Team:BCCS-Bristol/Modeling

From 2009.igem.org

(Difference between revisions)
(→Steve)
(→Antos)
Line 47: Line 47:
=== Antos ===
=== Antos ===
*BSim GRNs
*BSim GRNs
-
** BSimChemicalField generalisation and better integration with scene, rendering etc.
 
** <s>Proof of concept to check functionality.</s> [http://www.pnas.org/content/101/30/10955 Something like this]
** <s>Proof of concept to check functionality.</s> [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...
*** Update: it works! (r140) Need to run large scale simulation to check for long term synchronization...
*** Compare chemical field with degradation to vesicular transport.
*** Compare chemical field with degradation to vesicular transport.
-
** <s>Java implementation of Runge-Kutta 4th order solver.</s> r70
 
*** <s>Refactor ODEs from an interface to an abstract class if necessary.</s> EDIT: [https://2009.igem.org/Team:BCCS-Bristol/Modeling/Antos/ODE_intefaces interface] seems sufficient so far, however need to generalise ODEs to just one interface.
*** <s>Refactor ODEs from an interface to an abstract class if necessary.</s> EDIT: [https://2009.igem.org/Team:BCCS-Bristol/Modeling/Antos/ODE_intefaces interface] seems sufficient so far, however need to generalise ODEs to just one interface.
** <s>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)</s>[https://2009.igem.org/Team:BCCS-Bristol/Modeling/Antos#ODE_Solvers_and_Libraries_already_in_existence done]
** <s>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)</s>[https://2009.igem.org/Team:BCCS-Bristol/Modeling/Antos#ODE_Solvers_and_Libraries_already_in_existence done]
** <s>Implement the solvers into BSim.</s> Done for single bacterium
** <s>Implement the solvers into BSim.</s> Done for single bacterium
** <s>Implement other solvers (more efficient).</s> r70
** <s>Implement other solvers (more efficient).</s> r70
-
*** <s>The ability to choose between solvers.</s> This will be in a parameter file or some equivalent settings when importing an ODE file.
+
*** <s>The ability to choose between solvers.</s>  
** Extend to Stochastic ODEs. However, how much stochasticity is inherent in our system? autoinducer chemical field is intrinsically random due to motion of bacteria.
** 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.
 
-
*** <s>Investigate the feasibility of SBML parameters or a similar XML based format.</s> 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.
 
-
** <s>Investigate and implement GRN (ODE) and chemical field interaction.</s> r139
 
-
*** <s>Study implementation of 3D diffusion in BSim.</s> Seems to work fine
 
-
*** <s>Implement diffusion in/out terms for membrane diffusion.</s> 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.
 
-
*** <s>Colour changes</s> 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
 
-
**<s>New rendering framework</s> r182
 
-
*** Add boundaries when they're implemented again.
 
-
*** Re-implement chemical field(s).
 
-
**<s>Rod shape rotation.</s> r125
 
-
**<s>Basic BSimChemicalField drawing in 3D - will help with grns with a diffusing chemical.</s> r124
 
-
*** <s>but needs to be improved in terms of speed</s> Done (removed lighting on chemical field :-s) this is pretty much the limit of optimisations possible without more in depth OpenGL work.
 
-
**<s>GRN/quorum field</s> Done, but needs visual improvements due to high dynamic range of chemical levels.
 
-
**<s>Investigate (OpenGL?) volume rendering (Tom - Vidi?) maybe better for arbitrary (GRN diffusion) chemical fields</s> A definite possibility in OpenGL, probably possible in P3D for (large?) speedups.
 
*GRNs and vesicles
*GRNs and vesicles
-
** Read more about the mechanics of different GRNs (specifically switches).
+
** Read more about the mechanics switch, bistable and 'counter' GRNs and methods of modelling them.
-
** Find out how they interact with the external environment.
+
-
** <s>Investigate the possiblity of using a different time-step to the fixed one in BSim.</s> 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 the mechanics of our GRNs with respect to vesicle budding and communication.
** Investigate methods for numerically solving stochastic ODEs.
** Investigate methods for numerically solving stochastic ODEs.

Revision as of 13:38, 15 September 2009

BCCS-Bristol
iGEM 2009

Contents

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
    • 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.
      • 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.
    • 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
Retrieved from "http://2009.igem.org/Team:BCCS-Bristol/Modeling"