We had different approaches to model the biological system. We found interesting to explain at least two ways that we went throught. It is important to understand that both models aim at different goals in the process of understanding our system.

BOB (Based On Bibliography) Approach

Our first approach is quite rough and simple but effective. The goal here was to guess the behavior of our Bacteri'OClock, considering the overall system. Since it is a preliminary approach, we could not yet fill the model with data from the wet lab. This is why our work is mainly based on a bibliographic work, which allow us to use parameters and datas from scientific articles.

The keys points of this approach:

• Simplicity for itself is not so much important, what we were looking for was understandability at first.
• We used linear equations as much as possible: when it as already been proved in a paper than one interaction is efficiently modeled with an elementary expression, we tried to keep it.
• Too many parameters in a model means less relevancy. In addition, the more parameters you have, the hardest it becomes to tune the system in order to have the behavior you are looking for.

APE (APE Parameters Estimation) Approach

[http://en.wikipedia.org/wiki/Recursive_acronym Wondering what APE is standing for?]

The second approach was motivated by our will to characterize our system in the most precise way. What is at stake here is to determine the real parameters that govern the dynamics of our system.

• Each step is taken into account at a fundamental kinetic processes level or at a more global level by a Hill function which is a simple way to take into account multiple interactions and more especially cooperative binding.
• Specific experiments focused on finding relevant parameters have been designed and planned.
• Some noise parameters are included in the set of parameters to estimate, in order to try to translate the natural entropy into the model.

Depreciated pages

• Bibliographic References
• Preliminary approach
• Hill approach
• Estimation
• Roadmap