Team:BCCS-Bristol/Modeling

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Revision as of 21:34, 13 September 2009

BCCS-Bristol
iGEM 2009

Links

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. [1]
  - 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.~~ 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

@@ Line 12: / Line 12: @@
 * Wiki
 * Implement Paris GRNs
-* Movie output
 * Add paper references to bacterium behaviour and default parameter values (using [https://2008.igem.org/Team:BCCS-Bristol/Modeling-Parameters page from last year])
-* Particle mixins
-* Define parameters and the scene in a main loop a la AgentCell - minimal constructors - lots of sets(), the main() loops should be human-readable!! [[Team:BCCS-Bristol/Modeling/HowBSimWorks|BSim is gonna be super fast to prototype]].
 * Thread interaction loops; verify performance
-* http://vyshemirsky.blogspot.com/2007/11/sample-from-gamma-distribution-in-java.html
-* 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)