Team:BCCS-Bristol/Modeling

From 2009.igem.org

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* Implement Paris GRNs
* Implement Paris GRNs
* Wiki
* Wiki
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* Scene scale?

Revision as of 10:35, 8 September 2009

BCCS-Bristol
iGEM 2009

Contents

Links

  • Modelling ideas
  • [http://code.google.com/p/bsim-bccs/ Google Code subversion repository]

Todo list

Steve

  • Check physics/interactions/runLength
  • Thread interaction loops, vesicleBuffer?
  • Implement Paris GRNs
  • Wiki
  • Scene scale?


  • Microtubules
  • Change to private access control to discourage getters and setters

"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)


  • Define parameters and the scene in a main loop a la AgentCell?
  • Compile with parameters?
  • use jYAML for BSimParameters?
  • BSimParameters.load(file) .sets() static variables in appropriate classes?
  • Add paper references to default parameter values (using page from last year) and bacterium behaviour

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
    • BSimChemicalField generalisation and better integration with scene, rendering etc.
    • 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.
    • Java implementation of Runge-Kutta 4th order solver. r70
      • 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
    • Implement the solvers into BSim. Done for single bacterium
    • Implement other solvers (more efficient). r70
      • The ability to choose between solvers. This will be in a parameter file or some equivalent settings when importing an ODE file.
    • Extend to Stochastic ODEs. However, how much stochasticity is inherent in our system? autoinducer chemical field is intrinsically random due to motion of bacteria.
    • Interface BSim with external parameters (maybe similar to current parameter files) used to define an ODE system.
      • Investigate the feasibility of SBML parameters or a similar XML based format. SBML may be overcomplicated for our current needs. Low priority for now.
      • Similarly investigate the format used by XPP (may be more succinct, also is specifically for ODEs).
      • If we use JYaml for parameters this may be possible through that.
    • Investigate and implement GRN (ODE) and chemical field interaction. r139
      • Study implementation of 3D diffusion in BSim. Seems to work fine
      • Implement diffusion in/out terms for membrane diffusion. r139 - diffusion in/out based on the two relative concentrations
    • GRN interaction with vesicle budding and chemical transport (on the surface of the vesicle and inside it).
    • Incorporate a method for seeing the effects of GRN activity.
      • Colour changes works but needs reimplementation in new renderer
      • Time series: could have pop-out, need to fix the data export to allow exporting a time series.
  • New and updated BSim documentation?
  • BSim graphics
    • New rendering framework r182
      • Add boundaries when they're implemented again.
      • Re-implement chemical field(s).
    • Rod shape rotation. r125
    • Basic BSimChemicalField drawing in 3D - will help with grns with a diffusing chemical. r124
      • but needs to be improved in terms of speed Done (removed lighting on chemical field :-s) this is pretty much the limit of optimisations possible without more in depth OpenGL work.
    • GRN/quorum field Done, but needs visual improvements due to high dynamic range of chemical levels.
    • Investigate (OpenGL?) volume rendering (Tom - Vidi?) maybe better for arbitrary (GRN diffusion) chemical fields A definite possibility in OpenGL, probably possible in P3D for (large?) speedups.
  • GRNs and vesicles
    • Read more about the mechanics of different GRNs (specifically switches).
    • Find out how they interact with the external environment.
    • Investigate the possiblity of using a different time-step to the fixed one in BSim. Can use a longer or shorter time-step if required, however need to finish other parts to see if this would be relevant/important.
    • Investigate the effect of different time steps (GRNs operate on a time scale relatively long compared to that of BSim).
    • 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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