Paris/Modeling

From 2007.igem.org

(Difference between revisions)
Line 1: Line 1:
-
MODELISATION OF THE SYNTHETIC ORGANISME
+
MODELIZATION OF THE SYNTHETIC ORGANISME
[[Paris_Modeling_fr|French Page]]
[[Paris_Modeling_fr|French Page]]
Line 15: Line 15:
-
==Rythmeand organise the biological constructs==
+
==Rythme and organise the biological constructs==
-
  Il faut essayer de [http://openwetware.org/wiki/Parts_characterization/Characterization_approaches caractériser] les biobriques qu’on va utiliser, avant de les assembler, de manière à alimenter la modélisation en valeurs de paramètres, puis d’utiliser la modélisation pour construire, et voir ce qui correspond ou non à la modélisation, et essayer de comprendre pourquoi. (On a en ainsi une démarche de chercher comment les choses marchent en les construisant, puis en observant  l’écart avec la théorie, et en cherchant une explication pour affiner le modèle)
+
  We need to [http://openwetware.org/wiki/Parts_characterization/Characterization_approaches caracterise] the biobricks we're about to use, BEFORE assembling them, so that we can feed the model with parameter values. The We use the model to construct, and see if it fits or not the model, and try to understand why. (It's a new way of research in biology : instead of tearing complicated system a part, you try to first build simple ones, and by observing the difference with theory, a new explanation will sharpen the model
-
=QUE Modéliser ?=
+
=Model WHAT ?=
-
==Modélisation macroscopique==
+
==Macroscopic Modelization ==
-
J’entends par macroscopique, la modélisation qui se place au niveau de la culture cellulaire, avec des paramètres qu’on peut mesurer extérieurement.  
+
By macroscopique, I mean the modelization at cellular cultur level, with parameter that you can measure outside the cell.
-
Démarche : il faut récuperer les paramètres d’entrée et de sortie de chacun des élements du système, les introduire dans la modélisation, récuperer le taux de transformation cre-lox désiré, et modifier le promoteur de cre en utilisant les promoteurs biobricks, qui ont été caractérisé.
+
We need to get the parameter input and output values of the different elements of the system, introduce them in the model, get the desired cre lox transformation rate, and modifie the cre promoteur, or it's RBS  by using caracterised biobricks.
-
*Paramètres à chercher dans la littérature puis à [http://openwetware.org/wiki/Parts_characterization/Measurement_techniques mesurer] in vitro nous même :
+
Parameters to look for in the litterature then to [http://openwetware.org/wiki/Parts_characterization/Measurement_techniques measure] in vitro by ourself :
-
*Absorbtion de l’acide aminé vital par une cellule.
+
*Absorbtion of the vital AA by a cell
-
*Production de l’acide aminé vital par une cellule
+
*Production of the vital AA by a cell
-
*Zone de diffusion de  l’acide aminé dans le milieu
+
*Diffusion zone of the AA
-
*Taille léthal d’une cellule sans FTSZ ( pour une cellule productrice d’AA) (comment le mesurer ? en Cycles cellulaires ?( 4 ou 5 d’après Ariel)  mais vitesse de cycle identique que pour une cellule normale(avec FTSZ)?
+
*Lethal width of a cell without FTSZ ( for a AA producing cell) (how do you measure it? cell cycle? 4 OR 5 says Ariel. Same cycle speed as for a normal cell (without FTSZ)?
-
*Taille léthal d’une cellule sans FTSZ ( pour une cellule productrice de triglycéride) (mêmes questions)
+
*Lethal width of a cell without FTSZ ( for a triglyceride producing cell)?
-
Taux de recombinaison crelox (avec le  promoteur de référence (lien) ou un qu’on aura caractérisé)
+
*Cre lox recombination rate
 +
Always try to use a reference promoteur or RBS for the caracterisation
-
Pour chacune de ces points, créer une page et la documenter
 
