Team:Newcastle/Modeling/Population/Pseudo/Bacteria Code
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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. | 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. | ||
== Subtilis (Vegetative Cell) == | == Subtilis (Vegetative Cell) == |
Revision as of 02:14, 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.
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 detected, it will make a decision to be a metal sequestering cell, or not.
- 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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