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

From 2009.igem.org

(Difference between revisions)
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* setState - set a textual representation of the current state of the cell.  
* setState - set a textual representation of the current state of the cell.  
* suicide - death of a cell - makes the thread inactive.
* suicide - death of a cell - makes the thread inactive.
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=== Variables ===
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* alive - if it is alive or not
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* availableCadmium - cadmium available.
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* availableFood - nutrients available.
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* bugRecord - access to the database record for this cell.
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* canGerminate - if it is a sequestering cell.
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* dao - a database access object.
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* debug - a debug message printer.
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* divideFoodReq - size that the cell needs to grow to do divide.
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* internalCadmium - cadmium inside the cell.
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* internalFood - nutrients inside the cell (used).
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* parent - identification number of parent cell.
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* random - random number generator.
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* x - spacial coordinate.
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* y - spacial coordinate.
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* z - spacial coordinate.
== Subtilis (Vegetative Cell) ==
== Subtilis (Vegetative Cell) ==
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* willSequester - decides if it is going to sequester cadmium.
* willSequester - decides if it is going to sequester cadmium.
* willSporulate - decides if it will sporulate this turn currently runs JSim model.
* willSporulate - decides if it will sporulate this turn currently runs JSim model.
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=== Variables ===
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* allSet - state check.
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* hasSpaceForDaughter - can it divide.
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* isSequestering - if it is sequestering.
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* isSporulating - if it is spourlating.
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* sporeCounter - sporulation stage number.
== Motile ==
== Motile ==
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* willGerminate - Determines if it is to germinate on this turn.
* willGerminate - Determines if it is to germinate on this turn.
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=== Variables ===
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* germCounter - germination stage number.
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Revision as of 02:23, 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.

Cell (Superclass, common features)

Methods

  • takeTurn - allow the cell's states to run their life cycles.
  • hasSufficentFood - check if there is enough food to duplicate.
  • importCadmium - import cadmium from the environment (MntH)
  • exportCadmium - export cadmium to the environment (CadA)
  • importFood - import nutrients from the environment.
  • isLiving - checks to see if it is alive, and using CPU power.
  • log - write timestamped log data to the database.
  • run - run as a thread (ie looping).
  • setState - set a textual representation of the current state of the cell.
  • suicide - death of a cell - makes the thread inactive.

Variables

  • alive - if it is alive or not
  • availableCadmium - cadmium available.
  • availableFood - nutrients available.
  • bugRecord - access to the database record for this cell.
  • canGerminate - if it is a sequestering cell.
  • dao - a database access object.
  • debug - a debug message printer.
  • divideFoodReq - size that the cell needs to grow to do divide.
  • internalCadmium - cadmium inside the cell.
  • internalFood - nutrients inside the cell (used).
  • parent - identification number of parent cell.
  • random - random number generator.
  • x - spacial coordinate.
  • y - spacial coordinate.
  • z - spacial coordinate.

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.

Variables

  • allSet - state check.
  • hasSpaceForDaughter - can it divide.
  • isSequestering - if it is sequestering.
  • isSporulating - if it is spourlating.
  • sporeCounter - sporulation stage number.

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.

Variables

  • germCounter - germination stage number.



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