-
 
+
==Microscopique or Genetic Modelization ==
-
==Modélisation Microscopique ou génétique==
+
It's the modelisation of what happens IN the cell : of the genetic network, with the quantity of the different proteins as parameter
-
C’est la modélisation de ce qui se passe DANS la cellule, modélisation du réseau génétique, avec comme paramètres la quantité des différentes protéines ayant un rôle dans notre système.
+
How can we measure the moduls'efficiency? Thanks to [http://parts2.mit.edu/r/parts/htdocs/AbstractionHierarchy/ Pops] and Rips (Ribosome per seconde). We need  reference unity measures. For the [http://partsregistry.org/partsdb/pgroup.cgi?pgroup=RBS Ribosome binding site], we should always compare the RBS used to [http://partsregistry.org/Part:BBa_B0034 this one]. Is it also possible to have a reference promotor?
-
 
+
-
Comment mesurerl’efficacité des modules ? Grâce aux [http://parts2.mit.edu/r/parts/htdocs/AbstractionHierarchy/ Pops] et aux Rips. Il faut en effet des unité de mesure de référence. De plus il faut des modules de référence. Pour les [http://partsregistry.org/partsdb/pgroup.cgi?pgroup=RBS Ribosome binding site], il faut toujours comparer le RBS utilisé à [http://partsregistry.org/Part:BBa_B0034 celui-ci]. Est ce possible d'avoir aussi un promoteur de référence?
+

Revision as of 17:32, 1 July 2007

MODELIZATION OF THE SYNTHETIC ORGANISME

French Page

What do we want to do ? The goal is to model the cellular growth, and to prove it is possible, to find the range of paramaters that enables it, and then to optimise the triglycerid production. Is it Possible for a cell producing the Amino Acide, to feed at the same time the mother cell, and the triglyciride factory one? For this, we need to find the good theoritical balance between the different elements of the population. This balance is determined by the firing rate of the cre/lox system, which is genetically engineered

Contents

Why a modélisation ?

Minimise the biological steps

Make the system work by finding the possible parameters, and save time when doing wetwork, in order to directly make make the construct the most likely to work. ( For instance, immediately use the good promoters or RBS) Some might say the system is "simple enough" to build, so that it can be hand crafted. It might work so. But if we don't try to model a simple system, and try to make it stick as much as possible to reality, how can we ever hope to do it for a more complex one?

Biosynthetic spirit IGEM

If you listen toEndy,biosynthetic is not making a biological construct. It's HOW you make it, it's the process you use to build it. It's giving the possibility to first virtually create the system before carrying it out: by assembling the biobricks as judiciously as possible, by exactly knowing the link between input and ouput. It has to be reflected in the construction process.


Rythme and organise the biological constructs

We need to [http://openwetware.org/wiki/Parts_characterization/Characterization_approaches caracterise] the biobricks we're about to use, BEFORE assembling them, so that we can feed the model with parameter values. The We use the model to construct, and see if it fits or not the model, and try to understand why. (It's a new way of research in biology : instead of tearing complicated system a part, you try to first build simple ones, and by observing the difference with theory, a new explanation will sharpen the model

Model WHAT ?

Macroscopic Modelization

By macroscopique, I mean the modelization at cellular cultur level, with parameter that you can measure outside the cell. We need to get the parameter input and output values of the different elements of the system, introduce them in the model, get the desired cre lox transformation rate, and modifie the cre promoteur, or it's RBS by using caracterised biobricks.

Parameters to look for in the litterature then to [http://openwetware.org/wiki/Parts_characterization/Measurement_techniques measure] in vitro by ourself :


  • Absorbtion of the vital AA by a cell
  • Production of the vital AA by a cell
  • Diffusion zone of the AA
  • Lethal width of a cell without FTSZ ( for a AA producing cell) (how do you measure it? cell cycle? 4 OR 5 says Ariel. Same cycle speed as for a normal cell (without FTSZ)?
  • Lethal width of a cell without FTSZ ( for a triglyceride producing cell)?
  • Cre lox recombination rate

Always try to use a reference promoteur or RBS for the caracterisation


Microscopique or Genetic Modelization

It's the modelisation of what happens IN the cell : of the genetic network, with the quantity of the different proteins as parameter How can we measure the moduls'efficiency? Thanks to [http://parts2.mit.edu/r/parts/htdocs/AbstractionHierarchy/ Pops] and Rips (Ribosome per seconde). We need reference unity measures. For the [http://partsregistry.org/partsdb/pgroup.cgi?pgroup=RBS Ribosome binding site], we should always compare the RBS used to [http://partsregistry.org/Part:BBa_B0034 this one]. Is it also possible to have a reference promotor?