Realization of living cell's simulator for the synthetic biology



Tutors : Yves Gendrault, Morgan Madec
Team : Paul Bonnet, Romain Cherpantier, Hélène Moulet

Responsible : Hélène Moulet




Synthetic biology is a science whose goal is to tend towards the assembly of elements of living, it is a bit like Lego:

  • We take bits of genes, each of which has a particular property, called Biobrick (or parts). These are the lego pieces.
  • They are assembled together to form sets that each have a particular function: the motorcycle or the police officer in lego.
  • Finally we can assemble these sets to obtain a complete biological system: the policeman on his motorcycle.


Our project consisted in the realization of a computer simulator which makes it possible to obtain models corresponding to the Biobricks in the form of equations of behavior of particles moving and reacting together in a cell.

The name of the simulator: Smarties, derives from our choice of modeling of the cell (see III /)








  • Choice of species and related parameters . * Display of species on the GUI screen (below) . * The type and modalities of the desired reactions are then chosen in the other tabs of the interface.





    Possibility to model a large number of reactions and to save the results files in an automated way.



    ===== III/Behind the GI, a program written in C =====
    Modeling of the grid cell containing:
    * Particles: colored smarties. * Specialized areas in which particles can react, ex: nucleus, ribosomes.

    * Time is discreet, we talk about clock strokes or iterations of the program. * Each smarties moves one box (up / down / right or left) at each iteration. * When two smarties are on the same square or when one goes to a colored area, there may be interactions (the interaction modalities are set through the GUI).


    Exemples : Two reactions were coded, the complexations (nA + mB + pC = A <sub> n </ sub> B <sub> m </ sub> C <sub> p </ sub > … and protein synthesis . * 'Red' and 'green' entering the same box gives 'blue' can model the
    complexation A + B = AB * Protein synthesis in 4 steps: - a red smarties goes on the purple square in which it passes three iterations: modelization of the reaction time of the synthesis of mRNA in the nucleus. - during this time, several green smarties emerge from the purple square: synthesis of several mRNA - a green smarties passes 5 iterations in the blue square: protein synthesis in a ribosome - during this time, several yellow smarties come out of the ribosome: they are the synthesized proteins


    ===== IV/ Interpret the results of the simulator: an analysis of the graphs obtained ======
    From the graphical interface, results curves are obtained: * Abscissas: number of iterations of the program * Ordered: concentrations of the different species Equations of behavior are obtained using regression software. We can thus: * Check the correct operation of the simulator (results close to known theoretical results)
    * Develop new mathematical models explaining the behavior of particles.
    We can go further, retrieve data from many simulations (from data tables provided by the program) and analyze what we want:
    to the left: approximation by a sum of two exponentials of the reaction coefficients of the three complexations as a function of reaction and anti-reaction probabilities.
    below: study the noise due to the probability of anti-reaction in a reaction A + B = AB.









    This project will be taken up by another group (n ° 7 generalists) as part of its participation in the IGEM competition.