to create a behaviousal description of those patterns instead of a structural design. This to facilitate the usage of these construct.

This idea is different from other modeling method by not trying to modelize biologic systems but having the biologic system simulating the model(doing possibly more than the model but not less).

We starded by analysing older igem project looking for common used biobrick circuit and define the behaviour of those circuits.

Example of patterns

Mechanism

Pattern description

Pattern code
Transposon
  • in : one sequence with 2 extraction site
  • out : 1 sequence extracted and the original sequence regenerated
  • behaviours : extract a part of a sequence and potentialy active another
Phage
  • in : 1 sequence with 2 insertion site and 1 plasmid with 2 attachment sites
  • out : 1 sequence combination of the two first
  • behaviours : insert a subsequence in a DNA sequence

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