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

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(New page: {{:Team:Newcastle/CSS}} {{:Team:Newcastle/Header}} {{:Team:Newcastle/Left}} = Cells Pseudo code = This will give a brief outline of what our simulated bacterial cells will do throughout t...)
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= Cells Pseudo code =
= 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 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).
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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) ==
== Subtilis (Vegetative Cell) ==
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* If there is sufficient nutrients, size, etc to duplicate, make a daughter cell
* 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).
** Creates a database request that in turn makes Microbase create a new 'job' (cell).
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=== Methods ===
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* taketurn - perform one loop of life cycle.
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* findSpace - try to find a space to divide into.
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* getSet - various sequestering and sporulating checks.
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* hasCadmiumOD - checks if there is an amount of cadmium in the cell that would kill it.
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* isSequestering - checks if it is going to be sequestering.
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* isSporulating - checks if it is sporulating.
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* isRunOver - checks the database to bee if the run has been terminated.
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* sporulatingTurn - advances through sporulation.
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* willSequester - decides if it is going to sequester cadmium.
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* willSporulate - decides if it will sporulate this turn currently runs JSim model.
== Motile ==
== Motile ==
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* Checks if the current run has been ended.
* Checks if the current run has been ended.
* It may decide to become change back into the vegetative state.
* It may decide to become change back into the vegetative state.
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=== Methods ===
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* taketurn - perform one loop of life cycle. Decide to vegetate.
== Biofilm ==
== Biofilm ==
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* Checks if the current run has been ended.
* Checks if the current run has been ended.
* It may decide to become change back into the vegetative state.
* It may decide to become change back into the vegetative state.
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=== Methods ===
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* taketurn - perform one loop of life cycle. Decide to disperse the cells.
== Spore ==
== Spore ==
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** Advance through a germination step.
** Advance through a germination step.
** If all germination steps have taken place, change back into the vegetative state.
** If all germination steps have taken place, change back into the vegetative state.
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=== Methods ===
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* taketurn - perform one loop of life cycle.
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* isCanGerminate - Checks if the spore can germinate (not a metal sequester spore).
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* willGerminate - Determines if it is to germinate on this turn.
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Revision as of 02:06, 22 October 2009

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).

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.



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