Team:BCCS-Bristol/Modeling
From 2009.igem.org
(Difference between revisions)
(→Antos) |
|||
Line 132: | Line 132: | ||
=== Antos === | === Antos === | ||
+ | *New and updated BSim documentation? | ||
+ | |||
+ | *BSim graphics | ||
+ | **<s>Rod shape rotation. </s> r125 | ||
+ | **<s>Basic BSimChemicalField drawing in 3D - will help with grns with a diffusing chemical.</s> Done (r124) but needs to be improved in terms of speed and extensibility. | ||
+ | **Investigate (OpenGL?) volume rendering (Tom - Vidi?) maybe better for arbitrary (GRN diffusion) chemical fields | ||
*GRNs and vesicles | *GRNs and vesicles | ||
** Read more about the mechanics of different GRNs (specifically switches). | ** Read more about the mechanics of different GRNs (specifically switches). | ||
** Find out how they interact with the external environment. | ** Find out how they interact with the external environment. | ||
- | ** Investigate the possiblity of using a different time-step to the fixed one in BSim. | + | ** <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 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. | ||
Line 145: | Line 151: | ||
*** Refactor ODEs from an [https://2009.igem.org/Team:BCCS-Bristol/Modeling/Antos/ODE_intefaces interface] to an abstract class if necessary. | *** Refactor ODEs from an [https://2009.igem.org/Team:BCCS-Bristol/Modeling/Antos/ODE_intefaces interface] to an abstract class if necessary. | ||
** <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] | ||
- | ** Implement the solvers into BSim. | + | ** <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 | ||
*** The ability to choose between solvers (in BSim, not hard-coded). | *** The ability to choose between solvers (in BSim, not hard-coded). |
Revision as of 18:09, 21 August 2009
BCCS-Bristol
iGEM 2009
iGEM 2009
Contents |
Workflow
- Study Team:BCCS-Bristol/Modeling/Ideas to understand high level development goals (you can add stuff to that page!)
- Decide the specifics of what needs to be done and add items to your to-do list. Ideally the items added should read like commit messages
- Commit to the subversion repository and
strike outthe item on your to-do list, adding a reference to the commit number if possible e.g:-
Rename BSimObject to BSimParticler19
-
Todo list
Steve
- Abstract for SCN (26th Aug) and ECCS (1st Sep)
- Contact Paris team, review gold medal requirements
- Identify what batch simulations we wish to carry out, see [1].
- Matlab/Simbiology GRN simulations?
- Analyse performance using TPTP, rerun BSim1.0 simulations w/o various collisions to assess statistical importance
- Simplify growth > vesiculation based on P_begin P_end
- "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)
- Processing export libraries
- CollisionPhysics > CollisionDetection/CollisionResponse?
- Study whether 3D implementation of newPosition in BSimBacteriaCreate is reasonable r28
- Refactor to use Vector and Matrix types from vecmath
- tumbleSpeed looks a bit suspect
- 3D diffusion for BSimChemicalField r29
- Add paper references to parameter values in the code using page from last year
-
3D tumbling in BSimBacteriar65 -
Improve knowledge of rigid body collisions[2] [3]
Mattia
- Last Year Bug Fixing:
New solution for reading gammaVals.txt (Old Problem: In Windows Vista semeed to be some reading problems)Mathematic corrections in calcDistFromBoundary(Wrong Mathematics)
- BSim 3D:
- Update Class BSimParticle r28 r51
Class parametersConstructorsetPositionsetCentrePossetDirectionnormalise3DVector
- Update Class BSimChemicalField r29 r35
Class parametersConstructorsetAsLinearredrawupdateField- Update Class BSimChemicalFieldThread
Class parametersConstructorrun
addChemicalgetConcentrationgetField
- Update Class BSImBacterium r30 r50 r55
iterateBacterium- iterateTumble
startNewPhasedoRun
- Update Class BSImBacteriaCreate r31 r48
createBacteriaSetcreateBacterium
- Update Class BSimDeadBacterium r32
runLogic
- Update Class BSimBeadsCreate r33
createBeadSetcreateBead
- Update Class BSimChemicalFieldCreate r36
createChemicalField
- Update Class BSimCollisionPhysics r37 r39 r46
Class parametersupdateProperties- Update Class BSimCollisionPhysicsThread
rundistBetweenPointsresolveExternalForceslinearMotionforce2Velocity3D
- Update Class BSimParameters r38 r41 r42 r58
- Update Class BSimScene r40 r56
resetScenerunAllUpdates
New Class BSimPlaneBoundaryCreater43 r 54New Class BSimSolidPlaneBoundaryr44 r49 r53- Update Class BSimParametersLoader r47 r57
processLine
New Class BSimWrapPlaneBoundaryr52
- Update Class BSimParticle r28 r51
- BSim Population Dynamics:
Emily
-
Issue with bacteria 'escaping' the boundariesr61- 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. [4]
- 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
- New and updated BSim documentation?
- BSim graphics
Rod shape rotation.r125Basic BSimChemicalField drawing in 3D - will help with grns with a diffusing chemical.Done (r124) but needs to be improved in terms of speed and extensibility.- Investigate (OpenGL?) volume rendering (Tom - Vidi?) maybe better for arbitrary (GRN diffusion) chemical fields
- 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.
- BSim GRNs
-
Java implementation of Runge-Kutta 4th order solver.r70- Refactor ODEs from an interface to an abstract class if necessary.
-
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 (in BSim, not hard-coded).
- Investigate possibility of using javax/vecmath and matrix ops to maybe make the larger routines more efficient.
- Extend to Stochastic ODEs.
- 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.
- Similarly investigate the format used by XPP (may be more succinct, also is specifically for ODEs).
- Investigate and implement GRN (ODE) and chemical field interaction.
- Study implementation of 3D diffusion in BSim.
- Implement diffusion in/out terms for membrane diffusion.
- 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 (eg colour changes, pop-out time series).
-