Calendar

Roadmap

• Aims of the modeling part
• First approach proposed
  • Hill functions
  • first model + score function
  • bibliography
  • findparam
  • experiments
• Second approach
  • bibliography
  • equations
  • results
  • experiments
• Continue the previous model
  • Synchronyzation
  • Estimation of the FIFO processes
  • Stochastic modeling (Gilespie)
• Test of robustness
  • repressilator
  • comparison
• Enhancing the system
  • Better FIFO behaviour
  • Other interactions to increase the robustness

July

• 07/31 - Have a full bibliography ⇒ DONE

August

• 06/07 - First model of the FIFO temporal order, of the backward control inducing the oscillations ⇒ DONE
• 08/07 - Model the synchronization between cells, using Biocham
• 08/15 - Summary about the ODE method, Space introduction into models (AC, Delaunay)
• 08/22 - Feedback: list missing things (parameters), Optimization, Robustness analysis

September

• 09/22- Checkpoint meeting

October

• 10/15 - Scheduled wiki ending (2 weeks before the real ending to finish details)
• 10/31 - Official wiki ending (date to be checked)

Todo

• On the previous model
  • add cells
  • have a population that changes over time
  • Parameters robustness (threshold, Pa) (screening)
  • Gillespie : rebuild the model with this new approach // noise
  • Quantification of FIFO (see Yann)
  • Quantification period (influent parameters...)

• Other ideas
  • biocham : comparison with adapted repressilator
  • system to add "random" links for model optimisation (quantification of quality : see that oscillation FIFO and synchronization still occur)
  • change place of tetR (on flgA...)
  • see mgs (gillespie or spatialization)
  • highly rigorous model with mRNA and ON/OFF