# Team:Paris/Modeling/Programs

(Difference between revisions)
 Revision as of 12:13, 16 September 2008 (view source)Hugo (Talk | contribs) (→Hill Functions)← Older edit Revision as of 13:11, 16 September 2008 (view source)Hugo (Talk | contribs) (→Hill Functions)Newer edit → Line 25: Line 25: Because the promoters on a "low copy plasmid" exists in the cell in ten exemplaries, in contrary to a protein, which, as long as it is produced (even weakly) exists in thousands of exemplaries, we can the quantities of ''TF'' and ''P'' are different by several orders of magnitude. Then, with the previous notations, if ''A'', ''B'' and ''C'' stands respectively for ''TF'', ''P'' and the complex ''TF> [[Images:approxhill.jpg]] +
[[Image:approxhill.jpg]]
that we can easily solve with : that we can easily solve with : -
[[Images:reshill.jpg]]
+
[[Image:reshill.jpg]]
Depending to the order ''' ''n'' ''' (also called ''cooperativity'', because it correponds to the possibilities of the transcription factor to binds in a group on the promoter), this function is a ''sigmoïd'', known as the ''Hill function''. The parameter ''' ''K'' ''', called ''activation constant'', is often replaced in the previous expression by the following notation Depending to the order ''' ''n'' ''' (also called ''cooperativity'', because it correponds to the possibilities of the transcription factor to binds in a group on the promoter), this function is a ''sigmoïd'', known as the ''Hill function''. The parameter ''' ''K'' ''', called ''activation constant'', is often replaced in the previous expression by the following notation -
[[Images:changeK.jpg]]
+
[[Image:changeK.jpg]]
It simplify the manipulations of the expression ; we can notice that ''' ''K'' ''' represents now the amount of ''TF'' needed to get half of the total ''P'' bound. It simplify the manipulations of the expression ; we can notice that ''' ''K'' ''' represents now the amount of ''TF'' needed to get half of the total ''P'' bound. -
[[Images:hilldef.jpg]]
+
[[Image:hilldef.jpg]]
==Finding Parameters== ==Finding Parameters==

## Complexations Caracterisation

The first hypothesis is that a complexation reaction is fully determined by the following :

and that the rates k+ et k- stay constant under all conditions. Then, the second hypothesis is that these equations are (kinetically speaking) elementary :

Then, since we guess that the only datas we will have are the quantities of A and B introduced (Ai and Bi), the only equations we will deal with is the following, entirely determining the concentration Ceq at steady-state (at least if we take the smallest real root of the equation, it is useless to demonstrate the unicity, or even the existence, of such a solution) :

## Hill Functions

The previous system of complexation applied in particular to the association of the Promoters (P) and its Transcription Factor (TF).

Because the promoters on a "low copy plasmid" exists in the cell in ten exemplaries, in contrary to a protein, which, as long as it is produced (even weakly) exists in thousands of exemplaries, we can the quantities of TF and P are different by several orders of magnitude. Then, with the previous notations, if A, B and C stands respectively for TF, P and the complex TF><P, we will get

that we can easily solve with :

Depending to the order n (also called cooperativity, because it correponds to the possibilities of the transcription factor to binds in a group on the promoter), this function is a sigmoïd, known as the Hill function. The parameter K , called activation constant, is often replaced in the previous expression by the following notation

It simplify the manipulations of the expression ; we can notice that K represents now the amount of TF needed to get half of the total P bound.

## Finding Parameters

Then, by solving the previous equations for a given set of K et n, we can have a approximation of the corresponding Ceq. The idea, in order to find the bests parameters which correspond to our measurements, is to run a basical program of quadratic optimisation. The final error would tell us if our modelisation is consistent.

((((the following is not coresponding to the new model, but we will use the same frame to expose the corresponding program)))))

(((((((This program aims at fill this data bank, from experimental data obtained by our wet lab. )))))))

(((((( After some trials, we have obtained interesting results in terms of precision. We are now trying to test the robustness of the estimations in order to quantify the influence of biological variance in the results as well as the influence of the number of points available. ))))))))

(((((
)))))

(((((( The corresponding code can be found there : Estimation of the parameters )))))))