Team:BCCS-Bristol/Modeling/ToDo

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BCCS-Bristol
iGEM 2009

Contents

Todo list

Steve

  • Wiki
  • Implement Paris GRNs
  • Add paper references to bacterium behaviour and default parameter values (using page from last year)
  • Thread interaction loops; verify performance

"Growth curves were measured for all of the mutants, and their log-phase doubling times were calculated. In general, more extreme vesiculation phenotypes corresponded to longer doubling times" (Outer Membrane Vesicle Production by Escherichia coli Is Independent of Membrane Instability)

Emily

  • Issue with bacteria 'escaping' the boundaries r61
    • When the bacteria have a large enough force and the time step is not small enough the bacteris are able to 'escape' the boundary.
    • Fix this by checking the distance and direction of all the bacteria close to the boundary. This will catch those that have crossed the boundary in one time step.
    • THIS COULD BE IMPROVED FURTHER - it allows for far greater forces however does not fix this problem in all cases.
  • Understand how bacteria "tumble" under magnetic force
    • It is believed that the magnetic force causes the bacteria to orientate in line with the field and so the tumble phase will not occur.
  • Implement directed bateria (bacteria under constant magnetic field)
    • Control only the direction of the bacteria - not the force. r116
    • Add some variation in the direction of each bacterium
      • The average alignment of the population is described by Langevin function for classical paramagnetism. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.mi.36.100182.001245]
      • The interaction of the population with a magnetic field is affected by the temperature.
  • Finish coding the magnetic force for variable magnetic force
    • Code the magnetic force as an additional force on the bacteria along with the internal and external forces. r82
    • Find realistic values for the magnetic force acting on the bacteria.
  • Code half-coated bead
    • Apply two different potentials to each half of the bead - one side has a potential well (the bacteria attach here) and the other side has no well (the bacteria will interact normally here).
  • Control which objects are affected by the magnetic force
    • Magnetotactic bacteria in a constant magnetic field
    • Magnetotactic bacteria in a variable magnetic field
    • E. coli attaching to a magnetic bead under a variable magnetic field

Antos

  • BSim GRNs
    • Proof of concept to check functionality. [http://www.pnas.org/content/101/30/10955 Something like this]
      • Update: it works! (r140) Need to run large scale simulation to check for long term synchronization...
      • Compare chemical field with degradation to vesicular transport.
      • Refactor ODEs from an interface to an abstract class if necessary. EDIT: interface seems sufficient so far, however need to generalise ODEs to just one interface.
    • Investigate other options in terms of external libraries (eg odeToJava - good but seems overcomplicated for current purposes; hundreds of lines of code for one solver routine)done
    • Extend to Stochastic ODEs. However, how much stochasticity is inherent in our system? autoinducer chemical field is intrinsically random due to motion of bacteria.
  • GRNs and vesicles
    • Read more about the mechanics switch, bistable and 'counter' GRNs and methods of modelling them.
    • Investigate the mechanics of our GRNs with respect to vesicle budding and communication.
    • Investigate methods for numerically solving stochastic ODEs.

Mattia

Tomski

  • BSimBatch
    • Update to incorporate refactoring of other classes
  • BSimExport
    • What information should be output (numerical data, visualisations, etc)
    • Options for visualisation - multiple output cameras, rotation of single camera, following of BSimParticle
    • Add options into GUI so that longer simulations can be saved more easily from user interface
    • Include new parameters in parameter file and BSimParameters
  • Compilation on BlueCrystal
    • Test jar file generated on BCCS workstation on BC
    • Find out how to compile code from command line, without dependancy on Eclipse
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