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Contents 1 Cells Pseudo code 1.1 Subtilis (Vegetative Cell) 1.1.1 Life Cycle 1.1.2 Methods 1.2 Motile 1.2.1 Life Cycle 1.2.2 Methods 1.3 Biofilm 1.3.1 Life Cycle 1.3.2 Methods 1.4 Spore 1.4.1 Life Cycle 1.4.2 Methods

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).

This will also give a brief description of the methods which are called during the life cycle. Methocs and variables are inherited from the superclass.

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).

Methods

• taketurn - perform one loop of life cycle.
• findSpace - try to find a space to divide into.
• getSet - various sequestering and sporulating checks.
• hasCadmiumOD - checks if there is an amount of cadmium in the cell that would kill it.
• isSequestering - checks if it is going to be sequestering.
• isSporulating - checks if it is sporulating.
• isRunOver - checks the database to bee if the run has been terminated.
• sporulatingTurn - advances through sporulation.
• willSequester - decides if it is going to sequester cadmium.
• willSporulate - decides if it will sporulate this turn currently runs JSim model.

Motile

Life Cycle

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

Methods

• taketurn - perform one loop of life cycle. Decide to vegetate.

Biofilm

Life Cycle

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

Methods

• taketurn - perform one loop of life cycle. Decide to disperse the cells.

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.

Methods

• taketurn - perform one loop of life cycle.
• isCanGerminate - Checks if the spore can germinate (not a metal sequester spore).
• willGerminate - Determines if it is to germinate on this turn.