• Home
• Team
• Project
• Parts
• Modelling
• Sponsors
• Lab Book

Project

• Overview
• Choices Rationale
• Characterisation
• Safety
• Judging Comments

Sub-projects

• Metal Intake/Efflux
• Metal Sensing
• Sporulation Tuning
• Population Dynamics
• Stochastic Switch
• Metal Sequester
• Chassis
• Promoter Library

Wet Lab

• Lab Book
• Protocols

Meetings

• Meetings Calendar

Planning

• Timeline
• Ideas

Links

• Helping other teams
• Ethics
• T-Shirts
• iGEM Meetup
• Our City
• Fun and Games
• Sponsors
• Useful Links
• Contact Us
• Press Coverage

Contents 1 Cells Pseudo code 1.1 Cell (Superclass, common features) 1.1.1 Methods 1.1.2 Variables 1.2 Subtilis (Vegetative Cell) 1.2.1 Life Cycle 1.2.2 Methods 1.2.3 Variables 1.3 Motile 1.3.1 Life Cycle 1.3.2 Methods 1.4 Biofilm 1.4.1 Life Cycle 1.4.2 Methods 1.5 Spore 1.5.1 Life Cycle 1.5.2 Methods 1.5.3 Variables

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.