Team:Newcastle/Modeling/Population/Pseudo/Bacteria Code

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Contents

Cells Pseudo code

This will give a brief outline of what our simulated bacterial cells will do throughout their 'lives'. The life cycles shown here loop continuously, until it has a reason to stop (eg if it is dead).

Subtilis (Vegetative Cell)

Life Cycle

  • Checks if the current run has been ended.
  • Checks if the cell is going to die from an overdose of cadmium.
  • Imports some nutrients and cadmium, etc from the environment.
  • Checks to see if cadmium has been detected inside the cell.
    • If detected, it will make a decision to be a metal sequestering cell, or not.
      • Runs a JSim instance using parameters from the cell and runs the Sin Operon CellML model.
  • If it is in the 'sporulating' state, advance closer to sporulating.
  • If there is not sufficient nutrients, size, etc to duplicate, it may decide to enter other states such as Biofilm, Motile or Spore.
  • If there is sufficient nutrients, size, etc to duplicate, make a daughter cell
    • Creates a database request that in turn makes Microbase create a new 'job' (cell).

Motile

Life Cycle

  • Checks if the current run has been ended.
  • It may decide to become change back into the vegetative state.

Biofilm

Life Cycle

  • Checks if the current run has been ended.
  • It may decide to become change back into the vegetative state.

Spore

Life Cycle

  • Checks if the current run has been ended.
  • If it is able to germinate (ie not a cadmium sequestering spore) and correct conditions.
    • Advance through a germination step.
    • If all germination steps have taken place, change back into the vegetative state.



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